@text
Kinemage Supplement to Branden & Tooze "Introduction to Protein Structure"
Chapter 3 -  ALPHA-DOMAIN STRUCTURES

		Contents of file C3ALPHA.KIN:
Kin.1- The 4-helix bundle of ROP protein (3.1a,b and 3.2b)
Kin.2- Myohemerythrin, 4-helix bundle and Fe ligands (3.3b,c)
Kin.3- Myoglobin, with 8 helices around a heme group (3.4)
Kin.4- Helix-helix packing by ridges into grooves (3.5, 3.6b)

	Many entire proteins, or domains within larger structures, are made up almost entirely of alpha-helices.  The simplest, and one of the commonest, helical domain structures is a bundle of 4 helices that lie antiparallel to each other and pack closely together at an angle of about 20¡.  This kind of interaction is illustrated here by the structures of ROP protein and myohemerythrin, and by a low-angle helix contact from subtilisin.  A larger helical domain, with some helix contacts at high angles, is illustrated by the "globin fold" of myoglobin.

	Kinemage 1 shows the 4-helix bundle structure of ROP protein, starting with just the Calpha backbone and labels on the N- and C-termini.  Rop is a dimer of two identical chains, each forming an antiparallel hairpin of two alpha-helices.  The two subunits are related by a 2-fold axis, which can be turned on.  Choose View2 to see the bundle end-on; note that the helix axes are not quite straight but coil slightly, to achieve tight packing along their whole length.
	Now turn on "sc Hphobic" to see how the hydrophobic sidechains (in gold) are almost all on the inside of the bundle, filling the space between the 4 helices.  In ROP this interior packing is unusually regular, with sets of 4 sidechains (one from each helix) forming distinct layers.  Then turn on "sc Hphilic" to show polar sidechains in cyan and charged sidechains in skyblue;  they are all on the outside of the protein, except for two Thr.

	Kinemage 2 shows the 4-helix bundle of myohemerythrin, with the alpha-helices colored pink, green, yellow, and blue to match Fig. 3.3a.  The two Fe atoms of the binuclear iron center are marked in gold, and the bridging O in red.  Click on the "ANIMATE"button to see first an end view of the 4-helix bundle and then a closeup of the sidechains that ligand the iron atoms, oriented as in Fig. 3.3c.   One Fe has 3 His ligands, the other has 2 His and a bound azide at the O2 site;  both carboxyl groups bridge between the two irons.  Myohemerythrin binds O2 reversibly, acting as an oxgyen-storage molecule for marine worms the way myoglobin does for vertebrates. (from PDB file 2MHR)

	Kinemage 3 shows a different type of all-helical domain structure, with the "globin fold" of myoglobin.  The heme group is in yellowtint, with a red iron, and Calpha backbones of the 8 alpha-helices (A through H) are color-coded to match Fig. 3.4, with A-D in pink, E-F in seagreen, and the final G-H antiparallel pair in skyblue.  Note that many close contacts between helices in this structure are nearly perpendicular.  The heme is bound in a hydrophobic pocket between helices E and F, with two His ligands to the Fe.  O2 binds reversibly to the Fe, on the righthand side next to His 64.

	Kinemage 4 illustrates the way in which ridges-into grooves packing of sidechains produces a low-angle contact between two helices.  The startup view looks from one side of the helix-helix contact, lined up along a row of Ala sidechains (in hotpink) which form a j, j+4 row on the lower helix - that is, those sidechains are separated by 4 residues.  That row fits between the two i, i+3 rows of sidechains (in cyan and skyblue) on the top helix.  Choose View2 to look at the helices on top of one another.  The sidechain rows are emphasized by color-coded lines, to show that they interdigitate and all lie parallel to each other, as in part 4 of Fig. 3.6b. 

@kinemage 1
@caption (B&T Fig. 3.1a,b and 3.2b)
The 4-helix bundle of ROP protein, with subunit a in white and subunit b in yellowtint; the N and C termini are labeled.  Choose View2 to see the bundle end-on, and then turn on first "sc Hphobic" (the hydrophobic sidechains, in gold) and then "sc Hphilic" (hydrophilics in cyan, and charges in skyblue).  (from PDB file 1ROP)
@onewidth 
@multibin 3 
@zoom 1.1
@zslab 130
@center 52.84 11.866 26.68
@matrix 
.658941 0.752191 -0.002274 -0.007317 0.003388 -0.999967 -0.752160 0.658935 0.007736 
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@2zslab 250
@2center 52.84 8.349 26.68
