@text
Kinemage Supplement to Branden & Tooze "Introduction to Protein Structure", 
Second Edition
Chapter 8 -  DNA RECOGNITION IN PROCARYOTES BY HELIX-TURN-HELIX MOTIFS

		Contents of file c8HthTF.kin:
*{Kin 1}* Lambda Cro, & 5 helix-turn-helix motifs superimposed (Fig. 8.3-8.5)
*{Kin 2}* Lambda repressor/DNA complex - overview of dimer (Fig. 8.6-8.9)
*{Kin 3}* Lambda repressor/DNA - details of interactions (Fig. 8.14-8.17)
*{Kin 4}* Animation of allosteric changes in Trp repressor (Fig. 8.18-8.20)
*{Kin 5}* Lac repressor tetramer - core & 4-helix domains (Fig. 8.21,8.22)
*{Kin 6}* PurR/guanine/DNA binding (Fig. 8.23)
*{Kin 7}* CAP protein dimer vs CAP/DNA, animation (Fig. 8.24)

     *{Kinemage 1}* shows the Calpha backbone of a dimer of the lambda Cro protein, with each helix-turn-helix ("h-t-h") DNA-binding motif emphasized in skyblue and red, as in Fig. 8.4.  The subunits dimerize through beta strands, making a 6-stranded antiparallel beta sheet, while the DNA-binding motifs are at opposite ends of the molecule.  For the top motif, five other helix-turn-helix motifs (from lambda repressor, 434 cro, 434 repressor, CAP protein, and Trp repressor) are superimposed onto this one.  Animate to see close-ups of these helix-turn-helix motifs.  First you look down the second, "recognition", helix (red), with the first helix horizontal in the plane of the screen.  Then you see the perpendicular view, looking down the first helix (approximately as in Fig. 8.3a).  The 2 h-t-h  helices are nearly perpendicular and touch only near their ends in an asymmetrical way, a rather unusual arrangement that is common to a large family of DNA-binding proteins and rare otherwise.  It is reminiscent of the Ca++ binding "E-F hand" motifs, but the sequence runs in the opposite direction.

     *{Kinemage 2}* is an overview of the lambda repressor/DNA complex.  The two protein subunits are in white with blue and red helix-turn-helix motifs, which bind in adjacent turns of the major groove.  (There is another, C-terminal, domain in each subunit of the intact dimer molecule of repressor, which was not included in the crystal structure determination.)  The DNA backbone is represented by virtual bonds from P to C4' to P (gold), the sugars with a branching virtual bond from C4' to C1' (gold), and each base pair with a shortened line (yellowtint) joining sugar C1' atoms across the double helix.
    In the start-up view, the DNA double-helix is angled so that you look down the major grooves in which the repressor mainly binds.  There is a nearly-exact twofold symmetry between the two subunits of the lambda repressor dimer and between the two halves of the operator site on the DNA, but for subunit b the N-terminal tail is shown wrapped around the DNA (it includes 3 lysines) while residues 1-5 of subunit a were disordered in the crystal.  Subunit b binds to the half of the DNA that has the consensus operator sequence, while the other half has a non-consensus sequence with 3 changes.  The DNA is nearly standard B-form, but it is bent very slightly around the protein.  View2 looks down the double helix from one end, with the repressor sitting on top.

     *{Kinemage 3}* shows some details of the interaction between lambda repressor and DNA, which is very similar to the 434 repressor/DNA shown in Fig. 7.16 and 7.17.  Only interacting side chains are shown, on the b subunit.  The base pairs are shown in full, but without the base-pair Hbonds and without an explicit connection to the DNA backbone;  those that make interactions are color coded: G green, C yellow, A pink, and T blue, while the others are in gray.
    Gln 44, Ser 45, and Asn 55 of both repressor subunits, and Thr 2 and Lys 4 of subunit b, make specific H-bonds with bases in the major groove.  View2 is a close-up of the Gln 44 interaction (similar to Fig. 8.15b), showing the H-bond network to Gln 33 and a phosphate O that helps determine the nature and orientation of hydrogen bonds to Adenine 4 on strand 2 of the DNA.  View3 shows the double side-chain interaction of Asn 55 and Lys 4 with G 14 of strand 1, and also the H-bond between Thr 2 and G 10.  View4 looks deep into the interface, to show how the methyl groups of Thymidines 5 and 15 (green atom balls) fit snugly in between hydrophobic side chains and up against the helix backbone at Gly 46 and Gly 48.
	View5 looks down the axis of helix 1 of the binding motif from its N-terminal end, in a region that is typical of the types of non-specific DNA-binding interactions made with the sugar-phosphate backbone.  The N-terminus of the alpha helix interacts both by a specific H-bond to one of the free NH groups in the first turn (as in Fig. 8.16), and also by means of the helix dipole, which is appropriately positive at the N-terminus for interacting with the negatively-charged phosphates.  That same phosphate group also has a salt link to a charged Lys side chain and an H-bond to a polar Tyr OH group.

     *{Kinemage 4}* shows the structure of Trp repressor and its allosteric conformational changes.  First note the unusual organization of this all-helical protein, with an intertwining of two subunits each of which is non-compact alone (you can turn off one of the subunits to see the other one by itself).
     Animate to switch from the apo form (dark colors) to the Trp-liganded form (medium colors) to the DNA-complex form (light colors) which binds both Trp and the operon DNA (the 3 forms were superimposed using the lower halves of the structures).  For the complexed structure, the helix-turn-helix motifs are shown with full main chain.  The most important change is movement of the two helix-turn-helix motifs further apart:  turn on "measures" on the Tools pulldown, and locate a Calpha that sticks out distinctively in the turn (such as Ile79). Click on the same Calpha in each of the two subunits for the apo structure to find their distance apart, then do the same for each of the 3 forms.  That end of the two recognition helices is 36A apart in the complex, suitable for fitting in the DNA major groove one turn apart, while the distance is only 30A in the apo repressor.  Turn on all three forms at once or in pairs to see this difference another way.  Turn on the DNA and animate again, to see that the apo form could not bind:  if the bottom half is oriented correctly the top half would intersect the DNA impossibly.
     Binding of Trp moves the helix-turn-helix "reading heads" most of the way apart.  Turn off DNA, choose View2 for a close-up of the Trp site, and turn on all 3 forms to see that Trp binding wedges the two subunits apart somewhat - note especially the offset of the two green helices.  Thus Trp binds preferentially to the more open conformation and acts as an allosteric effector to activate DNA binding.  Turn on "binding" to see that the Trp is sandwiched between two Arg side-chains and also forms main-chain H-bonds.  Just below the Trp is Ala77, the site of a mutant (Ala77Val) that activates repressor constitutively even in the absence of Trp.  Temporarily turn on "mutant";  the Val side chain would clash with Thr53 in the more compact apo conformation, so it also tends to wedge the subunits apart and favor the active conformation.
     Now turn on just the DNA complex form, the DNA, and "binding".  Choose View3 for a close-up of sequence-specific binding between the Arg69 guanidinium and the N7 and O6 of Guanine 2;  the Arg is also oriented by a through-water H-bond to the neighboring phosphate.  Choose View4 for a close-up of non-specific binding to DNA-backbone phosphates made by Arg and Thr side chains, main-chain NH, and even an H-bond from the Trp ligand.  Choose View5 for a closeup of repressor-DNA binding (both specific and non-specific) through ordered water molecules, of which there are more cases for Trp repressor than for most other DNA complexes.

     *{Kinemage 5}* shows the core domains and 4-helix bundle domain for a tetramer of the lac repressor.  Each of the tight dimers binds the palindromic lac operator sequence of DNA (as for PurR, shown in the next kinemage) with a pair of N-terminal domains not present here.  The core domains (in greens and blues) are the regulating element that binds lactose, the co-repressor, whose presence allosterically changes the conformation to prevent DNA binding and to down-regulate expression of the lac operon.  View2 shows those core domains from the side, with their hinged connections toward the center;  they are both doubly-wound alpha/beta structures organized very like the arabinose-binding protein discussed in Chapter 6, and the lactose binds in the cleft between the two domains.  
     Choose View3 and turn off "core domain 2", to see a close-up of the 4-helix bundle that holds the two dimers together into a tetramer.  It is organized very much like the Rop protein helix-bundle in kinemage file c3Alpha.kin, with pairs of extremely close, regular alpha-helices joined by a wider hydrophobic core.  Turn on "4-hlx sidech" to see the pairs of orange Ala between the closely-paired helices and the gold Leu and Val that form the wider central hydrophobic core, organized in very definite layers.  The difference from ROP is that the close pair of helices are offset by half a turn, whereas in ROP they had adjacent turns aligned.

     *{Kinemage 6}* shows the PurR repressor binding to DNA; it is the primary regulator of purine synthesis and closely related to the lac repressor, but it is a dimer instead of a tetramer.  The first three views show different orientations of the overall complex, showing the considerable bending of the DNA and the fact that PurR interacts with the minor as well as the major groove.  View4 concentrates on the DNA-binding region, similar to Fig. 8.23, with each N-terminal domain putting a helix-turn-helix motif in the major groove and a fourth helix in the minor groove.  View5 is a close-up of interactions in the minor groove, including the Leu side chains that wedge apart the two central G-C base pairs and the Lys making a specific interaction with N3 of an Adenine.  View6 is a closeup of some of the helix-turn-helix DNA interactions, including nonspecific interactions of backbone NH and side-chain OHs with phosphate O and a sequence-specific double H-bond of Arg 26 (just past the helix-turn-helix) with N7 and O6 of a Guanine.
     View7 is a close-up of the regulatory purine binding site.  It is sandwiched between aromatics and bound by several H-bonds, in the cleft between the two domains of the "core" region (the part that resembles arabinose-binding protein).  Its binding changes the relative orientation of purR domains in such a way as to allosterically promote DNA binding.

     *{Kinemage 7}* shows the dimer of CAP protein ("gene activator protein", or "catabolite activator protein", or "cAMP-dependent repressor protein"). The protein dimerizes through interaction of two long helices at the interface, which form a parallel coiled-coil.  Each subunit has a large domain with an 8-stranded Greek key beta barrel inside which the cAMP binds (purple), and a smaller domain that contains the helix-turn-helix DNA-binding motif.  In the free form, the two subunits have rather different conformations, with the domains further apart in subunit b (greentint).  All four chain termini were disordered in the complex, but three of them were ordered in the free form;  those "tails" have been turned off for clarity.
