@text
 Kinemage Supplement to Branden & Tooze "Introduction to Protein Structure", Second Edition
Chapter 1 -  THE BUILDING BLOCKS

Modified 070830 for KiNG, kinemage 6 needs 4fxn.pdb

		Contents of file c1Basics-B-KiNG.kin:

*{Kin 6}* Exercise in finding dihedral angles & Calpha handedness (Fig. 1.7,1.2)

    [A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display.  Operations on the displayed kinemage respond immediately:  the entire image can be rotated in real time, parts of the display can be turned on or off, any point can be identified by picking it, and the change between different forms can be animated.  The image can be recentered, zoomed, put in stereo, or the front and back clipped away;  distances, angles, and dihedrals can be measured.  The kinemage can be edited on-screen:  colors changed, multiple viewpoints saved, button names edited, lines pruned away or new ones drawn, etc.  If you need an introduction to those functions, try the Demo5_4a-KiNG.kin file.
   A kinemage is prepared and specified by an author, teacher, researcher, or anyone else in order to better communicate ideas that depend on 3-dimensional information.  The kinemages are distributed as plain text files of commented display lists and accompanying explanations.  They are viewed and explored in an openended way by the reader using the simple graphics program called MAGE (by David C. Richardson), which runs on Macintosh, PC, or Unix computers, or use KiNG (by Ian Davis & Vincent Chen) which is a Java application and runs whereever Java is implemented.  A utility (called PREKIN) helps authors prepare the kinemages.
    The kinemages for this Supplement were prepared by Jane S. Richardson and David C. Richardson and are copyrighted by them, but are freely available for educational, research, or personal use.  Updated programs and more information are available at http://kinemage.biochem.duke.edu]