@2matrix 
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@group {ROP sub a} 
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{ca ala a 12}45.349 5.842 24.519
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{ca glu a 24}55.836 6.398 40.397
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{ca cys a 38}56.459 12.769 33.56
{ca glu a 39}53.627 14.342 35.557
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{ca his a 42}50.56 11.869 32.172
{ca asp a 43}48.29 14.988 32.098
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{ca asp a 46}44.852 11.992 29.884
{ca glu a 47}43.928 14.889 27.599
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{ca tyr a 49}42.407 9.745 26.038
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{ca ser a 51}39.618 13.599 23.424
{ca cys a 52}39.406 10.104 21.85
{ca leu a 53}36.52 9.107 24.156
{ca ala a 54}34.524 12.206 23.155
{ca arg a 55}35.135 11.7 19.427
{ca phe a 56}34.677 7.924 19.184
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{ N} P 32.39 2.582 17.546
{ C} P 34.677 7.924 19.184
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{sg cys a 52}41.986 9.393 21.061
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{ce1 phe a 14}49.906 -1.367 28.597
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{ce1 phe a 56}38.342 8.335 16.79
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{ca leu a 9}P 40.896 4.17 22.436
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{cd1 leu a 20}50.034 8.236 38.047
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{ca leu a 22}P 56.55 5.505 35.19
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{cg leu a 22}58.23 6.609 33.577
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{cd1 leu a 23}55.588 11.439 38.172
{cg leu a 23}P 54.461 10.489 38.363
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{cg leu a 29}64.535 5.498 40.244
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{cb ile a 37}59.542 15.712 32.189
{cg1 ile a 37}60.418 16.996 32.085
{cd1 ile a 37}61.837 16.577 31.595
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{cg2 ile a 37}59.045 15.312 30.699
{ca met a 1}P 32.39 2.582 17.546
{cb met a 1}33.271 2.428 18.81
{cg met a 1}34.257 3.54 18.961
{sd met a 1}35.104 3.15 20.545
{ce met a 1}33.734 3.285 21.683
{ca met a 11}P 45.913 2.263 23.2
{cb met a 11}46.416 2.423 21.761
{cg met a 11}47.89 2.638 21.767
{sd met a 11}48.459 1.988 20.093
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{cb ala a 8}42.43 4.441 18.296
{ca ala a 12}P 45.349 5.842 24.519
{cb ala a 12}44.218 6.76 24.103
{ca ala a 31}P 64.659 11.924 39.9
{cb ala a 31}64.717 10.933 38.704
{ca ala a 35}P 59.242 13.158 37.504
{cb ala a 35}59.353 13.015 39.06
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{cb tyr a 49}42.711 9.037 27.387
{cg tyr a 49}41.613 8.079 27.8
{cd1 tyr a 49}41.238 6.971 27.065
{ce1 tyr a 49}40.251 6.083 27.515
{cz tyr a 49}39.715 6.304 28.789
{oh tyr a 49}38.738 5.493 29.312
{cg tyr a 49}P 41.613 8.079 27.8
{cd2 tyr a 49}41.111 8.23 29.108
{ce2 tyr a 49}40.092 7.392 29.555
{cz tyr a 49}39.715 6.304 28.789
{ca ser a 17}P 48.181 4.12 32.611
{cb ser a 17}47.572 2.71 32.475
{og ser a 17}46.189 2.803 32.788
{ca ser a 40}P 53.068 16.767 32.66
{cb ser a 40}54.065 17.819 32.247
{og ser a 40}53.605 18.665 31.182
{ca ser a 51}P 39.618 13.599 23.424
{cb ser a 51}40.77 14.352 22.832
{og ser a 51}40.555 14.847 21.531
{ca thr a 2}P 34.312 0.62 14.917
{cb thr a 2}34.953 1.126 13.554
{og1 thr a 2}36.104 1.971 13.955
{cb thr a 2}P 34.953 1.126 13.554
{cg2 thr a 2}33.901 1.999 12.806
{ca thr a 7}P 41.844 -0.251 19.327
{cb thr a 7}42.59 -0.89 18.086
{og1 thr a 7}41.836 -2.163 17.962
{cb thr a 7}P 42.59 -0.89 18.086
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{ca thr a 19}P 52.827 7.233 32.205
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{og1 thr a 19}50.893 8.616 31.729
{cb thr a 19}P 52.301 8.482 31.506
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{cb lys a 25}59.427 4.036 37.973
{cg lys a 25}58.658 2.738 37.795
{cd lys a 25}59.416 1.781 36.869
{ce lys a 25}58.542 0.543 36.615
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{cg arg a 13}42.412 3.179 29.406
{cd arg a 13}41.298 2.195 29.422
{ne arg a 13}40.026 2.768 28.991
{cz arg a 13}39.296 2.232 27.995
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{cg arg a 55}36.337 11.685 17.176
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{cg asp a 32}64.877 16.986 40.907