     Animate to see the conformational change on binding to DNA.  Most of the dimer stays the same (they were superimposed using the two long helices at the dimer interface), but the small domain of subunit 2 rotates inward (some atoms move by more than 10A), making the two subunits more equivalent.  Choose View2 to emphasize the strong bend of the DNA.  This DNA sequence is very AT-rich, and is believed to be bent in solution.  In this complex, the protein and DNA make extensive interactions, over a wider interface than would be possible if the DNA were straight.  The N-terminal end of the first helix (skyblue) of the h-t-h motif points at DNA backbone, while the N-terminal end of the second helix (red) points into the major groove (View3).  Choose View4 and turn off "DNA" to concentrate on subunit b (greens) and see the relative domain motion of the conformational change.


    Copyright 1999 Jane S. and David C. Richardson.  Permission freely granted for educational, research, and personal use.  For program updates and more information, see http://kinemage.biochem.duke.edu.
@kinemage 1
@caption (B&T Fig. 8.3-8.5)
Lambda Cro protein - dimer, with helix-turn-helix ("h-t-h") motifs emphasized in skyblue and red. Animate for a tour of views, starting with a close-up of the helix-turn-helix in subunit o, looking down the second helix with the first helix horizontal in the plane of the screen, with 5 other h-t-h motifs superimposed.  (from PDB files 1CRO, 1LRD, 2CRO, 1R69, 2GAP, 1TRO)
@onewidth
@viewid {Cro dimer}
@zoom 1.00
@zslab 150
@ztran 0
@center -22.805 -37.033 -28.331
@matrix
-0.463305 -0.360981 -0.809346 -0.788376 0.584993 0.190385 0.404736 0.726276 -0.555619
@2viewid {down hlx 2}
@2zoom 1.77
@2zslab 150
@2center -34.580 -30.113 -18.415
@2matrix
0.465795 -0.879078 -0.101277 0.135102 -0.042461 0.989922 -0.874519 -0.474783 0.098987
@3viewid {down hlx 1}
@3zoom 1.77
@3zslab 130
@3center -34.580 -30.113 -18.415
@3matrix
0.866213 0.178282 0.466787 -0.036132 -0.909389 0.414375 0.498367 -0.375803 -0.781283
@master {rest}
@master {Lcro h-t-h}
@master {Lrep h-t-h}
@master {434cro h-t-h}
@master {434rep h-t-h}
@master {CAP h-t-h}
@master {TrpRp h-t-h}
@group {lambda Cro} animate moview= 1
@subgroup {sub o} dominant
@vectorlist {ca-ca} color= white master= {rest}
{ca met o 1}P -10.546 -31.594 -17.598
{"}-10.546 -31.594 -17.598
{ca glu o 2}-14.282 -31.313 -18.167
{ca gln o 3}-17.038 -32.941 -16.293
{ca arg o 4}-19.805 -34.669 -18.370
{ca ile o 5}-23.176 -35.450 -16.637
{ca thr o 6}-26.445 -36.795 -17.900
{ca leu o 7}-29.258 -34.194 -18.097
{ca lys o 8}-31.289 -36.184 -15.550
{ca asp o 9}-28.576 -36.314 -12.865
{ca tyr o 10}-27.735 -32.701 -13.242
{ca ala o 11}-31.242 -31.443 -12.972
{ca met o 12}-31.602 -33.653 -9.894
{ca arg o 13}-28.846 -32.180 -7.967
{ca phe o 14}-29.182 -28.666 -9.232
{ca gly o 15}-32.926 -28.419 -9.747
{ca gly o 37}P -35.731 -40.045 -21.877
{ca arg o 38}-33.503 -38.252 -24.503
{ca lys o 39}-29.788 -38.964 -24.270
{ca ile o 40}-28.527 -35.625 -23.348
{ca phe o 41}-25.224 -34.808 -21.596
{ca leu o 42}-24.219 -31.558 -20.035
{ca thr o 43}-20.525 -30.544 -20.216
{ca ile o 44}-19.153 -28.403 -17.455
{ca asn o 45}-15.879 -26.755 -18.342
{ca ala o 46}-13.124 -25.697 -15.899
{ca asp o 47}-14.661 -22.200 -15.662
{ca gly o 48}-18.140 -23.416 -14.811
{ca ser o 49}-19.553 -22.759 -18.208
{ca val o 50}-22.172 -25.427 -19.178
{ca tyr o 51}-23.209 -26.718 -22.636
{ca ala o 52}-25.467 -29.498 -23.814
{ca glu o 53}-25.600 -32.035 -26.581
{ca glu o 54}-27.736 -34.939 -27.593
{ca val o 55}-25.832 -38.126 -28.422
{ca lys o 56}-26.814 -40.942 -30.956
{ca pro o 57}-24.891 -43.976 -31.987
{ca phe o 58}-22.999 -44.390 -35.232
{ca pro o 59}-24.073 -46.201 -37.189
{ca ser o 60}-27.665 -45.779 -35.896
{ca asn o 61}-27.813 -49.388 -36.788
{ca lys o 62}-30.775 -51.578 -36.051
{ca lys o 63}-30.903 -51.039 -39.789
{ca thr o 64}-30.235 -52.897 -42.887
{ca thr o 65}-27.679 -55.277 -44.457
{ca ala o 66}-26.564 -56.825 -47.797
{arw}P -26.551 -43.059 -30.358
{ca pro o 57}-24.891 -43.976 -31.987
{arw}-25.338 -41.567 -32.486
{"}P -18.368 -26.520 -18.384
{ca asn o 45}-15.879 -26.755 -18.342
{arw}-16.946 -28.780 -17.337
{"}P -24.776 -34.945 -18.104
{ca thr o 6}-26.445 -36.795 -17.900
{arw}-24.547 -37.177 -16.318
@vectorlist {hlx 1 o} color= sky master= {Lcro h-t-h}
{ca gly o 15}P -32.926 -28.419 -9.747
{ca gln o 16}-34.772 -27.785 -12.919
{ca thr o 17}-34.903 -24.028 -12.425
{ca lys o 18}-31.148 -23.670 -12.480
{ca thr o 19}-30.592 -26.317 -15.177
{ca ala o 20}-32.897 -24.274 -17.433
{ca lys o 21}-30.992 -21.007 -16.756
{ca asp o 22}-27.621 -22.746 -17.315
{ca leu o 23}-28.825 -24.040 -20.669
{ca gly o 24}-30.701 -20.936 -21.614
@vectorlist {turn o} color= white master= {Lcro h-t-h}
{ca gly o 24}P -30.701 -20.936 -21.614
{ca val o 25}-34.150 -22.579 -22.281
{ca tyr o 26}-37.571 -22.379 -20.770
@vectorlist {hlx 2 o} color= red master= {Lcro h-t-h}
{ca tyr o 26}P -37.571 -22.379 -20.770
{ca gln o 27}-37.999 -24.961 -17.921
{ca ser o 28}-40.604 -27.168 -19.557
{ca ala o 29}-38.080 -27.941 -22.222
{ca ile o 30}-35.828 -29.605 -19.577
{ca asn o 31}-38.725 -31.605 -18.170
{ca lys o 32}-39.930 -32.708 -21.504
{ca ala o 33}-36.492 -33.921 -22.621
{ca ile o 34}-36.264 -35.952 -19.396
{ca his o 35}-39.812 -37.306 -19.618
{ca ala o 36}-38.899 -38.363 -23.129
{ca gly o 37}-35.731 -40.045 -21.877
@subgroup {sub b} dominant
@vectorlist {ca-ca} color= sea master= {rest}
{ca met b 1}P -8.384 -42.826 -20.406
{ca glu b 2}-9.697 -42.363 -23.899
{ca gln b 3}-8.985 -40.500 -27.119
{ca arg b 4}-11.724 -38.805 -29.012
{ca ile b 5}-11.333 -37.555 -32.556
{ca thr b 6}-13.699 -36.411 -35.315
{ca leu b 7}-14.600 -38.850 -38.128
{ca lys b 8}-13.066 -36.541 -40.722
{ca asp b 9}-9.758 -36.188 -38.836
{ca tyr b 10}-9.636 -39.887 -38.098
{ca ala b 11}-10.160 -40.549 -41.774
{ca met b 12}-7.148 -38.254 -42.608
{ca arg b 13}-5.005 -39.985 -40.092
{ca phe b 14}-5.807 -43.642 -41.158
{ca gly b 15}-7.675 -43.585 -44.564
{ca gly b 37}P -21.063 -32.822 -42.669
{ca arg b 38}-22.311 -35.063 -39.822
{ca lys b 39}-20.902 -34.391 -36.358
{ca ile b 40}-19.447 -37.785 -35.623
{ca phe b 41}-16.827 -38.377 -32.914
{ca leu b 42}-15.017 -41.720 -32.520
{ca thr b 43}-13.867 -42.838 -29.080
{ca ile b 44}-10.729 -44.704 -28.857
{ca asn b 45}-10.490 -46.928 -25.771
{ca ala b 46}-7.143 -47.790 -24.157
{ca asp b 47}-7.629 -51.347 -25.391
{ca gly b 48}-7.858 -50.152 -29.062
{ca ser b 49}-11.543 -50.661 -29.488
{ca val b 50}-13.268 -47.898 -31.435
{ca tyr b 51}-16.816 -46.693 -31.310
{ca ala b 52}-18.541 -43.733 -32.900
{ca glu b 53}-21.318 -41.365 -31.929
{ca glu b 54}-23.172 -38.570 -33.539
{ca val b 55}-23.497 -35.397 -31.574
{ca lys b 56}-25.977 -32.564 -31.906
{ca pro b 57}-26.473 -29.552 -29.670
{ca phe b 58}-29.188 -28.895 -27.058
{ca pro b 59}-31.465 -26.934 -27.164
{ca ser b 60}-29.662 -26.365 -30.361
{ca asn b 61}-26.914 -24.789 -28.141
{ca lys b 62}-28.241 -21.216 -28.057
{ca lys b 63}-27.907 -17.413 -27.517
{ca thr b 64}-31.772 -17.241 -26.781
{ca thr b 65}-34.807 -19.727 -26.291
{ca ala b 66}-38.175 -19.760 -24.248
{arw}P -25.257 -30.444 -31.664
{ca pro b 57}-26.473 -29.552 -29.670
{arw}-27.152 -31.920 -30.097
{"}P -11.792 -35.740 -33.844
{ca thr b 6}-13.699 -36.411 -35.315
{arw}-13.062 -38.311 -33.821
{"}P -10.028 -44.652 -26.696
{ca asn b 45}-10.490 -46.928 -25.771
{arw}-11.209 -46.814 -28.163
@vectorlist {hlx 1 b} color= sky master= {Lcro h-t-h}
{ca gly b 15}P -7.675 -43.585 -44.564
{ca gln b 16}-11.332 -44.669 -45.288
{ca thr b 17}-10.476 -48.349 -45.429
{ca lys b 18}-9.141 -48.596 -41.909
{ca thr b 19}-11.954 -46.319 -40.612
{ca ala b 20}-14.670 -48.545 -41.994
{ca lys b 21}-13.294 -51.695 -40.549
{ca asp b 22}-12.680 -50.119 -37.118
{ca leu b 23}-16.316 -49.000 -37.181
{ca gly b 24}-17.566 -52.186 -38.794
@vectorlist {turn b} color= sea master= {Lcro h-t-h}
{ca gly b 24}P -17.566 -52.186 -38.794
{ca val b 25}-19.208 -50.404 -41.793
{ca tyr b 26}-18.403 -49.975 -45.435
@vectorlist {hlx 2 b} color= red master= {Lcro h-t-h}
{ca tyr b 26}P -18.403 -49.975 -45.435
{ca gln b 27}-16.403 -47.177 -46.990
{ca ser b 28}-19.270 -45.514 -48.695
{ca ala b 29}-21.034 -45.093 -45.300
{ca ile b 30}-17.985 -43.333 -43.966
{ca asn b 31}-17.632 -41.196 -47.119
{ca lys b 32}-21.208 -40.196 -47.193
{ca ala b 33}-21.279 -39.169 -43.504
{ca ile b 34}-18.208 -36.973 -43.826
{ca his b 35}-19.451 -35.340 -47.055
{ca ala b 36}-22.872 -34.584 -45.529
{ca gly b 37}-21.063 -32.822 -42.669
@group {other 5} dominant 
@vectorlist {hlx 1} color= sky master= {Lrep h-t-h}
{ca ser b 32}P -33.478 -27.908 -10.077
{ca gln b 33}-34.837 -28.063 -13.644
{ca glu b 34}-35.359 -24.371 -12.804
{ca ser b 35}-31.567 -23.816 -12.629
{ca val b 36}-30.409 -26.603 -14.969
{ca ala b 37}-32.584 -24.687 -17.478
{ca asp b 38}-30.975 -21.232 -17.081
{ca lys b 39}-27.557 -22.856 -17.592
{ca met b 40}-28.851 -24.091 -20.973
{ca gly b 41}-30.865 -21.075 -22.095
@vectorlist {turn} color= white master= {Lrep h-t-h}
{ca gly b 41}P -30.865 -21.075 -22.095
{ca met b 42}-34.343 -22.658 -21.947
{ca gly b 43}-37.288 -22.872 -19.552
@vectorlist {hlx 2} color= red master= {Lrep h-t-h}
{ca gly b 43}P -37.288 -22.872 -19.552
{ca gln b 44}-38.220 -25.536 -17.034
{ca ser b 45}-40.634 -27.095 -19.580
{ca gly b 46}-37.936 -27.467 -22.227
{ca val b 47}-35.725 -29.217 -19.658
{ca gly b 48}-38.863 -31.004 -18.454
{ca ala b 49}-39.524 -32.389 -21.956
{ca leu b 50}-35.974 -33.708 -22.119
{ca phe b 51}-36.035 -35.527 -18.773
{ca asn b 52}-39.453 -37.081 -19.540
{ca gly b 53}-39.254 -38.453 -23.119
@vectorlist {hlx 1} color= sky master= {434rep h-t-h}
{ca asn  16 } P -32.849, -28.691 -10.016
{ca gln  17 } -34.641 -28.303 -13.389
{ca ala  18 } -35.005 -24.526 -13.061
{ca glu  19 } -31.273 -24.1 -12.449
{ca leu  20 } -30.372 -26.314 -15.403
{ca ala  21 } -32.802 -24.363 -17.648
{ca gln  22 } -31.156 -21.018 -16.752
{ca lys  23 } -27.647 -22.495 -17.278
{ca val  24 } -28.655 -23.818 -20.712
{ca gly  25 } -30.698 -20.678 -21.5
@vectorlist {turn} color= white master= {434rep h-t-h}
{ca gly  25 }P -30.698 -20.678 -21.5
{ca thr  26 } -33.969 -22.5 -22.211
{ca thr  27 } -37.420 -22.825 -20.625
@vectorlist {hlx 2} color= red master= {434rep h-t-h}
{ca thr  27 }P -37.420 -22.825 -20.625
{ca gln  28 } -38.284 -24.929 -17.571
{ca gln  29 } -40.757 -26.854 -19.781
{ca ser  30 } -38.032 -27.809 -22.314
{ca ile  31 } -36.043 -29.405 -19.483
{ca glu  32 } -39.131 -31.255 -18.248
{ca gln  33 } -39.879 -32.617 -21.717
{ca leu  34 } -36.319 -33.919 -22.118
{ca glu  35 } -36.451 -35.603 -18.683
{ca asn  36 } -39.848 -37.18 -19.506
{ca gly  37 } -38.502 -38.508 -22.838
@vectorlist {hlx 1} color= sky master= {434cro h-t-h}
{ca thr 16} P -32.746 -28.545 -10.212
{ca gln 17} -34.509 -28.41 -13.608
{ca thr 18} -34.851 -24.665 -13.065
{ca glu 19} -31.175 -24.109 -12.468
{ca leu 20} -30.352 -26.317 -15.481
{ca ala 21} -32.757 -24.181 -17.526
{ca thr 22} -31.298 -20.844 -16.332
{ca lys 23} -27.658 -21.864 -16.968
{ca ala 24} -28.449 -23.293 -20.420
{ca gly 25} -30.755 -20.418 -21.290
@vectorlist {turn} color= white master= {434cro h-t-h}
{ca gly 25}P -30.755 -20.418 -21.290
{ca val 26} -33.771 -22.541 -22.315
{ca lys 27} -37.318 -22.963 -21.013
@vectorlist {hlx 2} color= red master= {434cro h-t-h}
{ca lys 27}P -37.318 -22.963 -21.013
{ca gln 28} -37.78 -25.077 -17.907
{ca gln 29} -40.678 -26.78 -19.751
{ca ser 30} -38.023 -27.851 -22.269
{ca ile 31} -36.129 -29.861 -19.662
{ca gln 32} -39.202 -31.618 -18.225
{ca leu 33} -40.173 -32.762 -21.739
{ca ile 34} -36.665 -34.098 -22.322
{ca glu 35} -36.519 -35.738 -18.888
{ca ala 36} -40.073 -37.087 -19.289
{ca gly 37} -38.851 -38.686 -22.552
@vectorlist {hlx 1} color= sky master= {CAP h-t-h}
{ca thr a 168}P -34.014 -28.159 -9.884
{ca arg a 169}-35.010 -27.904 -13.517
{ca gln a 170}-35.086 -24.101 -13.053
{ca glu a 171}-31.326 -24.497 -12.579
{ca ile a 172}-30.729 -26.481 -15.810
{ca gly a 173}-32.623 -23.997 -18.011
{ca gln a 174}-30.658 -21.164 -16.452
{ca ile a 175}-27.487 -23.056 -17.379
{ca val a 176}-28.280 -24.309 -20.917
{ca gly a 177}-30.595 -21.675 -22.343
@vectorlist {turn} color= white master= {CAP h-t-h}
{ca gly a 177}P -30.595 -21.675 -22.343