   *{Kinemage 6}* uses a short segment from flavodoxin, for practice with dihedral angles, the "measure" tool, and amino-acid handedness.
   The startup view shows just 4 backbone atoms and the bonds between them - this is the minimum for defining a single dihedral angle.  Imagine it as a mechanical linkage with stiff bonds and rigid angles of about 120 degrees connecting each pair of bonds, but with something like a rotating sleeve that allows rotation around the central bond.  To see this rotation, in Mage: click and hold down the mouse in the horizontal scrollbar in the rotation window (on the arrow for slow motion, and on the scrollbar just inside the arrow for rapid motion); then click and hold at the opposite end to rotate back.  In KiNG: select menu item "Tools: Specialty: Suite Rotation to get its dial box on screen.  Select the ro1 dihedral, and drag in the dial region to change it.  Choose View2 to look down the central bond (move the image back and forth a bit to see both ends of that bond) and rotate the dihedral angle again.  This is a "phi" conformational angle, since it is rotation around the N-Calpha bond.  Watch the numerical value of phi change as you rotate, and see what the geometry looks like near 180 degrees and near 0 degrees;  which one is most extended?
     Turn on "measures ..." under the "Tools" pulldown menu;  the measure function reports the geometry of 4 successive atoms picked, including angles and dihedrals.  Choose View1 again.  Click on the bottom C atom, then on the 'N' atom (the "dist" part will give the distance between those last 2 atoms picked), then on the 'Calpha' atom (now "angle" will give the in-plane angle defined by the last 3 atoms picked), and finally on the 'C' atom (now "dhdrl" will give the dihedral angle defined by all 4 atoms).  In Mage turn the "measure" button on the righthand panel off and then on again, in KiNG type the "m" keyboard key twice (to restart the white lines), and then click on the 4 atoms in the opposite order to verify that the dihedral angle is the same when measured from either direction.
     Now press the "m" key on the keyboard to get rid of the white measure lines, and click here: *{Kin 6 v=3, m={flavodoxin} on, m={dihedral} off}* to put up a short portion of flavodoxin, including some alpha helix, some extended strand, and the connection between them.  Practice identifying backbone atom types N, Calpha, C and O by their geometry and relationships (first with the "side ch" button turned on, and then with it turned off).  The biggest clues are that the CO (or "carbonyl") sticks out, and that each entire peptide (the group of 5 atoms from one Calpha to the next) lies in one plane.  Practice telling N-to-C-terminal polypeptide chain direction from the fact that the peptide N atom precedes the Calpha, while the CO follows it.  Check yourself by clicking on an atom to get its atom name (just "ca" for the Calpha), residue name, and residue number on the information line at the bottom of the screen.  The backbone atom type at which the chain turns the most definite corner in 3 dimensions is the Calpha, which is the join between two successive planar peptides.  Click on atoms to find the residue numbers for the start and end of this entire segment of structure.  Now click on successive Calphas along the chain, and notice the distance between each Calpha pair:  to within about 0.1 Angstrom, it is always 3.8A.
     Choose View4 for a closeup of the extended, or beta-strand, part of the structure.  Turn "measures" back on, and starting at the first N (at the very beginning of the chain), click on the first 4 atoms in order along the backbone:  N, Calpha, C, and N (but not the O, which sticks out from the continuous line);  the dihedral angle displayed after that 4th atom-click is a psi angle (rotation around the Calpha-C bond) for Trp 6, and should read 132.9.  Then click on the next atom in order (the next Calpha) to get the near-180 omega dihedral angle around the 6-7 peptide bond:  what is its actual value?  Then click on the next atom in order (a C) to get the phi angle for Ser 7.  [Notice that at each step the white lines produced by the measures function show you which 4 atoms define the currently-displayed dihedral angle.  To measure the dihedral around a given bond, you must start one atom BEFORE that bond and finish one atom AFTER the bond.]
     Choose View5 for a closeup of the helical part.  By clicking your way along the backbone (starting at the C atom of residue Gly 10), measure the phi and psi angles of the fully-helical residues 11 to 13.  They should be close to -60, -40, and in between each phi,psi pair you should see a near-180 omega angle.
     Choose View6, to concentrate on the connection between the strand and helix (residues Gly 8, Thr 9, and Gly 10).  Because they are not fully in any piece of secondary-structure, their conformations are more variable.  Measure their phi,psi angles, looking for one with a positive phi value;  which residue is it?  what is that phi value?  Gly is uniquely able to adopt such conformations, because it has only an H in place of a Cbeta atom;  to see why that is true in this particular case, let's construct a hypothetical Cbeta onto this Gly.  
     Mage (using construction tools): First, with measures on, pick the N, C, Calpha, and Cbeta atoms of Thr 9, in that zigzag order, to define normal Cbeta geometry.  Now choose "draw new" under the "Edit" menu and turn on the new "construct4" button.  Click on the N, C, and then Calpha of the Gly you found with positive phi (Gly 10), and accept the "last measures" default in the resulting dialog box.  The construct-line tool draws a Cbeta for the Gly with the same geometry as the reference one you measured for Thr 9.  
     KiNG (using the mutation tool): Mutate the Gly to an Ala.  First, type "m" to turn off the measure highlights.  Then under the "Tools" menu select "Structural Biology" then "Sidechain mutator".  A dialog box comes up in which you need to navigate to where you downloaded the flavodoxin coordinate file 4fxn.pdb, choose this file.  Now a full model of flavodoxin overlays the original fragment.  Ctrl-click, option-click, or middle-click the Gly Calpha atom: select "Ala".  Now there are 2 more little dialog boxes:  a ÒModel managerÓ and a box labeled with this mutation.  Turn off "refit H's" in the button panel in order to see just the heavy atoms like the Cbeta.
     That hypothetical Cbeta is just 2.3 A away from another atom (an impossibly close bump distance):  which atom is too close?  (In KiNG, select "Probe dots" in the "Model manager" dialog box to visualize this collision.)
     We will now make what would be the Cbeta of a D-amino acid.

     Mage: Click the "eraselast" button to get rid of the new Cbeta, and click on the N, C, and Calpha of the Gly again, but this time in the construct dialog-box change the 125 dihedral value to -125 and then accept.  Turn the "construct" button back off, and press the 'm' key to get rid of the measure lines.
     KiNG:  Under "Tools" menu select "Kin editing":"Fudge Kins" which produces a "Fudge Kins" dialog box.  Select "Adjust Dihedral" and "Move One Point".  Turn on markers so you can see the atom picking steps.  Click in succession 4 particular points of Gly 10: n, c, ca, cb.  This last atom picked will be the moved one point. 
     You now have, in effect, a D-Ala residue at position 10.    Rotate to look at the D-Ala from its Calpha H direction (the 4th, now-empty, tetrahedral direction from the Calpha);  the Calpha should hump slightly toward you.  If you have trouble identifying that direction, choose View7.  From there, turn on the "corncrib, D" button for labels, and try the "corn crib" test for amino-acid handedness:  the 3 branches leaving the Calpha atom should read CO, then R ("r group" of the side chain, in this case your new green Cbeta), and then N around in a clockwise direction for a normal biological L-amino acid, but counter-clockwise for a D-amino acid such as this one you just made.  For comparison, try the same thing for the normal L-Thr at position 9:  center on its Calpha (turn "pickcenter" on, click that Calpha, and turn pickcenter back off), rotate to look from its H direction, and read off the CO, R, N branches, this time clockwise.  If it doesn't seem obvious at first, choose View8 and turn on the "corncrib, L" button for labels.  Practice identifying both L and D forms, until you can do it without the help of preset views and labels.  Remember that amino-acid handedness has strong effects on larger-scale structures:  if we were made of D-amino acids, our alpha helices would be lefthanded, our beta sheets would twist the other way, and our enzymes would be specific for molecules of the opposite chirality.