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{ca asp a 46}P 44.852 11.992 29.884
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{cg asp a 46}43.299 12.447 31.837
{od1 asp a 46}42.707 11.373 32.037
{cg asp a 46}P 43.299 12.447 31.837
{od2 asp a 46}42.813 13.551 32.107
{ca glu a 5}P 38.406 3.139 16.923
{cb glu a 5}36.992 3.727 16.837
{cg glu a 5}36.896 4.809 15.717
{cd glu a 5}35.476 5.105 15.28
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{cb glu a 24}54.759 5.423 40.78
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{ca glu a 28}P 61.035 6.163 43.836
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{cg glu a 28}59.377 4.163 43.908
{cd glu a 28}59.122 2.718 43.55
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{oe2 glu a 28}58.007 2.259 43.411
{ca glu a 33}P 63.237 16.922 36.904
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@kinemage 2
@caption  (B&T Fig. 3.3b,c)
The four-helix bundle of myohemerythrin, with the helices colored pink, green, yellow, and blue to match Fig. 3.3a.  The two Fe atoms are marked in gold and the bridging O in red.  View3 is from one end of the helix bundle.  Click on "ANIMATE" to see an end view of the bundle and then a closeup of the iron ligands, as in Fig. 3.3c.   One Fe has 3 His ligands, the other has 2 His and a bound azide at the oxygen site;  both carboxyl groups bridge between the two irons.  (from PDB file 2MHR)
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{ca gly 1} P 11.628 47.621 -.689
{ca gly 1} 11.628 47.621 -.689
{ca trp 2} 9.975 47.275 2.747
{ca glu 3} 7.316 49.777 3.826
{ca ile 4} 8.503 52.661 6.001
{ca pro 5} 6.222 53.175 8.99
{ca glu 6} 4.573 56.526 9.415
{ca pro 7} 4.866 57.627 12.233
{ca tyr 8} 8.291 56.107 12.446
{ca val 9} 7.781 53.598 15.25
{ca trp 10} 8.717 49.949 15.754
{ca asp 11} 5.91 47.411 15.382
{ca glu 12} 5.579 43.645 15.945
{ca ser 13} 6.201 42.974 12.228
{ca phe 14} 9.818 43.815 13.082
{ca arg 15} 10.144 41.26 15.925
{ca val 16} 13.202 39.003 15.928
{ca phe 17} 12.162 37.096 19.111
{ca tyr 18} 15.268 37.893 21.153
{ca asp 38} P 14.05 67.737 17.13
{ca asn 39} 17.035 67.676 14.787
{ca ser 40} 19.619 68.422 17.446
{ca lys 66} P 28.651 30.439 15.364
{ca tyr 67} 26.018 31.988 13.028
{ca ser 68} 27.179 31.354 9.446
{ca glu 69} 26.407 34.718 7.903
{ca leu 87} P 26.779 63.363 10.234
{ca ser 88} 26.296 66.623 12.066
{ca ala 89} 23.041 68.219 13.28
{ca pro 90} 20.78 69.427 11.752
{ca val 91} 20.889 66.29 9.671
{ca asp 92} 19.805 67.069 6.12
{ca lys 115} P 15.664 34.366 13.686
{ca gly 116} 15.851 30.988 15.531
{ca lys 117} 19.608 30.691 14.829
{ca leu 118} 21.088 32.493 17.865
@vectorlist {helix A} color=pink
{ca tyr 18} P 15.268 37.893 21.153
{ca glu 19} 14.002 40.175 23.908
{ca gln 20} 17.249 42.18 24.18
{ca leu 21} 17.621 42.673 20.436
{ca asp 22} 13.95 43.694 20.119
{ca glu 23} 14.385 46.329 22.835
{ca glu 24} 17.514 47.657 21.083
{ca his 25} 15.632 47.806 17.783
{ca lys 26} 12.801 49.78 19.409
{ca lys 27} 15.337 52.284 20.719
{ca ile 28} 16.935 52.789 17.285
{ca phe 29} 13.454 53.538 15.793
{ca lys 30} 12.917 55.997 18.673
{ca gly 31} 16.363 57.464 18.087
{ca ile 32} 15.447 58.309 14.484
{ca phe 33} 11.905 59.478 15.438
{ca asp 34} 13.467 61.944 17.964
{ca cys 35} 15.877 63.348 15.369
{ca ile 36} 12.828 63.814 13.117
{ca arg 37} 10.977 65.763 15.841
{ca asp 38} 14.05 67.737 17.13
@vectorlist {helix B} color=sea
{ca ser 40} P 19.619 68.422 17.446
{ca ala 41} 23.207 67.507 18.282
{ca pro 42} 22.146 65.594 21.434
{ca asn 43} 19.531 63.505 19.544
{ca leu 44} 22.003 62.587 16.767
{ca ala 45} 24.62 61.598 19.4
{ca thr 46} 22.05 59.399 21.148
{ca leu 47} 21.243 57.731 17.844
{ca val 48} 24.958 57.022 17.312
{ca lys 49} 25.3 55.648 20.849
{ca val 50} 22.296 53.287 20.818
{ca thr 51} 23.217 51.982 17.333
{ca thr 52} 26.835 51.326 18.373
{ca asn 53} 25.658 49.433 21.466
{ca his 54} 23.175 47.429 19.4
{ca phe 55} 25.74 46.353 16.774
{ca thr 56} 28.177 45.25 19.49
{ca his 57} 25.468 43.199 21.172
{ca glu 58} 23.988 41.648 18.004
{ca glu 59} 27.439 40.694 16.669
{ca ala 60} 28.388 39.177 20.073
{ca met 61} 25.275 36.985 19.836
{ca met 62} 25.963 36.003 16.205
{ca asp 63} 29.558 35.063 17.177
{ca ala 64} 28.545 33.09 20.198
{ca ala 65} 26.06 31.042 18.083
{ca lys 66} 28.651 30.439 15.364
@vectorlist {helix C} color=yellowtint
{ca glu 69} P 26.407 34.718 7.903
{ca val 70} 28.056 37.054 10.309
{ca val 71} 30.686 38.433 7.828
{ca pro 72} 28.381 40.081 5.265