{ca cys a 178}-34.095 -23.045 -22.083
{ca ser a 179}-37.196 -23.100 -19.828
@vectorlist {hlx 2} color= red master= {CAP h-t-h}
{ca ser a 179}P -37.196 -23.100 -19.828
{ca arg a 180}-38.303 -25.064 -16.767
{ca glu a 181}-40.851 -26.771 -19.090
{ca thr a 182}-38.834 -27.807 -22.167
{ca val a 183}-36.301 -29.215 -19.713
{ca gly a 184}-39.188 -31.264 -18.256
{ca arg a 185}-40.533 -32.142 -21.690
{ca ile a 186}-36.912 -33.308 -22.171
{ca leu a 187}-36.031 -34.820 -18.844
{ca lys a 188}-38.366 -37.773 -19.517
@vectorlist {hlx 1} color= sky master= {TrpRp h-t-h}
{ca ser a 67}P -31.977 -28.900 -10.109
{ca gln a 68}-34.246 -28.403 -13.180
{ca arg a 69}-34.529 -24.630 -12.544
{ca glu a 70}-30.750 -24.510 -12.294
{ca leu a 71}-30.369 -26.326 -15.625
{ca lys a 72}-32.839 -23.977 -17.351
{ca asn a 73}-31.009 -20.842 -16.127
{ca glu a 74}-27.619 -22.222 -17.240
{ca leu a 75}-28.831 -22.926 -20.810
{ca gly a 76}-31.136 -19.933 -21.283
@vectorlist {turn} color= white master= {TrpRp h-t-h}
{ca gly a 76}P -31.136 -19.933 -21.283
{ca ala a 77}-33.926 -22.520 -21.853
{ca gly a 78}-37.625 -22.701 -20.989
@vectorlist {hlx 2} color= red master= {TrpRp h-t-h}
{ca gly a 78}P -37.625 -22.701 -20.989
{ca ile a 79}-38.321 -25.175 -18.149
{ca ala a 80}-40.795 -26.871 -20.549
{ca thr a 81}-37.807 -28.044 -22.721
{ca ile a 82}-36.184 -29.572 -19.618
{ca thr a 83}-39.558 -31.352 -18.932
{ca arg a 84}-39.586 -32.766 -22.458
{ca gly a 85}-36.117 -34.203 -21.732
{ca ser a 86}-37.350 -35.666 -18.432
{ca asn a 87}-40.490 -37.276 -19.849
{ca ser a 88}-38.513 -38.669 -22.803
{ca leu a 89}-35.885 -40.273 -20.529
@group {h-t-h, dwn2} dominant animate moview= 2
@vectorlist {h1o} instance= {hlx 1 o} master= {Lcro h-t-h}
@vectorlist {t o} instance= {turn o} master= {Lcro h-t-h}
@vectorlist {h2o} instance= {hlx 2 o} master= {Lcro h-t-h}
@group {h-t-h, dwn1} dominant animate moview= 3
@vectorlist {h1o} instance= {hlx 1 o} master= {Lcro h-t-h}
@vectorlist {t o} instance= {turn o} master= {Lcro h-t-h}
@vectorlist {h2o} instance= {hlx 2 o} master= {Lcro h-t-h}

@kinemage 2
@caption (B&T Fig. 7.8, 7.16)
Complex of a lambda repressor dimer with DNA - simplified "virtual backbone" (gold) and base-pair lines (yellowtint) for the DNA, Calphas for the repressor, with the helix-turn-helix motifs highlighted in skyblue and red. View2 looks down the DNA axis. (from PDB file 1LRD)
@onewidth 
@zoom 1.14
@zslab 140
@center 11.845 -7.539 7.61
@matrix
-.686676 .152498 -.710788 .630607 -.361495 -.686772 -.361679 -.919818 .152063
@2zoom 1.4
@2zslab 260
@2matrix
.594571 .603803 -.530949 .704786 -.709209 -.017282 -.386988 -.363931 -.847228
@group {DNA}
@subgroup {strand 1} dominant
@vectorlist {mc 1} color= gold 
{c4* a 1 1} P 32.187 -1.67 32.865
{p a 1 2} 32.632 -4.068 29.822
{c4* a 1 2} 29.73 -6.418 29.964
{p t 1 3} 27.177 -8.391 27.554
{c4* t 1 3} 24.159 -8.157 29.753
{p a 1 4} 20.618 -9.559 28.83
{c4* a 1 4} 18.105 -7.47 30.887
{p c 1 5} 14.104 -7.752 30.397
{c4* c 1 5} 13.049 -4.137 31.298
{p c 1 6} 9.322 -3.182 30.369
{c4* c 1 6} 9.808 0.687 29.919
{p a 1 7} 6.127 1.45 28.768
{c4* a 1 7} 6.891 4.268 26.414
{p c 1 8} 5.438 7.009 23.924
{c4* c 1 8} 7.879 7.044 21.137
{p t 1 9} 6.933 8.824 17.849
{c4* t 1 9} 9.56 7.676 15.17
{p g 1 10} 9.949 8.865 11.808
{c4* g 1 10} 12.476 6.577 9.979
{p g 1 11} 13.191 6.267 6.189
{c4* g 1 11} 12.088 2.433 6.126
{p c 1 12} 12.21 0.667 3.043
{c4* c 1 12} 11.246 -2.797 4.513
{p g 1 13} 10.567 -6.329 2.792
{c4* g 1 13} 6.901 -6.528 2.992
{p g 1 14} 4.914 -8.837 0.564
{c4* g 1 14} 2.238 -6.996 0.16
{p t 1 15} -1.398 -7.999 -0.906
{c4* t 1 15} -4.12 -5.931 0.866
{p g 1 16} -7.591 -6.879 -0.536
{c4* g 1 16} -9.11 -3.457 -1.299
{p a 1 17} -12.254 -2.763 -3.642
{c4* a 1 17} -11.48 0.852 -4.616
{p t 1 18} -13.562 2.811 -7.38
{c4* t 1 18} -10.999 4.02 -9.677
{p a 1 19} -11.125 6.233 -12.976
{c4* a 1 19} -7.521 6.405 -14.179
{p t 1 20} -7.048 7.807 -17.769
{c4* t 1 20} -4.299 5.271 -19.091
@vectorlist {sug 1} color= gold
{c4* a 1 1} P 32.187 -1.67 32.865
{c1* a 1 1} 30.557 -3.168 33.72
{c4* a 1 2} P 29.73 -6.418 29.964
{c1* a 1 2} 27.74 -5.388 30.614
{c4* t 1 3} P 24.159 -8.157 29.753
{c1* t 1 3} 23.08 -6.109 29.759
{c4* a 1 4} P 18.105 -7.47 30.887
{c1* a 1 4} 17.865 -5.449 29.748
{c4* c 1 5} P 13.049 -4.137 31.298
{c1* c 1 5} 13.808 -2.515 29.845
{c4* c 1 6} P 9.808 0.687 29.919
{c1* c 1 6} 10.615 0.88 27.713
{c4* a 1 7} P 6.891 4.268 26.414
{c1* a 1 7} 8.193 4.048 24.493
{c4* c 1 8} P 7.879 7.044 21.137
{c1* c 1 8} 8.407 5.14 20.083
{c4* t 1 9} P 9.56 7.676 15.17
{c1* t 1 9} 9.322 5.408 14.663
{c4* g 1 10} P 12.476 6.577 9.979
{c1* g 1 10} 10.79 5.03 9.494
{c4* g 1 11} P 12.088 2.433 6.126
{c1* g 1 11} 9.76 2.144 6.075
{c4* c 1 12} P 11.246 -2.797 4.513
{c1* c 1 12} 8.926 -2.673 4.251
{c4* g 1 13} P 6.901 -6.528 2.992
{c1* g 1 13} 5.406 -5.003 2.08
{c4* g 1 14} P 2.238 -6.996 0.16
{c1* g 1 14} 1.516 -4.831 0.747
{c4* t 1 15} P -4.12 -5.931 0.866
{c1* t 1 15} -4.339 -3.951 -0.399
{c4* g 1 16} P -9.11 -3.457 -1.299
{c1* g 1 16} -8.232 -2.295 -3.123
{c4* a 1 17} P -11.48 0.852 -4.616
{c1* a 1 17} -9.974 0.694 -6.417
{c4* t 1 18} P -10.999 4.02 -9.677
{c1* t 1 18} -9.3 2.845 -10.497
{c4* a 1 19} P -7.521 6.405 -14.179
{c1* a 1 19} -7.424 4.405 -15.432
{c4* t 1 20} P -4.299 5.271 -19.091
{c1* t 1 20} -5.18 3.202 -19.781
@subgroup {strand 2} dominant 
@vectorlist {mc 2} color= gold
{c4* t 2 1} P -10.271 -10.39 -19.724
{p a 2 2} -6.677 -11.662 -18.322
{c4* a 2 2} -3.957 -9.69 -19.957
{p t 2 3} -0.737 -9.14 -17.626
{c4* t 2 3} -0.239 -5.161 -17.809
{p a 2 4} 2.483 -3.292 -16.863
{c4* a 2 4} 1.102 0.131 -16.196
{p t 2 5} 2.865 3.285 -14.714
{c4* t 2 5} -0.074 4.625 -12.594
{p c 2 6} 0.932 7.449 -10.224
{c4* c 2 6} -2.553 7.236 -8.731
{p a 2 7} -3.077 9.683 -5.75
{c4* a 2 7} -5.605 8.288 -3.294
{p c 2 8} -5.593 9.525 0.547
{c4* c 2 8} -5.38 5.827 1.801
{p c 2 9} -5.014 5.766 5.733
{c4* c 2 9} -3.833 2.206 6.286
{p g 2 10} -4.03 1.67 9.751
{c4* g 2 10} -2.9 -1.986 9.802
{p c 2 11} -2.214 -4.639 12.572
{c4* c 2 11} 1.328 -5.546 11.557
{p c 2 12} 3.501 -7.834 13.694
{c4* c 2 12} 7.054 -6.673 12.486
{p a 2 13} 9.948 -8.143 14.264
{c4* a 2 13} 12.368 -6.109 12.321
{p g 2 14} 16.384 -5.855 13.09
{c4* g 2 14} 16.67 -2.027 13.575
{p t 2 15} 19.56 0.131 15.176
{c4* t 2 15} 17.604 3.34 15.905
{p g 2 16} 20.357 5.484 17.706
{c4* g 2 16} 18.292 7.346 20.288
{p g 2 17} 20.04 9.538 22.938
{c4* g 2 17} 17.624 8.803 25.764
{p t 2 18} 18.317 9.978 29.52
{c4* t 2 18} 16.533 6.989 31.19
{p a 2 19} 16.377 6.219 34.974
{c4* a 2 19} 15.586 2.426 35.31
{p t 2 20} 16.253 0.302 38.592
{c4* t 2 20} 17.84 -2.872 37.384
@vectorlist {sug 2} color= gold
{c4* t 2 1} P -10.271 -10.39 -19.724
{1* t 2 1} -9.258 -8.459 -20.407
{c4* a 2 2} P -3.957 -9.69 -19.957
{c1* a 2 2} -4.463 -7.868 -18.584
{c4* t 2 3} P -0.239 -5.161 -17.809
{c1* t 2 3} -1.976 -4.061 -16.766
{c4* a 2 4} P 1.102 0.131 -16.196
{c1* a 2 4} -0.24 0.11 -14.287
{c4* t 2 5} P -0.074 4.625 -12.594
{c1* t 2 5} -0.659 3.113 -10.942
{c4* c 2 6} P -2.553 7.236 -8.731
{c1* c 2 6} -2.975 5.738 -7.044
{c4* a 2 7} P -5.605 8.288 -3.294
{c1* a 2 7} -4.24 6.666 -2.314
{c4* c 2 8} P -5.38 5.827 1.801
{c1* c 2 8} -3.579 4.46 1.715
{c4* c 2 9} P -3.833 2.206 6.286
{c1* c 2 9} -1.556 1.979 5.824
{c4* g 2 10} P -2.9 -1.986 9.802
{c1* g 2 10} -0.673 -1.649 9.483
{c4* c 2 11} P 1.328 -5.546 11.557
{c1* c 2 11} 2.913 -3.848 11.848
{c4* c 2 12} P 7.054 -6.673 12.486
{c1* c 2 12} 7.261 -4.666 13.683
{c4* a 2 13} P 12.368 -6.109 12.321
{c1* a 2 13} 12.436 -4.226 13.728
{c4* g 2 14} P 16.67 -2.027 13.575
{c1* g 2 14} 15.505 -1.313 15.432
{c4* t 2 15} P 17.604 3.34 15.905
{c1* t 2 15} 16.561 3.209 17.974
{c4* g 2 16} P 18.292 7.346 20.288
{c1* g 2 16} 18.185 5.772 22.014
{c4* g 2 17} P 17.624 8.803 25.764
{c1* g 2 17} 17.544 6.631 26.687
{c4* t 2 18} P 16.533 6.989 31.19
{c1* t 2 18} 17.71 4.982 31.076
{c4* a 2 19} P 15.586 2.426 35.31
{c1* a 2 19} 17.777 1.574 35.139
{c4* t 2 20} P 17.84 -2.872 37.384
{c1* t 2 20} 19.909 -2.508 36.62
@subgroup {base pairs} dominant
@vectorlist {bp} color= yellowtint
{c1* t 2 20} P U 20.899 -2.872 35.861
{c1* a 1 2} U 26.75 -5.024 31.373
{c1* t 1 3} P U 22.44 -5.182 30.408
{c1* a 2 19} U 18.417 0.647 34.49
{c1* t 2 18} P U 17.729 3.693 30.912
{c1* a 1 4} U 17.846 -4.16 29.912
{c1* c 1 5} P U 14.276 -1.369 29.449
{c1* g 2 17} U 17.076 5.485 27.083
{c1* c 1 6} P U 11.538 1.476 27.018
{c1* g 2 16} U 17.262 5.176 22.709
{c1* a 1 7} P U 9.215 3.945 23.697
{c1* t 2 15} U 15.539 3.312 18.77
{c1* c 1 8} P U 9.273 4.353 19.516
{c1* g 2 14} U 14.639 -0.526 15.999
{c1* a 2 13} P U 12.038 -2.994 13.848
{c1* t 1 9} U 9.72 4.176 14.543
{c1* c 2 12} P U 7.673 -3.534 13.194
{c1* g 1 10} U 10.378 3.898 9.983
{c1* g 1 11} P U 8.934 1.421 6.771
{c1* c 2 11} U 3.739 -3.125 11.152
{c1* c 1 12} P U 7.79 -2.552 4.87
{c1* g 2 10} U 0.463 -1.77 8.864
{c1* c 2 9} P U -0.698 1.118 5.363
{c1* g 1 13} U 4.548 -4.142 2.541
{c1* g 1 14} P U 0.894 -3.696 0.865
{c1* c 2 8} U -2.957 3.325 1.597
{c1* a 2 7} P U -4.252 5.387 -2.083
{c1* t 1 15} U -4.327 -2.672 -0.63
{c1* g 1 16} P U -7.573 -1.288 -3.615
{c1* c 2 6} U -3.634 4.731 -6.552
{c1* a 1 17} P U -8.835 0.99 -6.97
{c1* t 2 5} U -1.798 2.817 -10.389
{c1* a 2 4} P U -1.395 0.459 -13.804
{c1* t 1 18} U -8.145 2.496 -10.98
{c1* a 1 19} P U -6.727 3.321 -15.603
{c1* t 2 3} U -2.673 -2.977 -16.595
{c1* a 2 2} P U -4.547 -6.578 -18.723
{c1* t 1 20} U -5.096 1.912 -19.642
@group {Lambda repr}
@subgroup {sub a} dominant 
@vectorlist {Calpha a} color= white master= {Calphas} 
{pro A 6} P 4.917 -12.878 21.502
{leu A 7} 7.171 -14.734 19.108
{thr A 8} 6.414 -18.341 18.088
{gln A 9} 7.434 -21.207 20.413
{glu A 10} 10.09 -22.093 17.832
{gln A 11} 11.194 -18.465 17.478
{leu A 12} 11.715 -18.403 21.262
{glu A 13} 13.803 -21.578 20.875
{asp A 14} 16.165 -20.176 18.196
{ala A 15} 16.942 -17.153 20.373
{arg A 16} 17.718 -19.297 23.411
{arg A 17} 20.008 -21.42 21.245
{leu A 18} 21.776 -18.444 19.615
{lys A 19} 22.289 -16.658 22.921
{ala A 20} 23.703 -19.833 24.488
{ile A 21} 26.38 -19.901 21.747
{tyr A 22} 27.191 -16.218 22.345
{glu A 23} 27.475 -16.967 26.083
{lys A 24} 29.83 -19.922 25.434
{lys A 25} 32.006 -18.101 22.858
{lys A 26} 32.166 -14.507 24.112
{asn A 27} 35.515 -14.665 25.987
{glu A 28} 37.252 -16.775 23.285
{leu A 29} 36.121 -14.472 20.47
{gly A 30} 36.102 -11.655 22.995
{leu A 31} 32.791 -9.958 22.191
{ser A 32} 29.905 -8.157 23.855
{gly A 53} P 13.698 -13.524 21.764
{ile A 54} 12.044 -10.116 21.604
{asn A 55} 12.523 -9.401 17.866
{ala A 56} 12.578 -12.122 15.182
{leu A 57} 15.764 -13.373 13.614
{asn A 58} 15.732 -13.414 9.796
{ala A 59} 18.04 -14.747 7.078
{tyr A 60} 20.378 -11.751 6.685
{asn A 61} 20.709 -11.174 10.469
{ala A 62} 20.979 -14.912 11.181
{ala A 63} 23.608 -15.256 8.446
{leu A 64} 25.61 -12.321 9.91
{leu A 65} 25.472 -13.813 13.409
{ala A 66} 26.622 -17.262 12.252
{lys A 67} 29.79 -15.696 10.771
{ile A 68} 30.543 -13.442 13.757
{leu A 69} 30.158 -16.328 16.213
{lys A 70} 32.033 -18.781 13.922
{val A 71} 28.93 -20.987 13.894
{ser A 72} 26.66 -22.375 11.158
{val A 73} 23.022 -21.138 11.101
{glu A 74} 21.825 -24.746 11.637
{glu A 75} 23.388 -24.732 15.136
{phe A 76} 20.933 -22.093 16.361
{ser A 77} 18.152 -21.929 13.774
{pro A 78} 17.263 -25.055 11.819
{ser A 79} 14.273 -23.289 10.201
{ile A 80} 16.057 -20.211 8.896
{ala A 81} 18.799 -22.561 7.676
{arg A 82} 16.212 -24.416 5.562
{glu A 83} 14.915 -21.09 4.331
{ile A 84} 18.416 -20.046 3.214
{tyr A 85} 19.029 -23.385 1.487
{glu A 86} 15.88 -22.76 -0.541
{met A 87} 16.859 -19.352 -1.892
{tyr A 88} 20.178 -20.719 -3.14
{glu A 89} 18.25 -23.434 -4.981
{ala A 90} 17.194 -20.458 -7.135
{val A 91} 20.709 -19.008 -7.562
{ser A 92} 22.349 -22.403 -8.001
@vectorlist {helix 1a} color= sky master= {hlx-t-hlx} 
{ser A 32} P 29.905 -8.157 23.855
{gln A 33} 26.433 -7.167 22.601
{glu A 34} 27.95 -3.807 21.764