    Copyright 1999,2007 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 6
@caption
A short segment modified from flavodoxin for practice with dihedral angles, the "measure" tool, and amino-acid handedness.  Follow directions in text window.
@listcolordominant
@onewidth
@perspective
@viewid {dihedral}
@zoom 4.30
@zslab 170
@ztran 0
@center 37.350 10.122 11.378
@matrix
-0.546780 0.152090 0.823350 -0.284180 -0.958710 -0.011620 0.787580 -0.240330 0.567420
@2viewid {down bond}
@2zoom 4.30
@2zslab 170
@2center 37.350 10.122 11.378
@2matrix
0.259620 -0.947900 0.184640 -0.599050 -0.308050 -0.739090 0.757460 0.081270 -0.647810
@3viewid {overview}
@3zoom 1.00
@3zslab 183
@3center 32.810 8.600 9.210
@3matrix
-0.994955 0.076319 0.065110 -0.099660 -0.826220 -0.554462 0.011480 -0.558153 0.829658
@4viewid {close beta}
@4zoom 2.00
@4zslab 200
@4center 34.587 7.758 9.183
@4matrix
-0.983302 0.075400 0.165625 -0.156482 -0.814943 -0.558015 0.092900 -0.574614 0.813135
@5viewid {close hlx}
@5zoom 2.00
@5zslab 220
@5center 29.164 10.492 8.803
@5matrix
-0.798970 0.102180 0.592630 -0.245680 -0.954930 -0.166570 0.548900 -0.278680 0.788060
@6viewid {close turn}
@6zoom 2.00
@6zslab 200
@6center 31.399 6.755 6.501
@6matrix
-0.990994 0.082282 0.105640 -0.125150 -0.849710 -0.512182 0.047620 -0.520790 0.852355
@7viewid {Gly 10 H}
@7zoom 3.23
@7zslab 200
@7center 29.941 8.048 6.480
@7matrix
-0.215050 -0.723040 -0.656480 -0.965360 0.259080 0.030880 0.147750 0.640380 -0.753710
@8viewid {Thr 9 H}
@8zoom 3.23
@8zslab 200
@8center 31.247 4.572 5.606
@8matrix
-0.781350 -0.483060 0.395150 -0.515050 0.856670 0.028810 -0.352430 -0.181020 -0.918160
@master {flavodoxin}
@master {dihedral}
@group {flavodoxin} master= {flavodoxin} off
@subgroup {main ch} dominant
@vectorlist {mc} color= pink
{n trp 6}P 37.231 10.664 11.864
{ca trp 6}37.469 9.581 10.893
{c trp 6}36.171 8.792 10.724
{o trp 6}35.403 8.667 11.710
{c trp 6}P 36.171 8.792 10.724
{n ser 7}35.799 8.529 9.488
{ca ser 7}34.587 7.758 9.183
{c ser 7}34.829 6.799 8.020
{o ser 7}35.492 7.188 7.029
{c ser 7}P 34.829 6.799 8.020
{n gly 8}34.398 5.568 8.174
{ca gly 8}34.677 4.503 7.201
{c gly 8}33.588 4.343 6.149
{o gly 8}33.884 4.044 4.967
{c gly 8}P 33.588 4.343 6.149
{n thr 9}32.374 4.649 6.542
{ca thr 9}31.247 4.572 5.606
{c thr 9}30.392 5.839 5.587
{o thr 9}29.334 5.854 4.911
{c thr 9}P 30.392 5.839 5.587
{n gly 10}30.655 6.755 6.501
{ca gly 10}29.941 8.048 6.480
{c gly 10}29.148 8.400 7.740
{o gly 10}28.482 9.465 7.770
{c gly 10}P 29.148 8.400 7.740
{n asn 11}28.988 7.415 8.601
{ca asn 11}28.141 7.556 9.800
{c asn 11}28.647 8.612 10.783
{o asn 11}27.860 9.468 11.260
{c asn 11}P 28.647 8.612 10.783
{n thr 12}29.905 8.477 11.151
{ca thr 12}30.544 9.453 12.043
{c thr 12}30.713 10.781 11.321
{o thr 12}30.539 11.865 11.930