{ca his 73} 26.265 41.251 8.29
{ca lys 74} 29.085 42.899 10.235
{ca lys 75} 30.047 44.688 7.007
{ca met 76} 26.649 46.279 6.692
{ca his 77} 26.756 47.376 10.36
{ca lys 78} 30.246 48.871 9.985
{ca asp 79} 29.164 50.85 6.907
{ca phe 80} 26.08 52.285 8.651
{ca leu 81} 28.21 53.342 11.697
{ca glu 82} 30.693 55.001 9.355
{ca lys 83} 27.843 56.975 7.786
{ca ile 84} 25.951 58.215 10.897
{ca gly 85} 29.297 58.688 12.68
{ca gly 86} 30.047 61.363 10.131
{ca leu 87} 26.779 63.363 10.234
@vectorlist {helix D} color=sky
{ca asp 92} P 19.805 67.069 6.12
{ca ala 93} 16.494 65.702 4.897
{ca lys 94} 18.108 63.233 2.439
{ca asn 95} 20.164 61.575 5.203
{ca val 96} 17.184 61.349 7.621
{ca asp 97} 15.357 59.516 4.818
{ca tyr 98} 18.399 57.31 4.225
{ca cys 99} 18.402 56.371 7.93
{ca lys 100} 14.672 55.668 7.999
{ca glu 101} 14.941 53.356 5.036
{ca trp 102} 18.26 51.761 6.087
{ca leu 103} 16.927 50.503 9.449
{ca val 104} 13.737 49.077 7.955
{ca asn 105} 15.65 47.184 5.249
{ca his 106} 18.446 46.099 7.606
{ca ile 107} 16.049 44.505 10.048
{ca lys 108} 13.667 42.745 7.645
{ca gly 109} 16.297 41.852 5.039
{ca thr 110} 19.304 40.877 7.213
{ca asp 111} 18.555 40.618 10.946
{ca phe 112} 15.569 38.416 9.996
{ca lys 113} 17.972 35.777 8.74
{ca tyr 114} 19.172 35.019 12.296
{ca lys 115} 15.664 34.366 13.686
@subgroup dominant {Fe O} 
@vectorlist {FeO} color=white
{fe1 feo} P 22.031 43.794 12.338
{O feo} 21.193 45.019 13.358
{fe2 feo} 19.732 44.88 14.337
@vectorlist {Fe} color=gold
{fe1 feo} P U 21.931 43.794 12.338
U 22.131 43.794 12.338
P U 22.031 43.694 12.338
U 22.031 43.894 12.338
P U 22.031 43.794 12.238
U 22.031 43.794 12.438
{fe2 feo} P U 19.632 44.88 14.337
U 19.832 44.88 14.337
P U 19.732 44.78 14.337
U 19.732 44.98 14.337
P U 19.732 44.88 14.237
U 19.732 44.88 14.437
@vectorlist {O} color=red
{O feo} P U 21.093 45.019 13.358
U 21.293 45.019 13.358
P U 21.193 44.919 13.358
U 21.193 45.119 13.358
P U 21.193 45.019 13.258
U 21.193 45.019 13.458
@group dominant {myohem.2} animate moview= 3
@subgroup {ca} instance= {Calphas}
@subgroup {fe} instance= {Fe O}
@group dominant {lig close.1} animate moview= 4
@subgroup {ca} instance= {Calphas}
@subgroup {fe} instance= {Fe O}
@subgroup dominant {ligands}
@vectorlist {A sc} color= pinktint
{ca his 25} P 15.632 47.806 17.783
{cb his 25} 14.993 46.601 17.052
{cg his 25} 16.047 45.712 16.44
{nd1 his 25} 15.73 44.447 15.974
{ce1 his 25} 16.826 43.925 15.422
{ne2 his 25} 17.861 44.737 15.527
{cg his 25} P 16.047 45.712 16.44
{cd2 his 25} 17.347 45.9 16.155
{ne2 his 25} 17.861 44.737 15.527
@vectorlist {B sc} color= greentint
{ca his 54} P 23.175 47.429 19.4
{cb his 54} 21.983 47.989 18.572
{cg his 54} 21.265 46.887 17.819
{nd1 his 54} 20.698 45.751 18.348
{ce1 his 54} 20.298 45.018 17.329
{ne2 his 54} 20.584 45.642 16.16
{cg his 54} P 21.265 46.887 17.819
{cd2 his 54} 21.189 46.818 16.446
{ne2 his 54} 20.584 45.642 16.16
{ca glu 58} P 23.988 41.648 18.004
{cb glu 58} 23.264 42.427 16.939
{cg glu 58} 22.211 41.654 16.116
{cd glu 58} 21.602 42.5 15.036
{oe1 glu 58} 22.331 42.672 14.026
{cd glu 58} P 21.602 42.5 15.036
{oe2 glu 58} 20.454 42.979 15.111
@vectorlist {C sc} color= yellow
{ca his 73} P 26.265 41.251 8.29
{cb his 73} 25.638 40.288 9.332
{cg his 73} 24.478 40.851 10.088
{nd1 his 73} 23.387 40.106 10.442
{ce1 his 73} 22.533 40.859 11.101
{ne2 his 73} 23.011 42.115 11.206
{cg his 73} P 24.478 40.851 10.088
{cd2 his 73} 24.227 42.096 10.595
{ne2 his 73} 23.011 42.115 11.206
{ca his 77} P 26.756 47.376 10.36
{cb his 77} 26.988 46.483 11.571
{cg his 77} 25.852 45.625 12.037
{nd1 his 77} 26.028 44.704 13.058
{ce1 his 77} 24.897 44.085 13.316
{ne2 his 77} 23.98 44.599 12.48
{cg his 77} P 25.852 45.625 12.037
{cd2 his 77} 24.558 45.524 11.647
{ne2 his 77} 23.98 44.599 12.48
@vectorlist {D sc} color= cyan
{ca his 106} P 18.446 46.099 7.606
{cb his 106} 19.417 46.935 8.464
{cg his 106} 20.448 46.057 9.094
{nd1 his 106} 21.48 45.418 8.462
{ce1 his 106} 22.19 44.693 9.318
{ne2 his 106} 21.612 44.812 10.51
{cg his 106} P 20.448 46.057 9.094
{cd2 his 106} 20.501 45.636 10.372
{ne2 his 106} 21.612 44.812 10.51
{ca asp 111} P 18.555 40.618 10.946
{cb asp 111} 18.084 41.702 11.907
{cg asp 111} 19.132 42.711 12.275
{od1 asp 111} 20.313 42.633 11.991
{cg asp 111} P 19.132 42.711 12.275
{od2 asp 111} 18.747 43.678 12.996
@vectorlist {sc N} color=sky
{ne2 his 25} P U 17.761 44.737 15.527
U 17.961 44.737 15.527
P U 17.861 44.637 15.527