{ser A 35} 30.775 -5.127 19.541
{val A 36} 28.611 -7.889 18.031
{ala A 37} 26.29 -4.996 17.205
{asp A 38} 28.639 -2.611 15.353
{lys A 39} 29.817 -5.511 13.17
{met A 40} 26.224 -6.137 12.247
{gly A 41} 25.718 -2.405 11.853
@vectorlist {turn a} color=white master= {hlx-t-hlx} 
{gly A 41} P 25.718 -2.405 11.853
{met A 42} 23.108 -1.945 14.578
{gly A 43} 23.049 -0.9 18.248
@vectorlist {helix 2a} color=red master= {hlx-t-hlx} 
{gly A 43} P 23.049 -0.9 18.248
{gln A 44} 23.566 -3.195 21.251
{ser A 45} 19.858 -2.982 22.163
{gly A 46} 18.963 -4.336 18.703
{val A 47} 21.163 -7.387 19.285
{gly A 48} 19.817 -7.82 22.835
{ala A 49} 16.296 -7.841 21.382
{leu A 50} 17.334 -10.7 19.068
{phe A 51} 19.257 -12.741 21.627
{asn A 52} 16.421 -12.39 24.146
{gly A 53} 13.698 -13.524 21.764
@subgroup {sub b} dominant 
@vectorlist {Calpha b} color= white master= {Calphas} 
{ser B 1} P 4.538 4.776 9.386
{thr B 2} 3.128 5.037 5.858
{lys B 3} 5.989 6.453 3.869
{lys B 4} 7.501 4.68 0.832
{lys B 5} 11.182 5.078 -0.04
{pro B 6} 12.365 5.669 -3.602
{leu B 7} 14.211 2.824 -5.345
{thr B 8} 17.924 2.763 -6.075
{gln B 9} 19.233 2.989 -9.637
{glu B 10} 20.342 -0.66 -9.437
{gln B 11} 17.076 -1.773 -7.745
{leu B 12} 15.168 -0.11 -10.583
{glu B 13} 17.307 -1.924 -13.164
{asp B 14} 16.785 -5.374 -11.603
{ala B 15} 13.045 -4.618 -11.797
{arg B 16} 13.284 -3.67 -15.495
{arg B 17} 15.316 -6.851 -16.071
{leu B 18} 12.563 -8.789 -14.184
{lys B 19} 9.659 -7.477 -16.299
{ala B 20} 11.752 -8.033 -19.433
{ile B 21} 12.101 -11.696 -18.436
{tyr B 22} 8.398 -11.999 -17.564
{glu B 23} 7.623 -10.432 -20.937
{lys B 24} 9.656 -12.919 -22.983
{lys B 25} 8.435 -15.998 -21.051
{lys B 26} 4.812 -15.008 -20.43
{asn B 27} 3.295 -16.878 -23.371
{glu B 28} 5.68 -19.86 -23.268
{leu B 29} 4.916 -20.369 -19.541
{gly B 30} 1.43 -18.925 -20.065
{leu B 31} 0.964 -16.562 -17.142
{ser B 32} -0.463 -13.297 -15.94
{gly B 53} P 9.952 -0.337 -9.756
{ile B 54} 7.446 0.818 -7.118
{asn B 55} 8.444 -1.745 -4.422
{ala B 56} 11.938 -3.312 -4.206
{leu B 57} 12.531 -7.058 -4.434
{asn B 58} 14.134 -8.975 -1.579
{ala B 59} 15.829 -12.39 -1.533
{tyr B 60} 12.626 -14.342 -0.809
{asn B 61} 10.6 -12.727 -3.579
{ala B 62} 13.504 -12.754 -6.012
{ala B 63} 13.932 -16.513 -5.351
{leu B 64} 10.162 -17.07 -5.551
{leu B 65} 10.004 -15.07 -8.81
{ala B 66} 12.983 -17.001 -10.298
{lys B 67} 11.518 -20.424 -9.557
{ile B 68} 8.165 -19.248 -11.016
{leu B 69} 9.785 -17.943 -14.23
{lys B 70} 11.962 -21.07 -14.429
{val B 71} 15.056 -18.857 -14.441
{ser B 72} 17.971 -17.97 -12.15
{val B 73} 18.137 -14.658 -10.252
{glu B 74} 21.664 -13.641 -11.386
{glu B 75} 19.718 -13.098 -14.606
{phe B 76} 17.615 -10.294 -13.136
{ser B 77} 19.639 -9.456 -10.018
{pro B 78} 23.389 -9.971 -9.699
{ser B 79} 23.525 -8.123 -6.343
{ile B 80} 20.69 -10.081 -4.724
{ala B 81} 22.162 -13.29 -6.138
{arg B 82} 25.515 -12.349 -4.559
{glu B 83} 23.586 -11.559 -1.345
{ile B 84} 21.998 -15.036 -1.294
{tyr B 85} 25.42 -16.623 -2.006
{glu B 86} 26.719 -14.665 0.992
{met B 87} 23.969 -15.998 3.305
{tyr B 88} 24.466 -19.578 2.086
{glu B 89} 28.158 -19.51 3.083
{ala B 90} 26.807 -19.324 6.662
{val B 91} 25.058 -22.684 6.257
{ser B 92} 27.897 -24.299 4.342
@vectorlist {helix 1b} color= sky master= {hlx-t-hlx} 
{ser B 32} P -0.463 -13.297 -15.94
{gln B 33} 0.382 -11.085 -12.942
{glu B 34} -3.066 -12.404 -11.95
{ser B 35} -1.681 -15.971 -11.665
{val B 36} 1.97 -15.173 -10.879
{ala B 37} 0.391 -13.407 -7.864
{asp B 38} -1.641 -16.355 -6.497
{lys B 39} 1.514 -18.499 -6.662
{met B 40} 3.155 -15.943 -4.337
{gly B 41} 0.26 -15.153 -2.012
@vectorlist {turn b} color=white master= {hlx-t-hlx} 
{gly B 41} P 0.26 -15.153 -2.012
{met B 42} -0.3 -11.517 -3.055
{gly B 43} -2.536 -9.525 -5.397
@vectorlist {helix 2b} color=red master= {hlx-t-hlx} 
{gly B 43} P -2.536 -9.525 -5.397
{gln B 44} -1.924 -8.288 -8.919
{ser B 45} -0.917 -4.852 -7.534
{gly B 46} 1.75 -6.315 -5.26
{val B 47} 3.194 -8.198 -8.246
{gly B 48} 2.547 -5.058 -10.298
{ala B 49} 4.666 -2.955 -7.91
{leu B 50} 7.514 -5.436 -8.229
{phe B 51} 7.579 -5.532 -12.036
{asn B 52} 7.386 -1.711 -12.258
{gly B 53} 9.952 -0.337 -9.756

@kinemage 3
@caption
(B&T Fig. 7.16, 7.17)
Lambda repressor/DNA complex - details of interaction. View1-4 show base-specific interactions, and View5 shows non-specific interactions with the phosphate backbone. (from PDB file 1LRD)
@onewidth
@zoom 1.30
@zslab 200
@ztran 0
@center 2.500 -1.300 -4.500
@matrix
-0.670540 0.190179 -0.717083 0.664873 -0.274757 -0.694587 -0.329121 -0.942518 0.057789
@2viewid {Gln-Ade F8.15b}
@2zoom 2.50
@2zslab 260
@2ztran 0
@2center -1.500 -5.500 -12.300
@2matrix
-0.727978 0.222029 -0.648653 0.613338 -0.211879 -0.760870 -0.306374 -0.951741 0.018065
@3viewid {Thr2, Lys4 bdg}
@3zoom 1.50
@3zslab 200
@3ztran 0
@3center 4.700 0.800 -2.100
@3matrix
0.923039 -0.167726 -0.346217 0.249139 -0.425118 0.870174 -0.293133 -0.889462 -0.350615
@4viewid {T methyl holes}
@4zoom 2.20
@4zslab 200
@4ztran 0
@4center -0.100 -3.800 -3.000
@4matrix
0.817953 -0.099118 0.566682 -0.570183 -0.270573 0.775680 0.076447 -0.957584 -0.277831
@5viewid {nh-PO4 F8.16}
@5zoom 2.67
@5zslab 210
@5ztran 0
@5center -0.700 -12.632 -12.000
@5matrix
0.448826 0.856408 -0.255186 0.853692 -0.326514 0.405705 0.264128 -0.399942 -0.877659
@master {DNA bkbone}
@master {DNA bases}
@group {DNA str 1} dominant
@subgroup {sugar-phos}
@vectorlist {virt. bb} color= gold master= {DNA bkbone}
{p g 1 11}P 13.191 6.267 6.189
{c4* g 1 11}12.088 2.433 6.126
{p c 1 12}12.210 0.667 3.043
{c4* c 1 12}11.246 -2.797 4.513
{p g 1 13}10.567 -6.329 2.792
{c4* g 1 13}6.901 -6.528 2.992
{p g 1 14}4.914 -8.837 0.564
{c4* g 1 14}2.238 -6.996 0.160
{p t 1 15}-1.398 -7.999 -0.906
{c4* t 1 15}-4.120 -5.931 0.866
{p g 1 16}-7.591 -6.879 -0.536
{c4* g 1 16}-9.110 -3.457 -1.299
{p a 1 17}-12.254 -2.763 -3.642
{c4* a 1 17}-11.480 0.852 -4.616
{p t 1 18}-13.562 2.811 -7.380
{c4* t 1 18}-10.999 4.020 -9.677
{p a 1 19}-11.125 6.233 -12.976
{c4* a 1 19}-7.521 6.405 -14.179
{p t 1 20}-7.048 7.807 -17.769
@subgroup {no-con base} dominant
@vectorlist {non-contct} color= gray master= {DNA bases}
{c1* g 1 11}P 9.760 2.144 6.075
{n9 g 1 11}8.576 2.625 6.770
{c8 g 1 11}8.071 3.903 6.730
{n7 g 1 11}6.994 4.068 7.448
{c5 g 1 11}6.776 2.811 8.001
{c6 g 1 11}5.756 2.364 8.879
{o6 g 1 11}4.808 3.024 9.323
{c6 g 1 11}P 5.756 2.364 8.879
{n1 g 1 11}5.832 1.031 9.204
{c2 g 1 11}6.816 0.234 8.702
{n2 g 1 11}6.695 -1.045 9.141
{c2 g 1 11}P 6.816 0.234 8.702
{n3 g 1 11}7.807 0.612 7.904
{c4 g 1 11}7.726 1.910 7.579
{c5 g 1 11}6.776 2.811 8.001
{c4 g 1 11}7.726 1.910 7.579
{n9 g 1 11}8.576 2.625 6.770
{c1* c 1 12}P 8.926 -2.673 4.251
{n1 c 1 12}8.041 -1.498 4.320
{c2 c 1 12}6.878 -1.656 5.049
{o2 c 1 12}6.679 -2.763 5.579
{c2 c 1 12}P 6.878 -1.656 5.049
{n3 c 1 12}6.018 -0.618 5.157
{c4 c 1 12}6.241 0.584 4.576
{n4 c 1 12}5.388 1.587 4.696
{c4 c 1 12}P 6.241 0.584 4.576
{c5 c 1 12}7.423 0.735 3.830
{c6 c 1 12}8.272 -0.302 3.738
{n1 c 1 12}P 8.041 -1.498 4.320
{c6 c 1 12}8.272 -0.302 3.738
{c1* g 1 13}P 5.406 -5.003 2.080
{n9 g 1 13}5.450 -3.573 1.807
{c8 g 1 13}6.311 -2.872 1.009
{n7 g 1 13}6.020 -1.594 0.940
{c5 g 1 13}4.884 -1.450 1.727
{c6 g 1 13}4.089 -0.330 2.069
{o6 g 1 13}4.246 0.845 1.675
{c6 g 1 13}P 4.089 -0.330 2.069
{n1 g 1 13}3.022 -0.612 2.906
{c2 g 1 13}2.766 -1.855 3.374
{n2 g 1 13}1.697 -2.000 4.166
{c2 g 1 13}P 2.766 -1.855 3.374
{n3 g 1 13}3.488 -2.927 3.100
{c4 g 1 13}4.524 -2.659 2.268
{c5 g 1 13}4.884 -1.450 1.727
{n9 g 1 13}P 5.450 -3.573 1.807
{c4 g 1 13}4.524 -2.659 2.268
{c1* a 1 17}P -9.974 0.694 -6.417
{n9 a 1 17}-8.894 -0.227 -6.816
{c8 a 1 17}-8.887 -1.594 -6.719
{n7 a 1 17}-7.772 -2.130 -7.169
{c5 a 1 17}-7.007 -1.065 -7.608
{c6 a 1 17}-5.720 -0.996 -8.161
{n6 a 1 17}-4.924 -2.027 -8.423
{c6 a 1 17}P -5.720 -0.996 -8.161
{n1 a 1 17}-5.277 0.261 -8.451
{c2 a 1 17}-6.031 1.354 -8.212
{n3 a 1 17}-7.249 1.347 -7.682
{c4 a 1 17}-7.685 0.110 -7.391
{c5 a 1 17}-7.007 -1.065 -7.608
{n9 a 1 17}P -8.894 -0.227 -6.816
{c4 a 1 17}-7.685 0.110 -7.391
{c5 a 1 17}-7.007 -1.065 -7.608
{c1* t 1 18}P -9.300 2.845 -10.497
{n1 t 1 18}-8.874 1.450 -10.742
{c2 t 1 18}-7.594 1.278 -11.221
{o2 t 1 18}-6.867 2.261 -11.437
{c2 t 1 18}P -7.594 1.278 -11.221
{n3 t 1 18}-7.208 -0.007 -11.460
{c4 t 1 18}-8.015 -1.086 -11.187
{o4 t 1 18}-7.521 -2.233 -11.455
{c4 t 1 18}P -8.015 -1.086 -11.187
{c5 t 1 18}-9.305 -0.873 -10.645
{c5m t 1 18}-10.237 -1.993 -10.315
{n1 t 1 18}P -8.874 1.450 -10.742
{c6 t 1 18}-9.696 0.399 -10.457
{c5 t 1 18}-9.305 -0.873 -10.645
{c1* a 1 19}P -7.424 4.405 -15.432
{n9 a 1 19}-7.940 3.065 -15.090
{c8 a 1 19}-9.197 2.742 -14.640
{n7 a 1 19}-9.365 1.471 -14.412
{c5 a 1 19}-8.135 0.900 -14.760
{c6 a 1 19}-7.678 -0.426 -14.737
{n6 a 1 19}-8.416 -1.457 -14.327
{c6 a 1 19}P -7.678 -0.426 -14.737
{n1 a 1 19}-6.393 -0.632 -15.159
{c2 a 1 19}-5.615 0.399 -15.552
{n3 a 1 19}-5.990 1.691 -15.575
{c4 a 1 19}-7.259 1.876 -15.170
{c5 a 1 19}-8.135 0.900 -14.760
{n9 a 1 19}P -7.940 3.065 -15.090
{c4 a 1 19}-7.259 1.876 -15.170
@subgroup {contct bases} dominant
@vectorlist {G contact} color= sea master= {DNA bases}
{c1* g 1 14}P 1.516 -4.831 0.747
{n9 g 1 14}1.768 -3.567 0.091
{c8 g 1 14}2.824 -3.285 -0.752
{n7 g 1 14}2.887 -2.048 -1.134
{c5 g 1 14}1.838 -1.429 -0.473
{c6 g 1 14}1.385 -0.089 -0.484
{o6 g 1 14}1.881 0.873 -1.111
{c6 g 1 14}P 1.385 -0.089 -0.484
{n1 g 1 14}0.275 0.151 0.291
{c2 g 1 14}-0.317 -0.838 0.997
{n2 g 1 14}-1.380 -0.467 1.715
{c2 g 1 14}P -0.317 -0.838 0.997
{n3 g 1 14}0.064 -2.123 1.049
{c4 g 1 14}1.158 -2.350 0.291
{c5 g 1 14}1.838 -1.429 -0.473
{n9 g 1 14}P 1.768 -3.567 0.091
{c4 g 1 14}1.158 -2.350 0.291
{c1* g 1 16}P -8.232 -2.295 -3.123
{n9 g 1 16}-6.898 -2.391 -3.750
{c8 g 1 16}-6.233 -3.546 -4.006
{n7 g 1 16}-5.058 -3.354 -4.559
{c5 g 1 16}-4.968 -1.959 -4.667
{c6 g 1 16}-3.922 -1.154 -5.163
{o6 g 1 16}-2.843 -1.539 -5.642
{c6 g 1 16}P -3.922 -1.154 -5.163
{n1 g 1 16}-4.188 0.186 -5.118
{c2 g 1 16}-5.358 0.667 -4.610
{n2 g 1 16}-5.428 2.007 -4.627
{c2 g 1 16}P -5.358 0.667 -4.610
{n3 g 1 16}-6.359 -0.041 -4.132
{c4 g 1 16}-6.100 -1.361 -4.183
{n9 g 1 16}-6.898 -2.391 -3.750
{c5 g 1 16}P -4.968 -1.959 -4.667
{c4 g 1 16}-6.100 -1.361 -4.183
@vectorlist {T contact} color= sky master= {DNA bases}
{c1* t 1 15}P -4.339 -3.951 -0.399
{n1 t 1 15}-3.321 -3.168 -1.134
{c2 t 1 15}-3.476 -1.807 -1.271
{o2 t 1 15}-4.447 -1.209 -0.798
{c2 t 1 15}P -3.476 -1.807 -1.271
{n3 t 1 15}-2.527 -1.113 -1.955
{c4 t 1 15}-1.434 -1.697 -2.496
{o4 t 1 15}-0.581 -0.969 -3.100
{c4 t 1 15}P -1.434 -1.697 -2.496
{c5 t 1 15}-1.279 -3.092 -2.359
{c5m t 1 15}-0.084 -3.793 -2.941
{n1 t 1 15}P -3.321 -3.168 -1.134
{c6 t 1 15}-2.203 -3.738 -1.670
{c5 t 1 15}P -1.279 -3.092 -2.359
{c6 t 1 15}-2.203 -3.738 -1.670
@group {DNA str 2} dominant
@subgroup {sugar-phos}
@vectorlist {virt. bb} color= gold master= {DNA bkbone}
{o1p t 2 3}P -1.493 -9.483 -16.452
{p t 2 3}-0.737 -9.140 -17.626
{o2p t 2 3}0.410 -9.346 -18.510
{c4* a 2 2}P -3.957 -9.690 -19.957
{p t 2 3}-0.737 -9.140 -17.626
{c4* t 2 3}-0.239 -5.161 -17.809
{o3* t 2 3}1.563 -4.309 -16.264
{p a 2 4}2.483 -3.292 -16.863
{o1p a 2 4}3.528 -3.835 -15.769
{o2p a 2 4}P 3.104 -3.099 -18.116
{p a 2 4}2.483 -3.292 -16.863
{o5* a 2 4}1.512 -2.165 -16.304
{c4* a 2 4}1.102 0.131 -16.196
{p t 2 5}2.865 3.285 -14.714
{c4* t 2 5}-0.074 4.625 -12.594
{p c 2 6}0.932 7.449 -10.224
{c4* c 2 6}-2.553 7.236 -8.731
{p a 2 7}-3.077 9.683 -5.750
{c4* a 2 7}-5.605 8.288 -3.294
{p c 2 8}-5.593 9.525 0.547
{c4* c 2 8}-5.380 5.827 1.801
{p c 2 9}-5.014 5.766 5.733
{c4* c 2 9}-3.833 2.206 6.286
{p g 2 10}-4.030 1.670 9.751
{c4* g 2 10}-2.900 -1.986 9.802
{p c 2 11}-2.214 -4.639 12.572
{c4* c 2 11}1.328 -5.546 11.557
{p c 2 12}3.501 -7.834 13.694
@subgroup {no-con base} dominant
@vectorlist {non-contact} color= gray master= {DNA bases}
{c1* c 2 6}P -2.975 5.738 -7.044
{n1 c 2 6}-2.337 4.405 -6.987
{c2 c 2 6}-3.190 3.415 -6.497