{c thr 12}P 30.713 10.781 11.321
{n glu 13}30.795 10.677 10.017
{ca glu 13}30.869 11.903 9.232
{c glu 13}29.558 12.684 9.314
{o glu 13}29.576 13.931 9.469
{c glu 13}P 29.558 12.684 9.314
{n lys 14}28.454 11.958 9.242
{ca lys 14}27.136 12.605 9.358
{c lys 14}26.970 13.227 10.742
{o lys 14}26.501 14.386 10.860
@subgroup {side ch} dominant
@labellist {gly} color= cyan
{Gly} <8>34.677 4.503 7.201
{"} <10>29.941 8.048 6.480
@vectorlist {sc} color= cyan
{ca trp 6}P 37.469 9.581 10.893
{cb trp 6}38.599 8.640 11.338
{cg trp 6}38.946 7.624 10.223
{cd1 trp 6}39.862 7.727 9.239
{ne1 trp 6}39.803 6.591 8.402
{ce2 trp 6}38.909 5.807 8.859
{ne1 trp 6}39.803 6.591 8.402
{cg trp 6}P 38.946 7.624 10.223
{cd2 trp 6}38.364 6.362 10.045
{ce2 trp 6}38.909 5.807 8.859
{cz2 trp 6}38.492 4.596 8.330
{ch2 trp 6}37.497 3.946 9.058
{cd2 trp 6}P 38.364 6.362 10.045
{ce3 trp 6}37.375 5.702 10.761
{cz3 trp 6}36.957 4.481 10.231
{ch2 trp 6}37.497 3.946 9.058
{ca ser 7}P 34.587 7.758 9.183
{cb ser 7}33.478 8.735 8.813
{og ser 7}32.266 8.027 8.592
{ca thr 9}P 31.247 4.572 5.606
{cb thr 9}30.355 3.365 5.895
{og1 thr 9}29.479 3.665 6.971
{cb thr 9}P 30.355 3.365 5.895
{cg2 thr 9}31.122 2.071 6.170
{ca asn 11}P 28.141 7.556 9.800
{cb asn 11}27.941 6.212 10.506
{cg asn 11}27.136 5.243 9.636
{od1 asn 11}27.070 4.024 9.917
{cg asn 11}P 27.136 5.243 9.636
{nd2 asn 11}26.521 5.764 8.600
{ca thr 12}P 30.544 9.453 12.043
{cb thr 12}31.911 8.975 12.528
{og1 thr 12}31.772 7.711 13.165
{cb thr 12}P 31.911 8.975 12.528
{cg2 thr 12}32.549 9.957 13.509
{ca glu 13}P 30.869 11.903 9.232
{cb glu 13}31.239 11.611 7.781
{cg glu 13}31.308 12.901 6.968
{cd glu 13}31.768 12.631 5.538
{oe1 glu 13}31.648 11.482 5.047
{cd glu 13}P 31.768 12.631 5.538
{oe2 glu 13}32.207 13.594 4.862
{ca lys 14}P 27.136 12.605 9.358
{cb lys 14}25.992 11.620 9.106
{cg lys 14}24.607 12.280 9.129
{cd lys 14}24.282 13.051 7.849
{ce lys 14}23.010 13.888 7.992
{nz lys 14}22.967 14.919 6.945
@group {corncrib L} dominant off
@subgroup {} nobutton
@labellist {crib,l} color= white
{N} <9>32.374 4.649 6.542
{'R'} <9>30.355 3.365 5.895
{CO} <9>30.392 5.839 5.587
@group {corncrib D} dominant off
@subgroup {} nobutton
@labellist {crib,d} color= yellow
{N} <10>30.655 6.755 6.501
{'R'} <10>30.918 9.180 6.165
{CO} <10>29.148 8.400 7.740
@group {dihedral} master= {dihedral}
@subgroup {rotation} dominant
@labellist {st lbl} color= greentint
{C}36.171 8.792 10.724
{Calpha}37.469 9.581 10.893
{N}37.231 10.664 11.864
@vectorlist {rot} color= green
{c trp 6}P 36.171 8.792 10.724
{ca trp 6}37.469 9.581 10.893
@vectorlist {ro1} color= green 1bondrot -125.2 
{ca trp 6}P 37.469 9.581 10.893
{n trp 6}37.231 10.664 11.864
@vectorlist {ro} color= green
{n trp 6}P 37.231 10.664 11.864
{c tyr 5}37.479 11.931 11.580
@labellist {rot lbl} color= greentint
{C}37.479 11.931 11.580