U 17.861 44.837 15.527
P U 17.861 44.737 15.427
U 17.861 44.737 15.627
{ne2 his 54} P U 20.484 45.642 16.16
U 20.684 45.642 16.16
P U 20.584 45.542 16.16
U 20.584 45.742 16.16
P U 20.584 45.642 16.06
U 20.584 45.642 16.26
{ne2 his 73} P U 22.911 42.115 11.206
U 23.111 42.115 11.206
P U 23.011 42.015 11.206
U 23.011 42.215 11.206
P U 23.011 42.115 11.106
U 23.011 42.115 11.306
{ne2 his 77} P U 23.88 44.599 12.48
U 24.08 44.599 12.48
P U 23.98 44.499 12.48
U 23.98 44.699 12.48
P U 23.98 44.599 12.38
U 23.98 44.599 12.58
{ne2 his 106} P U 21.512 44.812 10.51
U 21.712 44.812 10.51
P U 21.612 44.712 10.51
U 21.612 44.912 10.51
P U 21.612 44.812 10.41
U 21.612 44.812 10.61
@vectorlist {sc O} color= red 
{oe1 glu 58} P U 22.231 42.672 14.026
U 22.431 42.672 14.026
P U 22.331 42.572 14.026
U 22.331 42.772 14.026
P U 22.331 42.672 13.926
U 22.331 42.672 14.126
{oe2 glu 58} P U 20.354 42.979 15.111
U 20.554 42.979 15.111
P U 20.454 42.879 15.111
U 20.454 43.079 15.111
P U 20.454 42.979 15.011
U 20.454 42.979 15.211
{od1 asp 111} P U 20.213 42.633 11.991
U 20.413 42.633 11.991
P U 20.313 42.533 11.991
U 20.313 42.733 11.991
P U 20.313 42.633 11.891
U 20.313 42.633 12.091
{od2 asp 111} P U 18.647 43.678 12.996
U 18.847 43.678 12.996
P U 18.747 43.578 12.996
U 18.747 43.778 12.996
P U 18.747 43.678 12.896
U 18.747 43.678 13.096
@vectorlist {bonds} color=purple
{ne2 his 54} P U 20.307 45.394 15.567
{fe2 feo} U 20.009 45.128 14.93
{fe2 feo} P U 19.143 44.835 14.712
{ne2 his 25} U 18.45 44.782 15.152
{n1 azi 120} P U 19.243 46.119 13.884
{fe2 feo} U 19.488 45.496 14.111
{fe2 feo} P U 19.396 44.47 13.88
{od2 asp 111} U 19.083 44.088 13.453
{fe2 feo} P U 19.964 44.268 14.586
{oe2 glu 58} U 20.222 43.591 14.862
{oe1 glu 58} P U 22.229 43.055 13.449
{fe1 feo} U 22.133 43.411 12.915
{fe1 feo} P U 22.677 44.061 12.385
{ne2 his 77} U 23.334 44.332 12.433
{ne2 his 73} P U 22.706 42.637 11.558
{fe1 feo} U 22.336 43.272 11.986
{fe1 feo} P U 21.894 44.128 11.738
{ne2 his 106} U 21.749 44.478 11.11
{od1 asp 111} P U 20.885 43.02 12.107
{fe1 feo} U 21.459 43.407 12.222
@subgroup {azide} dominant 
@vectorlist {azi} color= white 
{n1 azi 120} P 18.999 46.735 13.658
{n2 azi 120} 19.669 47.714 13.268
{n3 azi 120} 20.276 48.561 12.984
@vectorlist {N azi mk} color=sky
{n1 azi 120} P U 18.899 46.735 13.658
U 19.099 46.735 13.658
P U 18.999 46.635 13.658
U 18.999 46.835 13.658
P U 18.999 46.735 13.558
U 18.999 46.735 13.758
{n2 azi 120} P U 19.569 47.714 13.268
U 19.769 47.714 13.268
P U 19.669 47.614 13.268
U 19.669 47.814 13.268
P U 19.669 47.714 13.168
U 19.669 47.714 13.368
{n3 azi 120} P U 20.176 48.561 12.984
U 20.376 48.561 12.984
P U 20.276 48.461 12.984
U 20.276 48.661 12.984
P U 20.276 48.561 12.884
U 20.276 48.561 13.084
@group dominant {lig close.2} animate moview= 5
@subgroup {ca} instance= {Calphas}
@subgroup {fe} instance= {Fe O}
@subgroup {lig} instance= {ligands}
@subgroup {az} instance= {azide}
@kinemage 3
@caption (B&T Fig. 3.4)
The all-helical "globin fold" of myoglobin, with Calphas, helix labels, heme group (yellowtint), iron (red), and His Fe ligands (gold).  (from PDB file 1MBD)
@onewidth
@multibins 3
@zoom 1.05
@zslab 130
@center 15.470 20.118 4.946
@matrix 
.998195 -.059819 .00538 .028941 .557541 .829645 -.052628 -.827992 .558266
@2zoom 1.7
@2zslab 130
@2center 15.092 27.572 1.777
@2matrix 
.954142 -.237856 .181765 -.228413 -.185985 .955634 -.193498 -.953328 -.231786
@3zoom 1.06
@3zslab 160
@3center 12.805 20.291 5.358
@3matrix 
.45868 .01083 -.888536 .665377 .658572 .351508 .588971 -.75244 .294867 
@group {myoglobin} 
@subgroup dominant {Calphas}
@vectorlist {A-D} color=pink
{ca val 1}P 0.68 15.504 15.876
{ca leu 2}4.215 14.068 16.715
{ca ser 3}4.326 12.364 20.081
{ca glu 4}6.969 13.357 22.606
{ca gly 5}8.744 10.026 21.855
{ca glu 6}8.811 10.896 18.097
{ca trp 7}10.206 14.346 18.884
{ca gln 8}13.051 12.853 21.014
{ca leu 9}14.025 10.543 18.006
{ca val 10}14.139 13.614 15.659
{ca leu 11}16.147 15.762 17.997
{ca his 12}18.629 13.04 18.966
{ca val 13}19.691 12.639 15.413
{ca trp 14}19.541 16.357 14.645
{ca ala 15}22.093 16.971 17.52
{ca lys 16}24.487 14.67 15.536
{ca val 17}23.802 16.873 12.349
{ca glu 18}24.835 19.811 14.394
{ca ala 19}28.325 18.333 14.957
{ca asp 20}28.945 18.97 11.157
{ca val 21}26.276 21.39 9.809
{ca ala 22}28.334 22.379 6.724
{ca gly 23}29.171 18.956 5.615
{ca his 24}25.59 17.767 5.928
{ca gly 25}24.36 20.916 4.111
{ca gln 26}26.708 20.174 1.205