{o2 c 2 6}-4.369 3.690 -6.223
{c2 c 2 6}P -3.190 3.415 -6.497
{n3 c 2 6}-2.674 2.165 -6.360
{c4 c 2 6}-1.389 1.876 -6.668
{n4 c 2 6}-0.994 0.605 -6.497
{c4 c 2 6}P -1.389 1.876 -6.668
{c5 c 2 6}-0.533 2.886 -7.152
{n1 c 2 6}P -2.337 4.405 -6.987
{c6 c 2 6}-1.042 4.123 -7.277
{c5 c 2 6}-0.533 2.886 -7.152
{c1* a 2 7}P -4.240 6.666 -2.314
{n9 a 2 7}-3.151 5.814 -2.764
{c8 a 2 7}-1.970 6.157 -3.374
{n7 a 2 7}-1.189 5.127 -3.636
{c5 a 2 7}-1.904 4.034 -3.146
{c6 a 2 7}-1.612 2.653 -3.094
{n6 a 2 7}-0.515 2.068 -3.550
{c6 a 2 7}P -1.612 2.653 -3.094
{n1 a 2 7}-2.583 1.869 -2.530
{c2 a 2 7}-3.744 2.385 -2.040
{n3 a 2 7}-4.074 3.683 -2.069
{c4 a 2 7}-3.104 4.439 -2.610
{c5 a 2 7}-1.904 4.034 -3.146
{n9 a 2 7}P -3.151 5.814 -2.764
{c4 a 2 7}-3.104 4.439 -2.610
{c1* c 2 8}P -3.579 4.460 1.715
{n1 c 2 8}-2.302 4.254 1.026
{c2 c 2 8}-1.913 2.934 0.861
{o2 c 2 8}-2.567 2.000 1.328
{c2 c 2 8}P -1.913 2.934 0.861
{n3 c 2 8}-0.748 2.708 0.194
{c4 c 2 8}-0.003 3.718 -0.319
{n4 c 2 8}1.127 3.381 -0.952
{n1 c 2 8}P -2.302 4.254 1.026
{c6 c 2 8}-1.578 5.285 0.490
{c5 c 2 8}-0.418 5.072 -0.177
{c4 c 2 8}-0.003 3.718 -0.319
{c1* c 2 9}P -1.556 1.979 5.824
{n1 c 2 9}-0.481 2.275 4.855
{c2 c 2 9}0.245 1.203 4.365
{o2 c 2 9}-0.001 0.041 4.673
{c2 c 2 9}P 0.245 1.203 4.365
{n3 c 2 9}1.272 1.457 3.510
{c4 c 2 9}1.615 2.708 3.117
{n4 c 2 9}2.648 2.838 2.280
{c4 c 2 9}P 1.615 2.708 3.117
{c5 c 2 9}0.892 3.807 3.624
{n1 c 2 9}P -0.481 2.275 4.855
{c6 c 2 9}-0.112 3.539 4.462
{c5 c 2 9}0.892 3.807 3.624
{c1* c 2 11}P 2.913 -3.848 11.848
{n1 c 2 11}2.994 -2.385 11.677
{c2 c 2 11}4.099 -1.890 11.004
{o2 c 2 11}4.955 -2.625 10.537
{c2 c 2 11}P 4.099 -1.890 11.004
{n3 c 2 11}4.213 -0.543 10.856
{c4 c 2 11}3.290 0.330 11.335
{n4 c 2 11}3.451 1.649 11.113
{c4 c 2 11}P 3.290 0.330 11.335
{c5 c 2 11}2.180 -0.172 12.036
{n1 c 2 11}P 2.994 -2.385 11.677
{c6 c 2 11}2.086 -1.498 12.167
{c5 c 2 11}2.180 -0.172 12.036
@subgroup {contct bases} dominant
@vectorlist {G contact} color= sea master= {DNA bases}
{c1* g 2 10}P -0.673 -1.649 9.483
{n9 g 2 10}0.345 -0.852 8.953
{c8 g 2 10}0.347 0.536 8.981
{n7 g 2 10}1.353 1.086 8.372
{c5 g 2 10}2.072 -0.007 7.881
{c6 g 2 10}3.266 -0.055 7.135
{o6 g 2 10}3.936 0.893 6.742
{c6 g 2 10}P 3.266 -0.055 7.135
{n1 g 2 10}3.701 -1.326 6.856
{c2 g 2 10}3.023 -2.426 7.249
{n2 g 2 10}3.599 -3.567 6.890
{c2 g 2 10}P 3.023 -2.426 7.249
{n3 g 2 10}1.887 -2.433 7.944
{c4 g 2 10}1.474 -1.182 8.235
{n9 g 2 10}P 0.345 -0.852 8.953
{c4 g 2 10}1.474 -1.182 8.235
{c5 g 2 10}2.072 -0.007 7.881
@vectorlist {A contact} color= pink master= {DNA bases}
{c1* a 2 4}P -0.240 0.110 -14.287
{n9 a 2 4}-1.086 -0.852 -13.592
{c8 a 2 4}-0.840 -2.158 -13.295
{n7 a 2 4}-1.849 -2.769 -12.714
{c5 a 2 4}-2.828 -1.773 -12.611
{c6 a 2 4}-4.126 -1.794 -12.064
{n6 a 2 4}-4.698 -2.845 -11.500
{c6 a 2 4}P -4.126 -1.794 -12.064
{n1 a 2 4}-4.811 -0.625 -12.138
{c2 a 2 4}-4.265 0.495 -12.691
{n3 a 2 4}-3.046 0.550 -13.233
{c4 a 2 4}-2.376 -0.605 -13.147
{n9 a 2 4}P -1.086 -0.852 -13.592
{c4 a 2 4}-2.376 -0.605 -13.147
{c5 a 2 4}-2.828 -1.773 -12.611
@vectorlist {T contact} color= sky master= {DNA bases}
{c1* t 2 3}P -1.976 -4.061 -16.766
{n1 t 2 3}-3.198 -4.329 -15.968
{c2 t 2 3}-4.001 -3.237 -15.706
{o2 t 2 3}-3.709 -2.123 -16.133
{c2 t 2 3}P -4.001 -3.237 -15.706
{n3 t 2 3}-5.119 -3.477 -14.982
{c4 t 2 3}-5.434 -4.714 -14.538
{o4 t 2 3}-6.491 -4.886 -13.865
{c4 t 2 3}P -5.434 -4.714 -14.538
{c5 t 2 3}-4.596 -5.821 -14.828
{c5m t 2 3}-4.981 -7.181 -14.304
{n1 t 2 3}P -3.198 -4.329 -15.968
{c6 t 2 3}-3.494 -5.580 -15.529
{c5 t 2 3}-4.596 -5.821 -14.828
{c1* t 2 5}P -0.659 3.113 -10.942
{n1 t 2 5}-0.985 1.766 -10.509
{c2 t 2 5}-2.311 1.581 -10.093
{o2 t 2 5}-3.067 2.543 -10.178
{c2 t 2 5}P -2.311 1.581 -10.093
{n3 t 2 5}-2.715 0.364 -9.642
{c4 t 2 5}-1.859 -0.694 -9.557
{o4 t 2 5}-2.296 -1.800 -9.118
{c4 t 2 5}P -1.859 -0.694 -9.557
{c5 t 2 5}-0.501 -0.502 -9.927
{c5m t 2 5}0.471 -1.642 -9.842
{n1 t 2 5}P -0.985 1.766 -10.509
{c6 t 2 5}-0.125 0.701 -10.406
{c5 t 2 5}-0.501 -0.502 -9.927
@group {L repr b}
@subgroup {atom balls} dominant
@balllist {N} color= blue radius= .1
{nz lys B 4} 4.677 0.838 -2.080
{nz lys B 26} 2.217 -10.047 -21.382
{n gln B 33} 0.046 -11.607 -14.270
{ne2 gln B 33} 2.654 -7.071 -14.549
{ne2 gln B 44} -1.527 -5.559 -12.281
{nd2 asn B 55} 5.067 -2.838 -3.226
{n7 a 2 4} -1.849 -2.769 -12.714
{n6 a 2 4} -4.698 -2.845 -11.500
{n7 g 1 14} 2.887 -2.048 -1.134
{n7 g 1 16} -5.058 -3.354 -4.559
@balllist {O} color= red radius= .1
{og1 thr B 2} 1.147 4.268 6.947
{oe1 gln B 33} 0.913 -6.817 -13.113
{oe1 gln B 44} -3.490 -5.477 -11.181
{og ser B 45} -2.667 -4.398 -5.853
{od1 asn B 55} 6.290 -1.148 -2.525
{oh tyr B 22} 2.040 -11.222 -17.153
{o1p t 2 3} -1.493 -9.483 -16.452
{o2p t 2 3} 0.410 -9.346 -18.510
{o3* t 2 3} 1.563 -4.309 -16.264
{o1p a 2 4} 3.528 -3.835 -15.769
{o6 g 1 14} 1.881 0.873 -1.111
@balllist {C} color= green radius= .1
{c5m t 1 15} -0.084 -3.793 -2.941
{c5m t 2 5} 0.471 -1.642 -9.842
@subgroup {Calphas} dominant
@vectorlist {main ch} color= white
{ser B 1}P 4.538 4.776 9.386
{thr B 2}3.128 5.037 5.858
{lys B 3}5.989 6.453 3.869
{lys B 4}7.501 4.680 0.832
{lys B 5}11.182 5.078 -0.040
{pro B 6}12.365 5.669 -3.602
{leu B 7}14.211 2.824 -5.345
{thr B 8}17.924 2.763 -6.075
{gln B 9}19.233 2.989 -9.637
{glu B 10}20.342 -0.660 -9.437
{gln B 11}17.076 -1.773 -7.745
{leu B 12}15.168 -0.110 -10.583
{glu B 13}17.307 -1.924 -13.164
{asp B 14}16.785 -5.374 -11.603
{ala B 15}13.045 -4.618 -11.797
{arg B 16}13.284 -3.670 -15.495
{arg B 17}15.316 -6.851 -16.071
{leu B 18}12.563 -8.789 -14.184
{lys B 19}9.659 -7.477 -16.299
{ala B 20}11.752 -8.033 -19.433
{ile B 21}12.101 -11.696 -18.436
{tyr B 22}8.398 -11.999 -17.564
{glu B 23}7.623 -10.432 -20.937
{lys B 24}9.656 -12.919 -22.983
{lys B 25}8.435 -15.998 -21.051
{lys B 26}4.812 -15.008 -20.430
{asn B 27}3.295 -16.878 -23.371
{glu B 28}5.680 -19.860 -23.268
{leu B 29}4.916 -20.369 -19.541
{gly B 30}1.430 -18.925 -20.065
{leu B 31}0.964 -16.562 -17.142
{ser B 32}-0.463 -13.297 -15.940
{gly B 41}P 0.260 -15.153 -2.012
{met B 42}-0.300 -11.517 -3.055
{gly B 43}-2.536 -9.525 -5.397
{gly B 53}P 9.952 -0.337 -9.756
{ile B 54}7.446 0.818 -7.118
{asn B 55}8.444 -1.745 -4.422
{ala B 56}11.938 -3.312 -4.206
{leu B 57}12.531 -7.058 -4.434
{asn B 58}14.134 -8.975 -1.579
@vectorlist {hlx 1} color= bluetint
{ser B 32}P -0.463 -13.297 -15.940
{c ser B 32}-0.004 -12.892 -14.532
{o ser B 32}0.282 -13.820 -13.734
{c ser B 32}P -0.004 -12.892 -14.532
{n gln B 33}0.046 -11.607 -14.270
{gln B 33}0.382 -11.085 -12.942
{glu B 34}-3.066 -12.404 -11.950
{ser B 35}-1.681 -15.971 -11.665
{val B 36}1.970 -15.173 -10.879
{ala B 37}0.391 -13.407 -7.864
{asp B 38}-1.641 -16.355 -6.497
{lys B 39}1.514 -18.499 -6.662
{met B 40}3.155 -15.943 -4.337
{gly B 41}0.260 -15.153 -2.012
@vectorlist {hlx 2} color= pinktint
{gly B 43}P -2.536 -9.525 -5.397
{gln B 44}-1.924 -8.288 -8.919
{ser B 45}-0.917 -4.852 -7.534
{gly B 46}1.750 -6.315 -5.260
{val B 47}3.194 -8.198 -8.246
{gly B 48}2.547 -5.058 -10.298
{ala B 49}4.666 -2.955 -7.910
{leu B 50}7.514 -5.436 -8.229
{phe B 51}7.579 -5.532 -12.036
{asn B 52}7.386 -1.711 -12.258
{gly B 53}9.952 -0.337 -9.756
@subgroup {side ch} dominant
@vectorlist {side ch} color= yellowtint
{ca thr B 2}P 3.128 5.037 5.858
{cb thr B 2}1.765 5.518 6.480
{og1 thr B 2}1.147 4.268 6.947
{cb thr B 2}P 1.765 5.518 6.480
{cg2 thr B 2}0.858 6.425 5.665
{ca lys B 4}P 7.501 4.680 0.832
{cb lys B 4}6.469 4.350 -0.194
{cg lys B 4}5.214 3.690 0.405
{cd lys B 4}5.070 2.254 -0.103
{ce lys B 4}4.934 2.240 -1.624
{nz lys B 4}4.677 0.838 -2.080
{ca tyr B 22}P 8.398 -11.999 -17.564
{cb tyr B 22}7.672 -11.291 -16.390
{cg tyr B 22}6.171 -11.270 -16.578
{cd1 tyr B 22}5.559 -10.239 -17.290
{ce1 tyr B 22}4.178 -10.184 -17.478
{cz tyr B 22}3.395 -11.215 -16.977
{oh tyr B 22}2.040 -11.222 -17.153
{cg tyr B 22}P 6.171 -11.270 -16.578
{cd2 tyr B 22}5.355 -12.273 -16.071
{ce2 tyr B 22}3.971 -12.260 -16.259
{cz tyr B 22}3.395 -11.215 -16.977
{ca lys B 26}P 4.812 -15.008 -20.430
{cb lys B 26}4.187 -13.627 -20.641
{cg lys B 26}2.655 -13.710 -20.578
{cd lys B 26}2.030 -12.321 -20.578
{ce lys B 26}2.689 -11.449 -21.638
{nz lys B 26}2.217 -10.047 -21.382
{ca gln B 33}P 0.382 -11.085 -12.942
{cb gln B 33}0.479 -9.566 -12.868
{cg gln B 33}1.424 -9.002 -13.911
{cd gln B 33}1.636 -7.518 -13.808
{oe1 gln B 33}0.913 -6.817 -13.113
{cd gln B 33}P 1.636 -7.518 -13.808
{ne2 gln B 33}2.654 -7.071 -14.549
{ca gln B 44}P -1.924 -8.288 -8.919
{cb gln B 44}-2.957 -8.143 -10.041
{cg gln B 44}-2.376 -7.573 -11.289
{cd gln B 44}-2.508 -6.116 -11.551
{oe1 gln B 44}-3.490 -5.477 -11.181
{cd gln B 44}P -2.508 -6.116 -11.551
{ne2 gln B 44}-1.527 -5.559 -12.281
{ca ser B 45}P -0.917 -4.852 -7.534
{cb ser B 45}-1.789 -3.883 -6.816
{og ser B 45}-2.667 -4.398 -5.853
{ca ala B 49}P 4.666 -2.955 -7.910
{cb ala B 49}4.315 -2.749 -6.434
{ca ile B 54}P 7.446 0.818 -7.118
{cb ile B 54}5.901 0.728 -7.306
{cg1 ile B 54}5.479 1.423 -8.634
{cd1 ile B 54}3.970 1.196 -8.981
{cb ile B 54}P 5.901 0.728 -7.306
{cg2 ile B 54}5.154 1.285 -6.081
{ca asn B 55}P 8.444 -1.745 -4.422
{cb asn B 55}7.383 -2.721 -3.938
{cg asn B 55}6.219 -2.185 -3.191
{od1 asn B 55}6.290 -1.148 -2.525
{cg asn B 55}P 6.219 -2.185 -3.191
{nd2 asn B 55}5.067 -2.838 -3.226
@labellist {G lbl} color= yellowtint
{ G}2.547 -5.058 -10.298
{"}1.750 -6.315 -5.260
@group {interaction}
@subgroup {Hbonds} dominant
@vectorlist {Hb} color= purple
{nz lys B 26}P U 1.800 -9.885 -20.719
{o2p t 2 3}U 0.827 -9.508 -19.173
{oh tyr B 22}P U 1.579 -10.692 -17.536
{o2p t 2 3}U 0.871 -9.876 -18.127
{n gln B 33}P U -0.315 -11.109 -14.782
{o1p t 2 3}U -1.132 -9.981 -15.940
{ne2 gln B 44}P U -1.618 -4.774 -12.403
{n7 a 2 4}U -1.758 -3.554 -12.592
{oe1 gln B 44}P U -3.822 -4.754 -11.269
{n6 a 2 4}U -4.366 -3.568 -11.412
{ne2 gln B 44}P U -0.847 -5.910 -12.513
{oe1 gln B 33}U 0.233 -6.466 -12.881
{ne2 gln B 33}P U 2.850 -6.345 -14.823
{o1p a 2 4}U 3.332 -4.561 -15.495
{ne2 gln B 33}P U 2.399 -6.427 -14.949
{o3* t 2 3}U 1.818 -4.953 -15.864
{og ser B 45}P U -3.324 -4.111 -5.498
{n7 g 1 16}U -4.401 -3.641 -4.914
{nd2 asn B 55}P U 4.509 -2.636 -2.690
{n7 g 1 14}U 3.445 -2.250 -1.670
{od1 asn B 55}P U 5.793 -0.536 -2.388
{nz lys B 4}U 5.174 0.226 -2.217
{"}P U 3.921 0.847 -1.818
{o6 g 1 14}U 2.637 0.864 -1.373
{og1 thr B 2}P U 1.194 3.539 7.273
{n7 g 2 10}U 1.306 1.815 8.046

@kinemage 4
@caption
Trp repressor conformational changes, from apo to liganded to DNA complex - animate, or turn on multiples together. Subunit a is in blues, subunit b in greens; ligand is in pinks; helix-turn-helix motifs have full main chain for the DNA complex. Turn on DNA and "binding" to study interactions. (from PDB files 1TRO, 2WRP, 3WRP)
@onewidth
@viewid {side}
@zoom 1.1
@zslab 160
@center 24.441 9.411 14.052
@matrix
-0.776702 -.488075 .398139 -.595736 .36399 -.715968 .204527 -.79328 -.573476
@2viewid {Trp site}
@2zoom 2.48 
@2zslab 154
@2center 24.156 4.003 23.22
@2matrix
-0.62259 -.48163 .61678 -.57483 .81628 .05717 -.531 -.31895 -.78505
@3viewid {specific bdg}
@3zoom 4.83 
@3zslab 83
@3center 39.514 2.513 35.416
@3matrix
0.39695 -.8453 -.35762 -.82556 -.4991 .26334 -.40109 .1907 -.89597
@4viewid {non-spec bdg}
@4zoom 4.24
@4zslab 94
@4center 28.209 5.816 20.268
@4matrix
-0.819159 -.519357 .243402 -.480034 .388525 -.786522 .313917 -.761127 -.567573
@5viewid {thru-wat bdg}
@5zoom 4.34
@5zslab 120
@5center 32.936 4.643 33.566
@5matrix
0.515523 .495735 -.698914 .65279 .301151 .695107 .555068 -.814588 -.168361
@master {binding}
@master= {mutant}
@group {TrpRepr apo} animate
@subgroup {sub a} dominant
@vectorlist {ca sub a} color= blue
{ca ser 8}P 18.674 23.086 20.328
{ca ala 9}17.099 23.227 23.759
{ca ala 10}14.71 25.834 22.306
{ca met 11}13.405 23.387 19.681
{ca ala 12}13.426 20.278 21.949
{ca glu 13}9.649 20.04 21.543
{ca gln 14}9.674 19.879 17.744
{ca arg 15}12.514 17.383 17.910
{ca his 16}10.508 15.317 20.404
{ca gln 17}7.516 15.20 18.109
{ca glu 18}9.72 14.175 15.145
{ca trp 19}11.219 11.389 17.207
{ca leu 20}7.774 10.094 18.253
{ca arg 21}6.814 9.892 14.567
{ca phe 22}9.769 7.501 13.996
{ca val 23}8.808 5.414 17.057
{ca asp 24}5.208 5.087 15.830
{ca leu 25}6.376 4.102 12.332
{ca leu 26}8.701 1.41 13.700
{ca lys 27}5.938 0.28 15.996
{ca asn 28}3.726 -0.232 12.955
{ca ala 29}6.489 -1.97 10.969
{ca tyr 30}7.003 -4.557 13.744
{ca gln 31}3.296 -5.502 13.593
{ca asp 32}3.644 -5.848 9.779
{ca asn 33}6.908 -7.817 9.945
{ca leu 34}8.552 -4.963 8.002
{ca his 35}10.905 -4.037 10.806
{ca leu 36}14.053 -5.498 9.224
{ca pro 37}13.77 -3.62 5.962
{ca leu 38}12.747 -0.403 7.791
{ca leu 39}15.768 -0.609 10.065
{ca asn 40}18.169 -1.183 7.145
{ca leu 41}16.564 1.808 5.458
{ca met 42}16.744 4.137 8.462
{ca leu 43}20.135 3.234 9.969
{ca thr 44}23.718 2.961 8.797
{ca pro 45}25.807 -0.162 9.152
{ca asp 46}27.871 1.846 11.619
{ca glu 47}24.786 2.663 13.631
{ca arg 48}23.488 -0.932 13.611
{ca glu 49}26.945 -2.091 14.730
{ca ala 50}26.894 0.439 17.564
{ca leu 51}23.447 -0.606 18.786
{ca gly 52}24.57 -4.231 18.815
{ca thr 53}27.485 -3.19 20.955
{ca arg 54}25.296 -1.054 23.291
{ca val 55}23.325 -4.168 24.243
{ca arg 56}26.552 -5.742 25.473
{ca ile 57}27.557 -2.717 27.490
{ca val 58}24.229 -2.727 29.363
{ca glu 59}24.361 -6.465 29.851
{ca glu 60}27.865 -6.088 31.304
{ca leu 61}27.036 -3.006 33.438
{ca leu 62}24.131 -5.025 34.817
{ca arg 63}26.547 -7.883 35.431
{ca gly 64}28.923 -5.785 37.504
{ca glu 65}31.857 -8.177 36.977
{ca met 66}33.972 -6.09 34.579
{ca ser 67}35.658 -2.733 35.110
{ca gln 68}35.10 0.157 32.713
{ca arg 69}38.479 -0.438 31.006
{ca glu 70}38.055 -4.225 30.676
{ca leu 71}34.796 -3.166 29.083
{ca lys 72}36.681 -1.098 26.421
{ca asn 73}39.115 -3.941 25.806
{ca glu 74}36.707 -6.891 25.608
{ca leu 75}33.855 -5.072 23.892
{ca gly 76}35.86 -2.562 21.814
{ca ala 77}33.525 0.291 22.819
{ca gly 78}34.895 3.792 23.460
{ca ile 79}34.988 4.923 27.094
{ca ala 80}32.497 7.789 26.446
{ca thr 81}29.966 5.227 25.210
{ca ile 82}30.368 3.299 28.443
{ca thr 83}30.126 6.392 30.631
{ca arg 84}26.963 7.579 28.904
{ca ala 85}25.686 3.999 28.940
{ca ser 86}26.339 4.123 32.677
{ca asn 87}24.596 7.489 33.110
{ca ser 88}21.47 6.578 31.139
{ca leu 89}20.909 3.333 32.983
{ca lys 90}20.843 5.169 36.326
{ca ala 91}18.292 7.605 34.900
{ca ala 92}16.313 4.578 33.679
{ca pro 93}12.936 3.893 35.309
{ca ala 94}13.145 0.994 37.789
{ca glu 95}10.633 -0.966 35.721
{ca leu 96}12.996 -1.017 32.751
{ca arg 97}15.982 -1.971 34.911
{ca gln 98}14.062 -4.965 36.315
{ca trp 99}13.046 -6.023 32.804
{ca leu 100}16.559 -5.764 31.361
{ca glu 101}17.882 -7.872 34.305
{ca glu 102}15.199 -10.424 33.554
{ca val 103}15.994 -10.581 29.853
{ca leu 104}19.778 -9.964 29.619
{ca leu 105}20.599 -11.76 32.889
{ca lys 106}17.718 -14.216 33.257
{ca ser 107}17.802 -14.548 29.513
{ca asp 108}15.302 -14.755 26.688
@vectorlist {sc} color= sky off master= {binding}
{ca thr 53 }P 27.485 -3.19 20.955 {cb thr 53} 28.77 -2.494 20.379
{og1 thr 53} 29.286 -3.473 19.407
{cb thr 53}P 28.77 -2.494 20.379 {cg2 thr 53} 29.709 -2.03 21.489
{ca ala 77}P 33.525 .291 22.819 {cb ala 77} 32.264 -.081 23.563
@vectorlist {sc} color= orange master= {mutant} off
{cg1 val 77}P 31.277 1.081 23.621
{cb ala 77} 32.264 -0.081 23.563
{cg2 val 77} 31.63 -1.351 23.003
@subgroup {sub b} dominant
@vectorlist {ca sub b} color= green
{ca ser b 8}P 34.882 -5.422 9.098
{ca ala b 9} 33.575 -7.394 6.153
{ca ala b 10} 35.28 -10.435 7.722
{ca met b 11}33.208 -10.131 10.915
{ca ala b 12}29.926 -9.094 9.197
{ca glu b 13}28.309 -12.279 10.511
{ca gln b 14}29.07 -11.619 14.177
{ca arg b 15}27.945 -8.034 13.722
{ca his b 16}24.729 -9.284 12.109
{ca gln b 17}23.977 -11.544 15.034
{ca glu b 18}24.641 -8.698 17.514
{ca trp b 19}22.279 -6.459 15.598
{ca leu b 20}19.516 -9.106 15.598
{ca arg b 21}19.822 -9.319 19.393
{ca phe b 22}19.01 -5.568 19.604
{ca val b 23}16.057 -5.966 17.202
{ca asp b 24}14.626 -8.833 19.276
{ca leu b 25}15.038 -6.844 22.508
{ca leu b 26}13.253 -3.809 21.049
{ca lys b 27}10.613 -6.11 19.663
{ca asn b 28}9.995 -7.394 23.180
{ca ala b 29}10.017 -3.888 24.697
{ca tyr b 30}7.275 -2.716 22.297
{ca gln b 31}4.999 -5.569 23.456
{ca asn b 32}5.728 -4.54 27.088
{ca asp b 33}5.238 -0.809 26.456
{ca leu b 34}8.881 -0.307 27.508
{ca his b 35}9.977 0.957 24.123
{ca leu b 36}10.303 4.624 25.120
{ca pro b 37}12.625 4.04 28.039
{ca leu b 38}14.642 1.453 26.042
{ca leu b 39}15.124 3.884 23.179
{ca asn b 40}16.255 6.701 25.504
{ca leu b 41}18.668 4.222 27.055
{ca met b 42}20.098 2.916 23.780
{ca leu b 43}20.29 6.093 21.669
{ca thr b 44}21.747 9.566 21.993
{ca pro b 45}19.723 12.73 21.627
{ca asp b 46}21.744 13.315 18.472
{ca glu b 47}20.77 9.922 17.143
{ca arg b 48}17.07 10.343 18.005
{ca glu b 49}17.151 13.749 16.290
{ca ala b 50}18.709 12.175 13.203
{ca leu b 51}16.125 9.391 12.996
{ca gly b 52}13.348 11.967 13.246
{ca thr b 53}14.927 13.778 10.349
{ca arg b 54}15.402 10.555 8.302
{ca val b 55}11.633 10.024 8.316
{ca arg b 56}11.229 13.391 6.610
{ca ile b 57}13.837 12.659 3.985
{ca val b 58}12.066 9.432 2.971
{ca glu b 59}8.688 11.109 3.029
{ca glu b 60}10.072 13.835 0.754
{ca leu b 61}11.974 11.435 -1.561
{ca leu b 62}8.705 9.534 -1.901
{ca arg b 63}6.985 12.833 -2.632
{ca gly b 64}9.302 13.716 -5.495
{ca glu b 65}8.47 17.442 -5.322
{ca met b 66}11.726 18.764 -3.829
{ca ser b 67}15.248 18.714 -5.236
{ca gln b 68}18.154 17.315 -3.235
{ca arg b 69}19.37 20.827 -2.302
{ca glu b 70}15.92 22.155 -1.319
{ca leu b 71}15.939 19.039 0.819
{ca lys b 72}19.149 20.205 2.624
{ca asn b 73}17.738 23.698 3.066
{ca glu b 74}14.212 22.88 4.263
{ca leu b 75}15.097 19.812 6.311
{ca gly b 76}18.608 20.805 7.460
{ca ala b 77}19.975 17.337 6.617
{ca gly b 78}23.474 16.927 5.157
{ca ile b 79}23.659 15.973 1.476
{ca ala b 80}25.364 12.608 2.257
{ca thr b 81}22.377 11.666 4.422
{ca ile b 82}20.066 12.383 1.510
{ca thr b 83}22.199 10.49 -0.996
{ca arg b 84}22.401 7.424 1.229
{ca gly b 85}18.71 7.849 2.030
{ca ser b 86}18.20 7.816 -1.732
{ca asn b 87}20.392 4.735 -2.240
{ca ser b 88}18.805 2.654 0.524
{ca leu b 89}15.271 3.299 -0.629
{ca lys b 90}16.087 1.939 -4.099
{ca ala b 91}17.57 -1.175 -2.493
{ca ala b 92}14.385 -1.426 -0.402
{ca pro b 93}12.053 -4.366 -1.072
{ca val b 94}8.981 -3.284 -3.069
{ca glu b 95}6.731 -4.348 -0.199
{ca leu b 96}8.323 -1.786 2.105
{ca arg b 97}8.155 0.957 -0.530
{ca gln b 98}4.406 0.353 -0.979
{ca trp b 99}3.89 0.438 2.790
{ca leu b 100}5.855 3.656 3.311
{ca glu b 101}3.818 5.311 0.486
{ca glu b 102}0.665 4.159 2.220
{ca val b 103}1.712 5.485 5.612
{ca leu b 104}3.818 8.607 4.853
{ca leu b 105}1.781 9.631 1.788
{ca lys b 106}-1.628 8.094 2.48
{ca ser b 107} -1.007 8.873 6.106
{ca asp b 108} -1.519 7.169 9.438
@group {TrpRepr lig} animate
@subgroup {sub r} dominant
@vectorlist {Calphas} color= sky
{ca ser r 5}P 16.908 30.966 16.618
{ca pro r 6}15.488 30.507 20.121
{ca tyr r 7}13.967 27.177 21.234
{ca ser r 8}10.308 26.778 20.247
{ca ala r 9}7.814 24.73 22.279
{ca ala r 10}5.799 24.662 19.067
{ca met r 11}8.719 23.097 17.147
{ca ala r 12}9.30 20.711 20.053
{ca glu r 13}5.681 19.575 19.693
{ca gln r 14}6.172 18.895 16.014
{ca arg r 15}9.336 16.862 16.726
{ca his r 16}7.552 14.869 19.405
{ca gln r 17}4.679 13.917 17.071
{ca glu r 18}7.164 12.861 14.357
{ca trp r 19}9.038 10.641 16.838
{ca leu r 20}5.846 8.966 18.049
{ca arg r 21}4.878 8.406 14.385
{ca phe r 22}8.078 6.303 13.990
{ca val r 23}7.462 4.494 17.311
{ca asp r 24}3.877 3.612 16.314
{ca leu r 25}4.866 2.635 12.761
{ca leu r 26}7.467 0.208 14.122
{ca lys r 27}4.95 -1.18 16.634
{ca asn r 28}2.619 -2.06 13.714
{ca ala r 29}5.483 -3.441 11.634
{ca tyr r 30}6.256 -5.935 14.423
{ca gln r 31}2.576 -6.95 14.484
{ca asn r 32}2.752 -7.724 10.730
{ca asp r 33}6.198 -9.34 10.666
{ca leu r 34}7.573 -6.477 8.614
{ca his r 35}9.956 -5.191 11.322
{ca leu r 36}13.173 -6.477 9.622
{ca pro r 37}12.535 -4.802 6.239
{ca leu r 38}11.321 -1.648 8.001
{ca leu r 39}14.474 -1.41 10.153
{ca asn r 40}16.666 -2.10 7.109
{ca leu r 41}14.896 0.772 5.355
{ca met r 42}14.965 3.22 8.262
{ca leu r 43}18.491 2.784 9.636
{ca thr r 44}21.934 2.922 8.022
{ca pro r 45}24.319 -0.064 8.278
{ca asp r 46}26.445 1.95 10.785
{ca glu r 47}23.427 2.65 13.001
{ca arg r 48}22.481 -1.048 13.006
{ca glu r 49}26.073 -1.955 14.041
{ca ala r 50}25.996 0.726 16.778
{ca leu r 51}22.72 -0.651 18.211
{ca gly r 52}24.108 -4.203 18.320
{ca thr r 53}27.158 -2.861 20.247
{ca arg r 54}25.008 -0.812 22.618
{ca val r 55}23.062 -3.921 23.684
{ca arg r 56}26.373 -5.61 24.560
{ca ile r 57}27.488 -2.586 26.595
{ca val r 58}24.191 -2.482 28.536
{ca glu r 59}24.407 -6.241 29.229
{ca glu r 60}27.99 -5.95 30.575
{ca leu r 61}27.163 -2.86 32.650
{ca leu r 62}24.22 -4.703 34.288
{ca arg r 63}26.324 -7.759 34.860
{ca gly r 64}29.107 -5.872 36.661
{ca glu r 65}31.876 -8.441 35.966
{ca met r 66}33.973 -6.139 33.766
{ca ser r 67}35.318 -2.715 34.712
{ca gln r 68}34.496 0.106 32.265
{ca arg r 69}38.143 0.132 31.110
{ca glu r 70}38.072 -3.629 30.575
{ca leu r 71}34.909 -3.163 28.455
{ca lys r 72}36.655 -0.618 26.261
{ca asn r 73}39.529 -3.062 25.719
{ca glu r 74}37.168 -6.006 25.107
{ca leu r 75}34.563 -4.523 22.758
{ca gly r 76}36.55 -1.808 20.971
{ca ala r 77}34.105 0.896 22.184
{ca gly r 78}35.641 4.191 23.367
{ca ile r 79}35.236 5.399 26.930
{ca ala r 80}32.973 8.251 25.775
{ca thr r 81}30.555 5.656 24.351
{ca ile r 82}30.589 3.527 27.456
{ca thr r 83}30.004 6.591 29.643
{ca arg r 84}26.937 7.636 27.636
{ca gly r 85}25.592 4.102 28.189
{ca ser r 86}26.32 4.147 31.931
{ca asn r 87}24.718 7.573 32.367
{ca ser r 88}21.62 6.596 30.356
{ca leu r 89}21.23 3.367 32.360
{ca lys r 90}21.451 5.303 35.636
{ca ala r 91}18.709 7.668 34.369
{ca ala r 92}16.291 4.95 33.224
{ca pro r 93}13.099 3.96 35.016
{ca val r 94}13.777 1.269 37.627
{ca glu r 95}11.153 -0.986 35.991
{ca leu r 96}13.141 -0.917 32.698
{ca arg r 97}16.426 -1.774 34.521
{ca gln r 98}14.71 -4.654 36.354
{ca trp r 99}13.269 -5.994 33.088
{ca leu r 100}16.679 -5.74 31.312
{ca glu r 101}18.275 -7.726 34.182
{ca glu r 102}15.592 -10.409 33.711
{ca val r 103}16.027 -10.747 29.940
{ca leu r 104}19.743 -10.003 29.354
{ca leu r 105}21.309 -11.904 32.284
{ca lys r 106}21.242 -15.693 32.486
{ca ser r 107}19.377 -17.295 35.357
{ca asp r 108}21.782 -18.141 38.224
@vectorlist {lig} color= hotpink
{n trp w 1}P 20.494 7.296 25.216
{ca trp w 1}21.956 7.28 24.959
{c trp w 1}22.497 8.714 24.881
{o trp w 1}21.70 9.631 24.601
{c trp w 1}P 22.497 8.714 24.881
{oxt trp w 1}23.687 8.86 25.151
{ca trp w 1}P 21.956 7.28 24.959
{cb trp w 1}22.315 6.514 23.677
{cg trp w 1}23.659 5.86 23.732
{cd1 trp w 1}24.831 6.326 23.201
{ne1 trp w 1}25.862 5.454 23.456
{ce2 trp w 1}25.379 4.392 24.162
{cg trp w 1}P 23.659 5.86 23.732
{cd2 trp w 1}23.972 4.597 24.349
{ce2 trp w 1}25.379 4.392 24.162
{cz2 trp w 1}26.001 3.242 24.641
{ch2 trp w 1}25.223 2.349 25.324
{cd2 trp w 1}P 23.972 4.597 24.349
{ce3 trp w 1}23.221 3.674 25.045
{cz3 trp w 1}23.848 2.519 25.522
{ch2 trp w 1}25.223 2.349 25.324
@subgroup {sub s} dominant
@vectorlist {Calphas} color= sea
{ca ser s 5}P 42.255 -6.221 8.168
{ca pro s 6} 40.345 -8.235 5.56
{ca tyr s 7} 36.579 -8.833 5.87
{ca ser s 8} 35.695 -11.81 8.08
{ca ala s 9} 32.571 -13.935 7.559
{ca ala s 10}33.107 -14.966 11.169
{ca met s 11}32.987 -11.321 12.335
{ca ala s 12}29.977 -10.74 10.083
{ca glu s 13}28.219 -13.597 11.890
{ca gln s 14}28.929 -12.024 15.246
{ca arg s 15}27.566 -8.654 14.049
{ca his s 16}24.443 -10.306 12.690
{ca gln s 17}23.68 -12.054 16.002
{ca glu s 18}24.188 -8.774 17.911
{ca trp s 19}21.77 -6.959 15.576
{ca leu s 20}19.098 -9.639 15.942
{ca arg s 21}19.575 -9.444 19.738
{ca phe s 22}18.524 -5.745 19.555
{ca val s 23}15.626 -6.546 17.180
{ca asp s 24}14.319 -9.297 19.493
{ca leu s 25}14.832 -7.205 22.642