{ca asp 27}25.781 16.595 0.872
{ca ile 28}21.961 17.469 1.073
{ca leu 29}22.159 20.183 -1.63
{ca ile 30}24.361 18.089 -3.969
{ca arg 31}21.96 15.198 -3.668
{ca leu 32}18.994 17.5 -4.468
{ca phe 33}20.714 19.029 -7.476
{ca lys 34}21.927 15.758 -8.981
{ca ser 35}18.667 13.874 -8.391
{ca his 36}16.392 16.778 -9.496
{ca pro 37}18.298 19.027 -11.844
{ca glu 38}15.415 21.394 -12.273
{ca thr 39}16.015 22.601 -8.739
{ca leu 40}19.277 24.048 -9.531
{ca glu 41}17.803 26.393 -11.995
{ca lys 42}16.027 28.189 -9.145
{ca phe 43}19.403 29.427 -7.925
{ca asp 44}20.956 32.253 -9.895
{ca arg 45}23.727 31.976 -7.362
{ca phe 46}24.618 28.281 -8.163
{ca lys 47}23.416 27.663 -11.769
{ca his 48}26.887 27.886 -13.188
{ca leu 49}27.969 24.534 -11.393
{ca lys 50}27.731 21.626 -13.659
{ca thr 51}29.703 18.734 -12.118
{ca glu 52}29.574 17.123 -8.659
{ca ala 53}33.311 18.167 -8.047
{ca glu 54}32.518 21.742 -8.957
{ca met 55}29.619 21.649 -6.458
{ca lys 56}31.835 20.16 -3.696
{ca ala 57}34.501 22.836 -4.269
{ca ser 58}32.099 25.833 -3.965
@vectorlist {E-F} color=sea
{ca ser 58}P 32.099 25.833 -3.965
{ca glu 59}32.445 27.626 -0.686
{ca asp 60}29.282 29.739 -1.318
{ca leu 61}27.237 26.547 -1.842
{ca lys 62}28.439 25.233 1.497
{ca lys 63}27.43 28.578 3.066
{ca his 64}23.853 28.281 1.749
{ca gly 65}23.748 24.717 3.092
{ca val 66}24.428 26.117 6.569
{ca thr 67}21.723 28.835 6.044
{ca val 68}19.188 26.042 5.204
{ca leu 69}20.083 23.63 7.977
{ca thr 70}20.252 26.375 10.636
{ca ala 71}16.647 27.519 9.795
{ca leu 72}15.45 23.868 9.657
{ca gly 73}16.934 23.206 13.045
{ca ala 74}15.349 26.174 14.636
{ca ile 75}11.96 24.897 13.331
{ca leu 76}12.457 21.423 14.605
{ca lys 77}13.43 22.463 18.148
{ca lys 78}9.996 24.193 18.414
{ca lys 79}8.377 20.719 18.346
{ca gly 80}5.525 21.856 16.095
{ca his 81}5.111 25.434 17.642
{ca his 82}6.813 27.063 14.674
{ca glu 83}4.404 29.53 13.472
{ca ala 84}6.766 32.441 13.804
{ca glu 85}9.589 30.727 12.163
{ca leu 86}7.618 29.487 9.238
{ca lys 87}5.866 32.594 8.3
{ca pro 88}8.862 34.519 6.793
{ca leu 89}10.13 31.408 5.123
{ca ala 90}6.876 30.536 3.308
{ca gln 91}6.447 34.104 2.387
{ca ser 92}9.871 34.299 0.585
{ca his 93}9.623 30.85 -0.894
{ca ala 94}6.144 31.544 -2.363
{ca thr 95}6.663 35.031 -3.533
{ca lys 96}10.361 35.718 -4.148
{ca his 97}12.019 32.38 -4.759
{ca lys 98}9.008 30.58 -6.156
@vectorlist {G-H} color=sky
{ca lys 98}P 9.008 30.58 -6.156
{ca ile 99}9.601 27.139 -4.763
{ca pro 100}6.904 24.566 -5.439
{ca ile 101}5.779 22.433 -2.608
{ca lys 102}7.044 19.354 -4.587
{ca tyr 103}10.607 20.648 -4.408
{ca leu 104}10.238 20.748 -0.659
{ca glu 105}9.288 17.09 -0.915
{ca phe 106}12.451 16.459 -2.87
{ca ile 107}14.825 18.197 -0.316
{ca ser 108}12.949 16.265 2.407
{ca glu 109}13.91 12.964 0.676
{ca ala 110}17.642 14.221 0.27
{ca ile 111}17.7 15.052 4.094
{ca ile 112}16.533 11.588 5.002
{ca his 113}18.916 9.878 2.476
{ca val 114}21.936 11.776 3.974
{ca leu 115}20.964 11.203 7.562
{ca his 116}20.703 7.455 6.739
{ca ser 117}24.155 7.532 5.149
{ca arg 118}25.811 9.36 7.949
{ca his 119}24.044 8.119 11.166
{ca pro 120}22.775 4.587 10.584
{ca gly 121}22.916 3.665 14.346
{ca asp 122}20.943 6.526 15.388
{ca phe 123}18.692 6.445 12.195
{ca gly 124}16.843 3.117 12.383
{ca ala 125}13.303 2.755 11.064
{ca asp 126}11.741 4.242 14.117
{ca ala 127}13.763 7.489 13.772
{ca gln 128}13.279 7.522 9.984
{ca gly 129}9.455 7.338 10.463
{ca ala 130}9.63 10.189 13.057
{ca met 131}11.836 12.401 10.745
{ca asn 132}9.468 11.783 7.86
{ca lys 133}6.558 12.868 10.119
{ca ala 134}8.277 16.049 11.161
{ca leu 135}9.235 16.978 7.576
{ca glu 136}5.592 16.247 6.415
{ca leu 137}4.325 18.686 9.186
{ca phe 138}6.717 21.384 7.921
{ca arg 139}5.413 20.842 4.323
{ca lys 140}1.727 20.798 5.466
{ca asp 141}2.139 24.103 7.297
{ca ile 142}3.968 25.82 4.517
{ca ala 143}1.403 24.433 1.954
{ca ala 144}-1.409 26.135 4.032
{ca lys 145}0.43 29.444 3.764
{ca tyr 146}1.077 29.108 0.02
{ca lys 147}-2.69 28.479 -0.456
{ca glu 148}-3.56 31.582 1.378
{ca leu 149}-1.122 33.656 -0.757
{ca gly 150}-2.455 31.972 -4.062
{ca tyr 151}0.798 30.157 -5.01
{ca gln 152}0.55 26.719 -6.804
{ca gly 153}-2.504 24.983 -5.413
@subgroup dominant {hlx labels}
@labellist {labels} color=white
{ A} 16.147 15.762 17.997
{ B} 24.36 20.916 4.111
{ C} 19.277 24.048 -9.531
{ D} 32.518 21.742 -8.957
{ E} 16.647 27.519 9.795
{ F} 8.862 34.519 6.793
{ G} 17.7 15.052 4.094
{ H} 0.43 29.444 3.764
@subgroup dominant {His lig} 