{ca leu s 26}12.763 -4.383 21.138
{ca lys s 27}10.079 -6.857 20.024
{ca asn s 28}9.701 -7.989 23.673
{ca ala s 29}9.79 -4.415 24.959
{ca tyr s 30}6.764 -3.594 22.776
{ca gln s 31}4.964 -6.65 24.189
{ca asn s 32}5.54 -5.317 27.741
{ca asp s 33}4.881 -1.631 27.055
{ca leu s 34}8.497 -0.786 27.764
{ca his s 35}9.329 0.315 24.192
{ca leu s 36}9.46 4.087 24.991
{ca pro s 37}11.966 3.799 27.872
{ca leu s 38}13.986 1.244 25.893
{ca leu s 39}14.221 3.522 22.829
{ca asn s 40}15.105 6.498 25.046
{ca leu s 41}17.904 4.389 26.524
{ca met s 42}19.196 2.952 23.250
{ca leu s 43}19.158 5.978 20.938
{ca thr s 44}20.616 9.481 21.233
{ca pro s 45}18.353 12.557 20.945
{ca asp s 46}19.857 13.238 17.461
{ca glu s 47}19.064 9.708 16.271
{ca arg s 48}15.461 10.028 17.489
{ca glu s 49}15.12 13.349 15.579
{ca ala s 50}16.647 11.746 12.453
{ca leu s 51}14.155 8.839 12.571
{ca gly s 52}11.191 11.22 12.886
{ca thr s 53}12.487 13.106 9.790
{ca arg s 54}13.078 9.898 7.838
{ca val s 55}9.43 8.854 8.278
{ca arg s 56}8.362 12.208 6.798
{ca ile s 57}10.712 11.758 3.831
{ca val s 58}9.401 8.231 3.129
{ca glu s 59}5.783 9.463 3.352
{ca glu s 60}6.433 12.316 0.867
{ca leu s 61}8.38 10.058 -1.509
{ca leu s 62}5.47 7.554 -1.573
{ca arg s 63}2.972 10.318 -2.039
{ca gly s 64}4.746 11.815 -5.066
{ca glu s 65}3.268 15.343 -4.718
{ca met s 66}6.587 17.064 -3.976
{ca ser s 67}9.717 16.963 -6.125
{ca gln s 68}12.918 15.91 -4.318
{ca arg s 69}14.169 19.521 -4.48
{ca glu s 70}10.89 20.793 -3.044
{ca leu s 71}11.286 18.273 -0.18
{ca lys s 72}14.745 19.593 0.614
{ca asn s 73}13.355 23.139 0.757
{ca glu s 74}10.318 22.075 2.82
{ca leu s 75}11.849 19.794 5.459
{ca gly s 76}15.385 21.181 5.76
{ca ala s 77}16.89 17.779 4.8
{ca gly s 78}19.868 17.836 2.403
{ca ile s 79}19.698 16.202 -1.005
{ca ala s 80}22.166 13.501 0.094
{ca thr s 81}19.704 12.472 2.831
{ca ile s 82}16.736 12.422 0.516
{ca thr s 83}18.678 10.366 -2.037
{ca arg s 84}19.589 7.72 0.550
{ca gly s 85}15.862 7.486 1.362
{ca ser s 86}14.832 7.218 -2.299
{ca asn s 87}17.451 4.546 -3.008
{ca ser s 88}16.506 2.521 0.09
{ca leu s 89}12.798 2.707 -0.812
{ca lys s 90}13.535 1.482 -4.345
{ca ala s 91}15.483 -1.473 -2.865
{ca ala s 92}12.816 -2.532 -0.352
{ca pro s 93}10.577 -5.575 -0.684
{ca val s 94}7.408 -4.734 -2.624
{ca glu s 95}5.28 -6.008 0.29
{ca leu s 96}6.894 -3.402 2.614
{ca arg s 97}6.268 -0.571 0.076
{ca gln s 98}2.629 -1.668 -0.317
{ca trp s 99}2.151 -1.753 3.466
{ca leu s 100}3.761 1.721 3.891
{ca glu s 101}1.363 3.112 1.237
{ca glu s 102}-1.556 1.634 3.215
{ca val s 103}-0.515 3.069 6.589
{ca leu s 104}1.22 6.373 5.709
{ca leu s 105}-1.126 7.694 2.989
{ca lys s 106}-4.675 8.798 3.758
{ca ser s 107} -7.523 6.899 2.153
{ca asp s 108} -8.688 8.665 -1.047
@vectorlist {lig} color= hotpink
{n trp x 1}P 18.587 2.531 4.972
{ca trp x 1}18.997 3.937 4.727
{c trp x 1}20.459 3.991 4.266
{o trp x 1}21.207 3.036 4.559
{c trp x 1}P 20.459 3.991 4.266
{oxt trp x 1}20.779 4.966 3.589
{ca trp x 1}P 18.997 3.937 4.727
{cb trp x 1}18.804 4.826 5.963
{cg trp x 1}18.499 6.252 5.629
{cd1 trp x 1}19.373 7.305 5.61
{ne1 trp x 1}18.729 8.464 5.251
{ce2 trp x 1}17.412 8.189 5.029
{ne1 trp x 1}18.729 8.464 5.251
{cg trp x 1}P 18.499 6.252 5.629
{cd2 trp x 1}17.211 6.791 5.274
{ce2 trp x 1}17.412 8.189 5.029
{cz2 trp x 1}16.346 9.009 4.67
{ch2 trp x 1}15.122 8.416 4.525
{cd2 trp x 1}P 17.211 6.791 5.274
{ce3 trp x 1}15.963 6.229 5.116
{cz3 trp x 1}14.894 7.055 4.758
{ch2 trp x 1}15.122 8.416 4.525
@group {DNAcomplex} animate
@subgroup {sub a} dominant
@balllist {mc N} color= blue master= {binding} off radius= 0.100
{n gly a 78}36.046 2.892 22.876
@balllist {mc O} color= red master= {binding} off radius= 0.100
{o ile a 79}33.897 4.888 28.338
@vectorlist {mc} color= bluetint
{ca ser a 5}P 5.077 28.626 22.900
{ca pro a 6}5.311 30.636 19.685
{ca tyr a 7}8.914 29.457 19.568
{ca ser a 8}11.676 27.086 20.579
{ca ala a 9}9.683 24.959 23.007
{ca ala a 10}7.015 24.382 20.365
{ca met a 11}9.587 23.378 17.760
{ca ala a 12}10.971 20.703 20.074
{ca glu a 13}7.444 19.37 20.577
{ca glu a 14}7.007 18.864 16.800
{ca arg a 15}10.233 16.892 16.376
{ca his a 16}8.937 14.832 19.243
{ca gln a 17}5.661 14.039 17.424
{ca glu a 18}7.517 13.069 14.196
{ca trp a 19}9.549 10.604 16.262
{ca leu a 20}6.444 9.114 17.879
{ca arg a 21}5.275 8.463 14.299
{ca phe a 22}8.325 6.256 13.668
{ca val a 23}7.581 4.405 16.955
{ca asp a 24}4.01 3.685 15.836
{ca leu a 25}4.942 2.601 12.331
{ca leu a 26}7.507 0.15 13.778
{ca lys a 27}4.968 -1.287 16.192
{ca asn a 28}2.59 -2.007 13.254
{ca ala a 29}5.542 -3.548 11.317
{ca tyr a 30}6.234 -6.047 14.165
{ca gln a 31}2.493 -7.028 14.149
{ca asp a 32}2.806 -7.826 10.440
{ca asn a 33}6.249 -9.501 10.448
{ca leu a 34}7.726 -6.608 8.342
{ca his a 35}9.939 -5.23 11.132
{ca leu a 36}13.207 -6.359 9.540
{ca pro a 37}12.707 -4.945 6.037
{ca leu a 38}11.381 -1.762 7.699
{ca leu a 39}14.508 -1.385 9.862
{ca asn a 40}16.769 -2.224 6.829
{ca leu a 41}15.017 0.675 5.020
{ca met a 42}15.035 3.204 7.845
{ca leu a 43}18.567 2.707 9.307
{ca thr a 44}22.07 2.643 7.742
{ca pro a 45}24.452 -0.336 8.139
{ca asp a 46}26.792 1.731 10.424
{ca glu a 47}23.727 2.567 12.562
{ca arg a 48}22.681 -1.122 12.993
{ca glu a 49}26.272 -2.048 13.979
{ca ala a 50}26.468 0.744 16.571
{ca leu a 51}23.214 -0.448 18.171
{ca gly a 52}24.676 -3.934 18.369
{ca thr a 53}27.662 -2.541 20.377
{ca arg a 54}25.359 -0.486 22.717
{ca val a 55}23.235 -3.548 23.589
{ca arg a 56}26.387 -5.543 24.477
{ca ile a 57}27.597 -2.723 26.766
{ca val a 58}24.225 -2.399 28.565
{ca glu a 59}24.174 -6.222 29.102
{ca glu a 60}27.762 -6.384 30.465
{ca leu a 61}27.251 -3.288 32.717
{ca leu a 62}24.165 -5.006 34.154
{ca arg a 63}26.048 -8.246 34.721
{ca gly a 64}28.707 -6.39 36.767
{ca glu a 65}31.386 -9.111 36.419
{ca met a 66}33.798 -7.122 34.216
{ca ser a 67}35.426 -3.788 35.064
{c ser a 67}35.226 -3.016 33.730
{o ser a 67}35.361 -3.629 32.659
{c ser a 67}P 35.226 -3.016 33.730
{n gln a 68}34.999 -1.725 33.822
{ca gln a 68}34.80 -0.871 32.631
{c gln a 68}35.982 -0.90 31.681
{o gln a 68}35.88 -0.835 30.427
{c gln a 68}P 35.982 -0.90 31.681
{n arg a 69}37.242 -0.89 32.206
{ca arg a 69}38.405 -0.995 31.324
{c arg a 69}38.487 -2.345 30.648
{o arg a 69}39.061 -2.435 29.531
{c arg a 69}P 38.487 -2.345 30.648
{n glu a 70}37.986 -3.352 31.326
{ca glu a 70}37.957 -4.719 30.789
{c glu a 70}36.951 -4.819 29.627
{o glu a 70}37.207 -5.54 28.627
{c glu a 70}P 36.951 -4.819 29.627
{n leu a 71}35.826 -4.201 29.837
{ca leu a 71}34.743 -4.153 28.816
{c leu a 71}35.259 -3.447 27.562
{o leu a 71}35.096 -3.953 26.426
{c leu a 71}P 35.259 -3.447 27.562
{n lys a 72}35.846 -2.28 27.744
{ca lys a 72}36.388 -1.49 26.625
{c lys a 72}37.373 -2.284 25.788
{o lys a 72}37.357 -2.169 24.539
{c lys a 72}P 37.373 -2.284 25.788
{n asn a 73}38.326 -2.937 26.439
{ca asn a 73}39.347 -3.761 25.752
{c asn a 73}38.716 -4.916 24.980
{o asn a 73}39.022 -5.091 23.781
{c asn a 73}P 38.716 -4.916 24.980
{n glu a 74}37.756 -5.589 25.576
{ca glu a 74}37.027 -6.678 24.890
{c glu a 74}36.367 -6.256 23.573
{o glu a 74}36.396 -7.003 22.568
{c glu a 74}P 36.367 -6.256 23.573
{n leu a 75}35.766 -5.082 23.561
{ca leu a 75}34.942 -4.584 22.446
{c leu a 75}35.69 -3.733 21.447
{o leu a 75}35.072 -3.339 20.426
{c leu a 75}P 35.69 -3.733 21.447
{n gly a 76}36.924 -3.376 21.744
{ca gly a 76}37.707 -2.43 20.960
{c gly a 76}37.019 -1.069 20.987
{o gly a 76}37.085 -0.372 19.953
{c gly a 76}P 37.019 -1.069 20.987
{n ala a 77}36.455 -0.687 22.145
{ca ala a 77}35.701 0.574 22.285
{c ala a 77}36.449 1.634 23.046
{o ala a 77}37.516 1.348 23.631
{c ala a 77}P 36.449 1.634 23.046
{n gly a 78}36.046 2.892 22.876
{ca gly a 78}36.611 3.951 23.778
{c gly a 78}35.81 3.82 25.116
{o gly a 78}34.618 3.448 25.159
{c gly a 78}P 35.81 3.82 25.116
{n ile a 79}36.56 4.012 26.199
{ca ile a 79}35.949 4.085 27.548
{c ile a 79}34.826 5.102 27.538
{o ile a 79}33.897 4.888 28.338
{c ile a 79}P 34.826 5.102 27.538
{n ala a 80}34.926 6.241 26.828
{ca ala a 80}33.787 7.176 26.820
{c ala a 80}32.466 6.608 26.326
{o ala a 80}31.383 7.121 26.739
{c ala a 80}P 32.466 6.608 26.326
{n thr a 81}32.45 5.599 25.478
{ca thr a 81}31.215 4.894 25.031
{c thr a 81}30.649 4.101 26.202
{o thr a 81}29.408 3.956 26.382
{c thr a 81}P 30.649 4.101 26.202
{n ile a 82}31.541 3.423 26.938
{ca ile a 82}31.082 2.66 28.128
{c ile a 82}30.41 3.664 29.114
{o ile a 82}29.392 3.259 29.700
{c ile a 82}P 30.41 3.664 29.114
{n thr a 83}31.00 4.802 29.360
{ca thr a 83}30.471 5.868 30.214
{c thr a 83}29.095 6.333 29.812
{o thr a 83}28.139 6.535 30.610
{c thr a 83}P 29.095 6.333 29.812
{n arg a 84}28.898 6.523 28.502
{ca arg a 84}27.584 6.852 27.950
{c arg a 84}26.515 5.804 28.340
{o arg a 84}25.406 6.253 28.661
{c arg a 84}P 26.515 5.804 28.340
{n gly a 85}26.878 4.572 28.275
{ca gly a 85}26.074 3.41 28.656
{c gly a 85}25.687 3.535 30.152
{o gly a 85}24.53 3.305 30.535
{c gly a 85}P 25.687 3.535 30.152
{n ser a 86}26.747 3.791 30.934
{ca ser a 86}26.597 3.885 32.404
{c ser a 86}25.678 5.015 32.813
{o ser a 86}24.651 4.847 33.520
{c ser a 86}P 25.678 5.015 32.813
{n asn a 87}25.921 6.201 32.287
{ca asn a 87}25.094 7.374 32.585
{c asn a 87}23.655 7.215 32.112
{o asn a 87}22.733 7.77 32.740
{c asn a 87}P 23.655 7.215 32.112
{n ser a 88}23.477 6.535 30.990
{ca ser a 88}22.14 6.276 30.429
{c ser a 88}21.376 5.326 31.348
{o ser a 88}20.156 5.513 31.476
{c ser a 88}P 21.376 5.326 31.348
{n leu a 89}21.968 4.212 31.725
{ca leu a 89}21.37 3.278 32.680
{c leu a 89}20.944 4.017 33.955
{o leu a 89}19.789 3.826 34.377
{c leu a 89}P 20.944 4.017 33.955
{n lys a 90}21.782 4.911 34.442
{ca lys a 90}21.502 5.69 35.640
{c lys a 90}20.235 6.517 35.449
{o lys a 90}19.495 6.654 36.447
{c lys a 90}P 20.235 6.517 35.449
{n ala a 91}20.033 7.061 34.263
{ca ala a 91}18.839 7.867 33.989
{c ala a 91}17.598 7.046 33.610
{o ala a 91}16.59 7.733 33.272
{c ala a 91}P 17.598 7.046 33.610
{n ala a 92}17.648 5.741 33.509
{ca ala a 92}16.466 4.951 33.091
{ca pro a 93}13.206 4.225 34.958
{ca ala a 94}13.488 1.549 37.653
{ca glu a 95}10.918 -0.54 35.831
{ca leu a 96}13.097 -0.721 32.669
{ca arg a 97}16.174 -1.696 34.682
{ca gln a 98}14.269 -4.475 36.453
{ca trp a 99}12.947 -5.845 33.130
{ca leu a 100}16.384 -5.746 31.447
{ca glu a 101}18.009 -7.649 34.324
{ca glu a 102}15.166 -10.10 34.015
{ca val a 103}15.50 -10.658 30.246
{ca leu a 104}19.166 -10.19 29.324
{ca leu a 105}20.89 -11.403 32.470
{ca lys a 106}19.898 -15.052 32.539
{ca ser a 107}18.423 -15.514 29.074
{ca asp a 108}20.828 -13.07 27.430
@balllist {sc N} color= blue master= {binding} off radius= 0.100
{ne arg a 54}24.701 3.884 20.319
{nh1 arg a 54}22.716 4.867 19.681
{nh2 arg a 54}24.663 5.809 18.910
{ne2 gln a 68}31.287 2.024 34.615
{ne arg a 69}41.281 2.201 33.928
{nh1 arg a 69}39.514 2.513 35.416
{nh2 arg a 69}41.029 4.195 35.066
{nz lys a 72}41.272 2.249 27.312
{ne arg a 84}26.943 9.437 24.112
{nh1 arg a 84}27.471 10.909 22.597
{nh2 arg a 84}25.249 10.785 23.194
{nd2 asn a 87}27.237 8.211 34.022
@balllist {sc O} color= red master= {binding} off radius= 0.100
{oe1 gln a 68}32.888 3.036 33.443
{og1 thr a 81}32.184 4.898 22.810
{og1 thr a 83}32.656 6.462 31.059
{og ser a 86}27.863 4.056 34.458
{od1 asn a 87}27.802 9.804 32.449
@vectorlist {sc} color= sky master= {binding} off
{ca ala a 50}P 26.468 0.744 16.571
{cb ala a 50}26.281 2.257 16.326
{ca leu a 51}P 23.214 -0.448 18.171
{cb leu a 51}21.77 -0.449 17.616
{cg leu a 51}21.159 0.943 17.495
{cd1 leu a 51}20.045 0.999 16.466
{cg leu a 51}P 21.159 0.943 17.495
{cd2 leu a 51}20.612 1.382 18.874
{ca arg a 54}P 25.359 -0.486 22.717
{cb arg a 54}24.35 0.592 22.264
{cg arg a 54}25.013 1.788 21.595
{cd arg a 54}24.063 2.827 21.099
{ne arg a 54}24.701 3.884 20.319
{cz arg a 54}24.055 4.866 19.677
{nh1 arg a 54}22.716 4.867 19.681
{cz arg a 54}P 24.055 4.866 19.677
{nh2 arg a 54}24.663 5.809 18.910
{ca ser a 67}P 35.426 -3.788 35.064
{cb ser a 67}36.787 -3.496 35.687
{og ser a 67}37.73 -3.761 34.655
{ca gln a 68}P 34.80 -0.871 32.631
{cb gln a 68}34.383 0.514 33.108
{cg gln a 68}32.913 0.61 33.519
{cd gln a 68}32.367 1.952 33.797
{oe1 gln a 68}32.888 3.036 33.443
{cd gln a 68}P 32.367 1.952 33.797
{ne2 gln a 68}31.287 2.024 34.615
{ca arg a 69}P 38.405 -0.995 31.324
{cb arg a 69}39.766 -0.619 31.926
{cg arg a 69}39.786 0.731 32.636
{cd arg a 69}40.957 0.842 33.566
{ne arg a 69}41.281 2.201 33.928
{cz arg a 69}40.59 2.969 34.757
{nh1 arg a 69}39.514 2.513 35.416
{cz arg a 69}P 40.59 2.969 34.757
{nh2 arg a 69}41.029 4.195 35.066
{ca lys a 72}P 36.388 -1.49 26.625
{cb lys a 72}36.935 -0.145 27.054
{cg lys a 72}38.419 -0.211 27.488
{cd lys a 72}39.173 1.007 27.150
{ce lys a 72}40.67 0.896 27.244
{nz lys a 72}41.272 2.249 27.312
{ca ile a 79}P 35.949 4.085 27.548
{cb ile a 79}37.074 4.399 28.605
{cg1 ile a 79}36.538 3.961 30.015
{cd1 ile a 79}36.445 2.414 30.152
{cb ile a 79}P 37.074 4.399 28.605
{cg2 ile a 79}37.399 5.931 28.611
{ca ala a 80}P 33.787 7.176 26.820
{cb ala a 80}34.214 8.402 26.031
{ca thr a 81}P 31.215 4.894 25.031
{cb thr a 81}31.456 3.996 23.738
{og1 thr a 81}32.184 4.898 22.810
{cb thr a 81}P 31.456 3.996 23.738
{cg2 thr a 81}30.186 3.431 23.081
{ca ile a 82}P 31.082 2.66 28.128
{cb ile a 82}32.219 1.906 28.877
{cg1 ile a 82}33.087 1.085 27.877
{cd1 ile a 82}32.306 0.16 26.925
{cb ile a 82}P 32.219 1.906 28.877
{cg2 ile a 82}31.585 0.95 29.947
{ca thr a 83}P 30.471 5.868 30.214
{cb thr a 83}31.495 7.063 30.377
{og1 thr a 83}32.656 6.462 31.059
{cb thr a 83}P 31.495 7.063 30.377
{cg2 thr a 83}30.926 8.254 31.142
{ca arg a 84}P 27.584 6.852 27.950
{cb arg a 84}27.672 6.806 26.403
{cg arg a 84}28.025 8.094 25.744
{cd arg a 84}26.719 8.512 25.104
{ne arg a 84}26.943 9.437 24.112
{cz arg a 84}26.469 10.26 23.229
{nh1 arg a 84}27.471 10.909 22.597
{cz arg a 84}P 26.469 10.26 23.229
{nh2 arg a 84}25.249 10.785 23.194
{ca ser a 86}P 26.597 3.885 32.404
{cb ser a 86}28.005 4.047 33.043
{og ser a 86}27.863 4.056 34.458
{ca asn a 87}P 25.094 7.374 32.585
{cb asn a 87}25.744 8.665 32.168
{cg asn a 87}27.051 8.93 32.927
{od1 asn a 87}27.802 9.804 32.449
{cg asn a 87}P 27.051 8.93 32.927
{nd2 asn a 87}27.237 8.211 34.022
@vectorlist {sc} color= sky master= {binding} off
{ca ala a 77} P 35.701 0.574 22.285 
{cb ala a 77} 34.366 0.268 23.047 
{ca thr a 53} P 27.662 -2.541 20.377 
{cb thr a 53} 28.695 -1.435 19.851 
{og1 thr a 53} 29.287 -2.00 18.635 
{cb thr a 53} P 28.695 -1.435 19.851 
{cg2 thr a 53} 29.734 -1.077 20.926 
@vectorlist {sc} color= orange master= {mutant} off
{cg1 val a 77}P 33.735 1.571 23.541
{cb ala a 77} 34.366 .268 23.047
{cg2 val a 77} 33.409 -.504 22.137
@balllist {water} off color= red radius= 0.1 master= {binding}
{O HOH 219}37.964 0.297 35.259
{O HOH 278}30.813 7.336 22.396
{O HOH 296}32.237 5.338 33.398
{O HOH 325}34.805 8.105 30.412
@vectorlist {Hbonds} off color= purple master= {binding}
{nh2 arg a 54}P U 25.315 6.051 18.988
{o3* a f 12}U 27.059 6.70 19.197
{o2p c f 13}P U 26.865 4.348 20.116
{ne arg a 54}U 25.383 4.03 20.255
{ne1 lig c 1}P U 26.534 5.948 22.780
{o1p c f 13}U 27.714 6.367 21.938
{"}P U 28.90 6.756 21.760
{O HOH 278}U 30.175 7.142 22.184
{"}P U 31.152 6.732 22.498
{og1 thr a 81}U 31.845 5.502 22.708
{oe2 glu b 47}P U 23.519 6.868 17.662
{nh2 arg a 54}U 24.262 6.18 18.473
{oe1 glu b 47}P U 21.669 6.399 18.699
{nh1 arg a 54}U 22.367 5.378 19.353
{nh1 arg a 69}P U 39.089 2.916 35.800
{n7 g e 2}U 38.164 3.796 36.636
{o6 g e 2}P U 40.339 5.711 36.636
{nh2 arg a 69}U 40.818 4.659 35.546
{nh1 arg a 69}P U 39.113 1.94 35.375
{O HOH 219}U 38.365 0.87 35.300
{o1p g e 2}P U 36.074 -0.132 36.117
{O HOH 219}U 37.34 0.155 35.542
{og1 thr a 83}P U 33.197 6.875 30.896
{O HOH 325}U 34.264 7.692 30.575
{"}P U 35.462 8.291 30.567
{n6 a e 4}U 37.00 8.726 30.931
{O HOH 325}P U 34.914 8.668 30.813
{n7 a e 4}U 35.149 9.878 31.676
{og1 thr a 83}P U 32.544 6.163 31.682
{O HOH 296}U 32.349 5.637 32.775
{"}P U 32.427 4.665 33.411
{oe1 gln a 68}U 32.698 3.709 33.430
{O HOH 296}P U 31.794 5.12 33.894
{o1p t e 3}U 30.638 4.553 35.190
{"}P U 30.471 3.751 35.415
{ne2 gln a 68}U 31.011 2.608 34.886
{o1p t e 3}P U 29.579 4.261 35.362
{og ser a 86}U 28.479 4.13 34.782
{o ile a 79}P U 33.64 5.214 28.902
{og1 thr a 83}U 32.913 6.136 30.495
{og1 thr a 81}P U 32.544 4.509 22.353
{o1p t f 14}U 33.181 3.821 21.548
{n gly a 78}P U 35.485 3.013 22.476
{o1p t f 14}U 34.102 3.311 21.491
{n lig c 1}P U 20.637 6.769 25.242
{o leu b 41}U 20.374 5.097 25.408
{o leu b 43}P U 19.513 7.602 23.188
{n lig c 1}U 20.377 7.50 24.580
{o5* c j 13}P U 30.029 6.128 20.31
{O HOH 278} U 30.596 7.003 21.82
@balllist {trp N} color= blue master= {binding} off radius= 0.100
{n trp b 1}20.746 7.457 25.174
{ne1 trp b 1}25.986 5.753 23.170
@vectorlist {Trp} color= pink
{n trp b 1}P 20.746 7.457 25.174
{ca trp b 1}22.227 7.482 24.948
{c trp b 1}22.632 8.969 24.669
{ca trp b 1}P 22.227 7.482 24.948
{cb trp b 1}22.412 6.514 23.745
{cg trp b 1}23.788 5.916 23.674
{cd1 trp b 1}24.843 6.514 23.015
{ne1 trp b 1}25.986 5.753 23.170
{ce2 trp b 1}25.685 4.682 23.951
{ne1 trp b 1}25.986 5.753 23.170
{cg trp b 1}P 23.788 5.916 23.674
{cd2 trp b 1}24.29 4.711 24.214
{ce2 trp b 1}25.685 4.682 23.951
{cz2 trp b 1}26.506 3.704 24.513
{ch2 trp b 1}25.895 2.626 25.165
{cd2 trp b 1}P 24.29 4.711 24.214
{ce3 trp b 1}23.762 3.799 25.125
{cz3 trp b 1}24.517 2.684 25.477
{ch2 trp b 1}25.895 2.626 25.165
@subgroup {sub c} dominant
@vectorlist {mc} color= greentint
{ca ala c 10}P 34.682 -9.769 10.823
{ca met c 11}34.283 -7.912 14.100
{ca ala c 12}31.429 -6.783 11.846
{ca glu c 13}29.786 -10.201 11.501
{ca glu c 14}29.756 -10.212 15.283
{ca arg c 15}28.24 -6.777 15.662
{ca his c 16}25.569 -7.981 13.221
{ca gln c 17}24.448 -10.879 15.407
{ca glu c 18}24.182 -8.452 18.331
{ca trp c 19}22.052 -6.026 16.239
{ca leu c 20}19.646 -8.979 15.573
{ca arg c 21}19.522 -9.511 19.350
{ca phe c 22}18.517 -5.852 19.838
{ca val c 23}15.616 -6.358 17.296
{ca asp c 24}14.413 -9.245 19.416
{ca leu c 25}14.689 -7.309 22.730
{ca leu c 26}12.758 -4.447 21.189
{ca lys c 27}9.992 -6.784 20.051
{ca asn c 28}9.684 -7.983 23.673
{ca ala c 29}9.636 -4.382 24.984
{ca tyr c 30}6.687 -3.414 22.743
{ca gln c 31}4.838 -6.434 24.292
{ca asp c 32}5.386 -5.066 27.851
{ca asn c 33}4.782 -1.394 27.179
{ca leu c 34}8.493 -0.506 27.744
{ca his c 35}9.391 0.384 24.121
{ca leu c 36}9.613 4.14 24.798
{ca pro c 37}12.016 3.907 27.765
{ca leu c 38}14.025 1.243 25.813
{ca leu c 39}14.357 3.586 22.816
{ca asn c 40}15.314 6.578 25.018
{ca leu c 41}18.134 4.446 26.513
{c leu c 41}19.079 4.166 25.311
{o leu c 41}20.265 4.409 25.476
{c leu c 41}P 19.079 4.166 25.311
{n met c 42}18.516 3.536 24.282
{ca met c 42}19.392 3.019 23.208
{c met c 42}19.759 4.025 22.139
{o met c 42}20.787 3.748 21.466
{c met c 42}P 19.759 4.025 22.139
{n leu c 43}19.034 5.076 21.926
{ca leu c 43}19.262 6.036 20.830
{c leu c 43}19.621 7.367 21.474
{o leu c 43}19.144 7.645 22.594
{c leu c 43}P 19.621 7.367 21.474
{n thr c 44}20.248 8.228 20.694
{ca thr c 44}20.53 9.603 21.178
{ca pro c 45}18.287 12.684 20.791
{ca asp c 46}19.792 13.445 17.345
{ca glu c 47}19.178 9.893 16.064
{ca arg c 48}15.507 10.076 17.168
{ca glu c 49}15.086 13.412 15.252
{ca ala c 50}16.733 11.982 12.111
{ca leu c 51}14.394 8.912 12.186
{ca gly c 52}11.338 11.219 12.445
{ca thr c 53}12.602 12.938 9.280
{ca arg c 54}13.25 9.758 7.226
{ca val c 55}9.585 8.667 7.851
{ca arg c 56}8.367 11.992 6.354
{ca ile c 57}10.623 11.544 3.361
{ca val c 58}9.487 7.979 2.569
{ca glu c 59}5.805 8.956 3.060
{ca glu c 60}5.958 11.915 0.604
{ca leu c 61}8.017 9.999 -2.034
{ca leu c 62}5.32 7.323 -1.943
{ca arg c 63}2.455 9.926 -2.143
{ca gly c 64}4.016 11.453 -5.297
{ca glu c 65}2.328 14.863 -5.218
{ca met c 66}5.504 16.941 -4.833
{ca ser c 67}8.717 16.916 -6.943
{"}8.717 16.916 -6.943
{c ser c 67}9.759 16.759 -5.811
{o ser c 67}9.53 17.199 -4.662
{c ser c 67}P 9.759 16.759 -5.811
{n gln c 68}10.881 16.139 -6.102
{ca gln c 68}11.902 15.945 -5.002
{c gln c 68}12.453 17.301 -4.622
{o gln c 68}12.823 17.56 -3.455
{c gln c 68}P 12.453 17.301 -4.622
{n arg c 69}12.538 18.243 -5.542
{ca arg c 69}13.028 19.587 -5.183
{c arg c 69}12.032 20.255 -4.225
{o arg c 69}12.476 21.045 -3.378
{c arg c 69}P 12.032 20.255 -4.225
{n glu c 70}10.744 20.169 -4.480
{ca glu c 70}9.69 20.742 -3.635
{c glu c 70}9.766 20.171 -2.204
{o glu c 70}9.639 20.872 -1.196
{c glu c 70}P 9.766 20.171 -2.204
{n leu c 71}9.879 18.879 -2.118
{ca leu c 71}10.003 18.10 -0.891
{c leu c 71}11.221 18.519 -0.087
{o leu c 71}11.135 18.868 1.120
{c leu c 71}P 11.221 18.519 -0.087
{n lys c 72}12.402 18.63 -0.719
{ca lys c 72}13.559 19.071 0.122
{c lys c 72}13.377 20.458 0.703
{o lys c 72}13.937 20.798 1.783
{c lys c 72}P 13.377 20.458 0.703
{n asn c 73}12.792 21.371 -0.039
{ca asn c 73}12.486 22.732 0.422
{c asn c 73}11.417 22.711 1.522
{o asn c 73}11.544 23.428 2.518
{c asn c 73}P 11.417 22.711 1.522
{n glu c 74}10.449 21.838 1.441
{ca glu c 74}9.448 21.701 2.529
{c glu c 74}10.159 21.293 3.814
{o glu c 74}9.739 21.676 4.940
{c glu c 74}P 10.159 21.293 3.814
{n leu c 75}11.045 20.307 3.706
{ca leu c 75}11.704 19.73 4.873
{c leu c 75}12.868 20.533 5.438
{o leu c 75}13.381 20.112 6.504
{c leu c 75}P 12.868 20.533 5.438
{n gly c 76}13.477 21.287 4.567
{ca gly c 76}14.705 22.078 4.821
{c gly c 76}15.885 21.069 4.766
{o gly c 76}16.753 21.026 5.651
{c gly c 76}P 15.885 21.069 4.766
{n ala c 77}15.684 20.014 3.975
{ca ala c 77}16.679 18.954 3.816
{c ala c 77}17.594 19.188 2.584
{o ala c 77}17.285 20.056 1.769
{c ala c 77}P 17.594 19.188 2.584
{n gly c 78}18.627 18.379 2.569
{ca gly c 78}19.569 18.376 1.372
{c gly c 78}18.959 17.424 0.342
{o gly c 78}18.322 16.426 0.724
{c gly c 78}P 18.959 17.424 0.342
{n ile c 79}19.084 17.725 -0.955
{ca ile c 79}18.529 16.822 -1.973
{c ile c 79}19.127 15.43 -1.874
{o ile c 79}18.437 14.423 -2.121
{c ile c 79}P 19.127 15.43 -1.874
{n ala c 80}20.371 15.297 -1.387
{ca ala c 80}20.982 13.958 -1.259
{c ala c 80}20.222 13.078 -0.266
{o ala c 80}20.308 11.845 -0.380
{c ala c 80}P 20.222 13.078 -0.266
{n thr c 81}19.636 13.715 0.750
{ca thr c 81}18.864 12.938 1.754
{c thr c 81}17.604 12.355 1.120
{o thr c 81}17.33 11.22 1.467
{c thr c 81}P 17.604 12.355 1.120
{n ile c 82}16.957 13.134 0.248
{ca ile c 82}15.773 12.578 -0.511
{c ile c 82}16.194 11.395 -1.368
{o ile c 82}15.524 10.359 -1.492
{c ile c 82}P 16.194 11.395 -1.368
{n thr c 83}17.302 11.598 -2.101
{ca thr c 83}17.903 10.576 -2.930
{c thr c 83}18.175 9.272 -2.162
{o thr c 83}17.886 8.171 -2.639
{c thr c 83}P 18.175 9.272 -2.162
{n arg c 84}18.584 9.417 -0.891
{ca arg c 84}18.869 8.232 -0.045
{c arg c 84}17.582 7.464 0.212
{o arg c 84}17.515 6.248 0.137
{c arg c 84}P 17.582 7.464 0.212
{n ala c 85}16.548 8.241 0.421
{ca ala c 85}15.191 7.667 0.668
{c ala c 85}14.696 6.939 -0.591
{o ala c 85}14.194 5.801 -0.565
{c ala c 85}P 14.696 6.939 -0.591
{n ser c 86}14.898 7.619 -1.729
{ca ser c 86}14.504 7.05 -3.034
{c ser c 86}15.193 5.733 -3.298
{o ser c 86}14.583 4.649 -3.570
{c ser c 86}P 15.193 5.733 -3.298
{n asn c 87}16.517 5.77 -3.188
{ca asn c 87}17.347 4.564 -3.387
{c asn c 87}17.00 3.473 -2.394
{o asn c 87}17.003 2.287 -2.753
{c asn c 87}P 17.00 3.473 -2.394
{n ser c 88}16.741 3.823 -1.128
{ca ser c 88}16.336 2.763 -0.146
{c ser c 88}15.002 2.148 -0.496
{o ser c 88}14.794 0.945 -0.306
{c ser c 88}P 15.002 2.148 -0.496
{n leu c 89}14.024 2.924 -0.952
{ca leu c 89}12.726 2.344 -1.372
{c leu c 89}12.932 1.393 -2.559
{o leu c 89}12.302 0.337 -2.521
{c leu c 89}P 12.932 1.393 -2.559
{n lys c 90}13.759 1.726 -3.552
{ca lys c 90}14.035 0.814 -4.703
{c lys c 90}14.64 -0.505 -4.272
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@subgroup {bases} dominant
@balllist {base N} color= blue master= {binding} off radius= 0.100
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