@vectorlist {His} color=gold
{ca his 64}P 23.853 28.281 1.749
{cb his 64}23.443 28.259 0.286
{cg his 64}21.912 28.349 0.217
{nd1 his 64}21.239 29.408 0.72
{ce1 his 64}19.988 28.872 0.461
{ne2 his 64}19.782 27.654 -0.107
{cg his 64}P 21.912 28.349 0.217
{cd2 his 64}21.173 27.3 -0.267
{ne2 his 64}19.782 27.654 -0.107
{ca his 93}P 9.623 30.85 -0.894
{cb his 93}9.774 29.558 -0.14
{cg his 93}11.242 29.428 0.382
{nd1 his 93}11.718 30.313 1.33
{ce1 his 93}13.133 29.869 1.471
{ne2 his 93}13.369 28.841 0.659
{cg his 93}P 11.242 29.428 0.382
{cd2 his 93}12.183 28.506 -0.059
{ne2 his 93}13.369 28.841 0.659
@subgroup dominant {heme} 
@vectorlist {heme} color=yellowtint
{cha hem 538}P 16.869 31.03 0.421
{c1a hem 538}16.709 30.487 1.66
{c2a hem 538}16.89 31.086 2.972
{c3a hem 538}16.554 30.238 4.011
{chb hem 538}P 15.626 27.85 4.026
{c4a hem 538}16.079 28.95 3.366
{c3a hem 538}P 16.554 30.238 4.011
{cma hem 538}16.567 30.474 5.544
{c2a hem 538}P 16.89 31.086 2.972
{caa hem 538}17.347 32.488 3.128
{cba hem 538}16.236 33.467 3.63
{cga hem 538}15.122 33.606 2.556
{o1a hem 538}15.296 34.151 1.479
{cga hem 538}P 15.122 33.606 2.556
{o2a hem 538}14.061 33.141 3.071
{chb hem 538}P 15.626 27.85 4.026
{c1b hem 538}15.113 26.751 3.376
{c2b hem 538}14.652 25.566 4.108
{c3b hem 538}14.334 24.622 3.118
{chc hem 538}P 14.216 24.682 0.674
{c4b hem 538}14.486 25.32 1.851
{c2b hem 538}P 14.652 25.566 4.108
{cmb hem 538}14.636 25.489 5.667
{c3b hem 538}P 14.334 24.622 3.118
{cab hem 538}13.893 23.203 3.384
{cbb hem 538}14.411 22.459 4.394
{chc hem 538}P 14.216 24.682 0.674
{c1c hem 538}14.487 25.253 -0.582
{c2c hem 538}14.36 24.555 -1.816
{c3c hem 538}14.819 25.393 -2.879
{chd hem 538}P 15.581 27.805 -2.763
{c4c hem 538}15.096 26.652 -2.143
{c2c hem 538}P 14.36 24.555 -1.816
{cmc hem 538}13.917 23.085 -1.874
{c3c hem 538}P 14.819 25.393 -2.879
{cac hem 538}14.921 25.111 -4.367
{cbc hem 538}14.637 23.948 -5.
{chd hem 538}P 15.581 27.805 -2.763
{c1d hem 538}16.063 29.003 -2.139
{c2d hem 538}16.58 30.136 -2.942
{c3d hem 538}16.998 30.983 -1.986
{cha hem 538}P 16.869 31.03 0.421
{c4d hem 538}16.683 30.414 -0.714
{c2d hem 538}P 16.58 30.136 -2.942
{cmd hem 538}16.619 30.235 -4.451
{c3d hem 538}P 16.998 30.983 -1.986
{cad hem 538}17.689 32.316 -2.21
{cbd hem 538}19.23 32.063 -2.306
{cgd hem 538}20.063 33.291 -2.723
{o1d hem 538}20.026 33.709 -3.846
{cgd hem 538}P 20.063 33.291 -2.723
{o2d hem 538}20.619 33.815 -1.805
{c1a hem 538}P 16.709 30.487 1.66
{n a hem 538}16.206 29.133 1.939
{c4a hem 538}16.079 28.95 3.366
{c3a hem 538}16.554 30.238 4.011
{c1b hem 538}P 15.113 26.751 3.376
{n b hem 538}14.91 26.616 2.009
{c4b hem 538}14.486 25.32 1.851
{c3b hem 538}14.334 24.622 3.118
{c1c hem 538}P 14.487 25.253 -0.582
{n c hem 538}14.938 26.541 -0.791
{c4c hem 538}15.096 26.652 -2.143
{c3c hem 538}14.819 25.393 -2.879
{c1d hem 538}P 16.063 29.003 -2.139
{n d hem 538}16.16 29.164 -0.837
{c4d hem 538}16.683 30.414 -0.714
{c3d hem 538}16.998 30.983 -1.986
@vectorlist {Fe} color=red
{fe hem 538}P 15.271 27.962 .622
15.271 27.962 .622
P U 14.271 27.962 .622
U 16.271 27.962 .622
P U 15.271 26.962 .622
U 15.271 28.962 .622
P U 15.271 27.962 -.378
U 15.271 27.962 1.622
@kinemage 4
@caption (B&T Fig. 3.5 and 3.6b)
Low-angle, close contact between helices 105-116 (white) and 133-145 (yellowtint) in subtilisin.  In the startup view a j,j+4 row of side chains (hotpink) on the bottom helix fits between the i,i+3 rows (cyan and skyblue) on the top helix.  Choose View2 to see how the rows (emphasized by color-coded lines) relate to the two helices.  (from PDB file 1SBT)
@multibins 5
@zoom 1.18
@zslab 280
@matrix 
-.157215 -.254875 -.954109 -.221543 -.932396 .285581 -.962393 .256273 .09012
@2zoom 1.18 
@2zslab 340
@2center 23.400 35.863 38.745 
@2matrix 
-.22038 -.944087 -.245221 .299907 .173642 -.938032 .928164 -.280267 .244869
@group {helix mc}
@vector {i:105-16} color=white
{105} 12.9 32. 37.
{105 ca} 13.3 31.9 38.3
14.3 30.5 38.3
15.1 30.5 39.3
M 14.3 30.5 38.3
14.3 29.7 37.4
{106 ca} 15. 28.5 37.3
16.4 28.9 36.9
17.5 28.4 37.4
M 16.4 28.9 36.9
16.5 29.9 35.9
{107 ca} 17.6 30.4 35.3
18.5 31. 36.3
19.7 30.6 36.5
M 18.5 31. 36.3
17.9 32. 37.1
{ile 108 ca} 18.7 32.7 38.2
19.3 31.7 39.3
20.5 31.6 39.5
M 19.3 31.7 39.3
18.5 30.9 40.
{109 ca} 19. 30. 41.
20.1 29. 40.3
21.2 28.9 41.
M 20.1 29. 40.3
20. 28.8 39.
{110 ca} 21. 28.1 38.2
22.3 29. 38.3
23.3 28.5 38.8
M 22.3 29. 38.3
22.3 30.3 37.9
{ile 111 ca} 23.6 31. 38.
24. 30.7 39.3
25.2 30.2 39.5
M 24. 30.7 39.3
23.2 31. 40.3
{112 ca} 23.5 30.7 41.8
24.3 29.6 42.2
25.4 29.8 42.7
M 24.3 29.6 42.2
23.8 28.3 42.2
{113 ca} 24.5 27.2 42.3
25.8 27.1 41.7
26.7 26.5 42.2
M 25.8 27.1 41.7
25.9 27.9 40.5
{114 ca} 27.1 28.1 39.8
28.2 29. 40.5
29.4 28.9 40.3
M 28.2 29. 40.5
27.7 30. 41.1
{115 ca} 28.4 31. 42.
28.9 30.1 43.2
30.1 29.9 43.3
M 28.9 30.1 43.2
28. 29.5 43.8
{116 ca} 28.3 28.8 45.
29.4 27.6 44.7
@vector {j:133-45} color=yellowtint
{133} 14.6 42.3 36.
{133 ca} 15.4 43. 36.9
16.4 42.2 37.5
17.6 42.4 37.7
M 16.4 42.2 37.5
16. 41. 38.
{134 ca} 16.9 39.9 38.8
17.9 39.4 37.8
19.1 39.4 38.
M 17.9 39.4 37.8
17.5 38.9 36.7
{135 ca} 18.3 38.2 35.7
19.7 38.9 35.6
20.7 38.3 36.
M 19.7 38.9 35.6
19.5 40.2 35.2
{136 ca} 20.6 41.1 35.1
{c} 21.2 41.5 36.5
{o} 22.5 41.5 36.5
M 21.2 41.5 36.5
20.5 41.3 37.5
{137 ca} 21.1 41.3 38.9
22.2 40.1 39.
23.3 40.5 39.2
M 22.2 40.1 39.
21.7 39. 38.9
{138 ca} 22.7 37.9 39.
23.8 37.9 38.
25. 37.7 38.3
M 23.8 37.9 38.
23.4 38.2 36.8
{139 ca} 24.2 38.2 35.7
25.4 39. 36.1
26.6 38.8 36.
M 25.4 39. 36.1
25.2 40.3 36.9
{140 ca} 26.2 41. 37.3
27. 40.2 38.3
28.2 40.1 38.2
M 27. 40.2 38.3
26.4 39.7 39.4
{141 ca} 27. 38.9 40.4
28. 38. 39.8
29.3 38. 40.
M 28. 38. 39.8
27.7 37. 38.9
{142 ca} 28.8 36. 38.5
30. 36.6 38.
31.1 36. 38.2
M 30. 36.6 38.
30. 37.7 37.3
{143 ca} 31.2 38.3 36.8
31.9 39.1 37.9
33.1 39.3 38.
M 31.9 39.1 37.9
31.1 39.5 38.9
{144 ca} 31.5 40.3 40.
32.5 39.5 40.8
33.7 39.8 41.1
M 32.5 39.5 40.8
32. 38.3 41.1
{145 ca} 32.8 37.3 41.9
34. 37. 41.
@label off {label ends} color=white
{ 105} 13.3 31.9 38.3
{ 116} 28.3 28.8 45.
{ 133} 15.4 43. 36.9
{ 145} 32.8 37.3 41.9
@group {i3 to j4}
@vector {i+3 row} color=sky
{ile 108 ca} M 18.7 32.7 38.2
{ile 108 cb} 17.7 33.7 38.9
{ile 108 cg1} 17.3 34.7 37.8
{ile 108 cd1} 16.8 35.9 38.5
{ile 108} M 17.7 33.7 38.9
{ile 108 cg2} 18.3 34.3 40.1
{ile 111 ca} M 23.6 31. 38.
{ile 111 cb} 23.3 32.8 37.8
{ile 111} 22.9 33. 36.4
{ile 111} 23. 34.5 36.2
{ile 111} M 23.3 32.8 37.8
{ile 111} 24.9 33.2 37.9
@vector {side row} color=cyan
{112} 23.5 30.7 41.8
{112} 22.3 31. 42.6
{112} 21.8 32.7 42.4
{112} 22.5 33.3 43.2
{112} 23.9 33.3 43.2
M 22.5 33.3 43.2
{112} 22. 34.3 44.
{ile 115} M 28.4 31. 42.
{ile 115} 27.5 32.3 42.3
{ile 115} 27. 33. 41.1
{ile 115} 26.2 34.3 41.6
M 27.5 32.3 42.3
{ile 115} 28.3 33.1 43.3
@label {labels} color=white
{ i-3} 17.7 33.7 38.9
<108 cb>{ i} 23.3 32.8 37.8
<111 cb>{ j-4} 16.9 39.9 38.8
<134 ca>{ j} 22.7 37.9 39.
<138 ca>{ j+4} 28.8 36. 38.5
<142 ca>@vector {j+4 row} color=hotpink
{ala 134} 16.9 39.9 38.8
{ala 134} 16. 38.9 39.3
{ala 138} M 22.7 37.9 39.
{ala 138} 21.8 36.6 39.
{ala 142} M 28.8 36. 38.5
{ala 142} 28.2 35. 37.5
@vector {side row} color=red
{135} 18.3 38.2 35.7
{135} 17.7 38.3 34.2
{135} 18.3 37.3 33.3
{135} 18.3 35.9 34.
M 18.3 37.3 33.3
{135} 17.6 37.3 31.9
{139} M 24.2 38.2 35.7
{139} 23.6 39.1 34.7
{139} 24.6 39.5 33.5
M 23.6 39.1 34.7
{139} 22.4 38.3 34.
@group {row lines}
@subgroup {i,i+3} dominant
@vectorlist {108-111} color=sky
P U 15.596 34.642 38.775
U 18.471 33.959 38.119
U 21.476 33.277 37.462
U 25.004 32.458 36.675
@vectorlist {112-115} color=cyan
P U 29.431 31.914 41.952
U 26.477 32.505 42.484
U 23.523 33.095 43.016
U 20.569 33.686 43.548
@subgroup {j,j+4} dominant
@vectorlist {134-142} color=hotpink
P U 14.114 39.503 39.578
U 18.107 38.226 38.989
U 22.1 36.95 38.4
U 26.093 35.674 37.811
U 30.086 34.397 37.222
@vectorlist {135-9} color=red
P U 24.398 38.3 33.915
U 20.05 38.3 34.1
U 15.702 38.3 34.285