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

		Contents of file C1BASIC.KIN:
Kin.1- Polypeptide fragment, with rotatable phi, psi, and chi angles (Fig. 1.6)

     This kinemage shows a 5-residue fragment of polypeptide chain, to show its geometry and atom names and to allow rotation of one residue's worth of the variable dihedral angles Phi, Psi, and Chi.  Hydrogen atoms (in brown) are included, so this illustrates the full chemical geometry of a protein.  Turn them off (with the "H" button box) to see the heavy atoms alone, more typical of what is directly known for most crystal structures since hydrogen atoms diffract x-rays very weakly.  Atoms are depicted in this type of "skeletal" or "stick" representation as the intersections or ends of lines which show the chemical connectivity of the molecule.  In this case, non-carbon atoms are marked in color:  red for O and blue for N.  For a skeletal model, one aspect of the basic physical nature of the molecule - namely the chemical bonding arrangement - is explicitly clear, and the model does not hide parts of itself.  On the other hand, another important physical aspect - the packing and steric constraints - can only be inferred by relative position of the atoms.  Don't forget to rotate the image often, by dragging with the mouse anywhere in the graphics window.
     Selected atom labels can be turned on, or the angle labels turned off, with the botton box controls on the right side of the screen.  They identify the atom names along the backbone, or they label the variable dihedral angles that determine conformation.  (Of course, an atom can also be identified just by clicking on it, but then the residues will have specific numbers, such as 45 for the Phe, rather than being called n, n+1, etc.)
     The dihedral angles Phi (around the N-Calpha bond) and Psi (arouns the Calpha-C bond) of the central Phe residue can be rotated using the sliders in the righthand panel.  Clicking in the bar to right or left of the "thumbmark" will change the angle by 10 degrees at a time; clicking on the right or left arrows will change it by one degree.  The lower angle value above the slider changes as you change the angle, while the top one stays at the original value.  As you change one of the angles, look for positions at which atoms on either side are too close together (that is what determines the allowed conformations).  For instance, try setting phi to 0 and psi to 180 - does that look possible?  What bumps?
     The central Phe (residue n) is shown in cyan with a full sidechain.  The Calpha-Cbeta bonds are grouped separately and colored seagreen, both to better illustrate the tetrahedral geometry of the Calpha atom and also to point out that the Cbeta position is fixed with respect to the polypeptide backbone.  Were it not for the unique amino acid glycine which lacks a Cbeta, one would probably consider the Cbeta as part of the mainchain rather than the sidechain.  View2 looks down the Cbeta - Calpha bond, showing that the starting conformation is one of the three staggered positions of Chi1 expected from simple steric considerations around a carbon-carbon single bond.  (One can always return to the starting view by choosing "View1" on the "Views" pulldown menu.)  Try rotating Chi1 and Chi2.

More advanced tricks you may want to try - 
     From the Menu bar at the top of the screen, pull down the "Other" menu, and select "measures".  This activates a way to select atoms in succession and get distance between the last two points, the angle between the last three points and the dihedral angle between the last four points selected.  A button box is created on the control strip at the right of the screen that lets one turn the measuring function on and off.  (Toggling the button box off, then on, allows a fresh start without drawing a line from the last selection.)  Try this to measure specific values of the dihedrals along the mainchain (Phi, Psi, Omega) and/or the dihedrals going out the side chain (Chi 1, Chi 2, etc.).  Remember that a dihedral is the rotation angle around the central bond of the 4 atoms which define it.
     Select "draw new" under Other menu, check "monitor last line", then after returning to the graphics display, hit the "drawlineson" button and make a line, for instance, between O and On+1, then click drawlineson back off.  Now as phi and psi angles are changed, the distance of that line will be adjusted and displayed.

@kinemage 1
@caption (B&T Fig. 1.6)
Polypeptide fragment with rotatable Phi, Psi, and Chi angles.  Mainchain is white, Calpha-Cbeta bonds are seagreen, Phe sidechain is cyan, and H atoms are brown.  N and O atoms are marked in blue and red.  Angles can be rotated using the sliders in the righthand panel.
@zoom 1.08
@zslab 220
@center 27.732 14.188 2.696
@matrix
-.531301 -.64732 -.54653 -.363856 .75694 -.542817 .765067 -.08954 -.637697
@2zoom 1.08
@2zslab 200
@2center 27.732 14.188 2.696
@2matrix
-.912591 -.121955 -.390261 -.226881 .945094 .235203 .340151 .303189 -.890155

@group {to n-2} dominant
@subgroup {mainchain} 
@vectorlist {PHI} color=white 1bondrot -133.5

{ca phe 45} P 27.732 14.188 2.696 {n phe 45} 28.153 12.815 2.58

@vectorlist {mc} color=white
{ca asn 43}P 31.235 10.157 -1.075
{c asn 43}30.363 9.898 0.175
{o asn 43}29.83 8.807 0.431
{c asn 43}P 30.363 9.898 0.175
{n asn 44}30.329 10.926 0.929
@vectorlist {mc O} color= red  nobutton
{o asn 43}P U 29.73 8.807 0.431 U 29.93 8.807 0.431
P U 29.83 8.707 0.431 U 29.83 8.907 0.431
P U 29.83 8.807 0.331 U 29.83 8.807 0.531

@group {Ala  n-1} dominant
@subgroup {mainchain} 
@vectorlist {mc} color=white
{n ala 44} P 30.329 10.926 0.929
{ca ala 44}29.68 10.998 2.281
{c ala 44}29.441 12.481 2.513
{o ala 44}30.374 13.253 2.64
{c ala 44} P 29.441 12.481 2.513
{n phe 45}28.153 12.815 2.58
@vectorlist {ca-cb} color= sea master= {ca-cb}
{ca ala 44}P 29.68 10.998 2.281
{cb ala 44}30.579 10.298 3.287
@vectorlist {dummy} master= {side ch}
@vectorlist {mc N} color= blue  nobutton
{n ala 44}P U 30.229 10.926 0.929 {n ala 44}U 30.429 10.926 0.929
P U 30.329 10.826 0.929 {n ala 44}U 30.329 11.026 0.929
P U 30.329 10.926 0.829 {n ala 44}U 30.329 10.926 1.029
@vectorlist {mc O} color= red  nobutton
{o ala 44}P U 30.274 13.253 2.64 {o ala 44}U 30.474 13.253 2.64
P U 30.374 13.153 2.64 {o ala 44}U 30.374 13.353 2.64
P U 30.374 13.253 2.54 {o ala 44}U 30.374 13.253 2.74
@vectorlist {H} color=brown nobutton master= {H}
{n ala 44}P 30.329 10.926 0.929 {d ala 44}30.784 11.813 0.848
{ca ala 44}P 29.68 10.998 2.281 {ha ala 44}28.831 10.413 2.219
{cb ala 44} P 30.579 10.298 3.287 {hb1 ala 44} 31.47 10.751 3.313 
{cb ala 44} P 30.579 10.298 3.287 {hb2 ala 44} 30.701 9.342 3.019 
{cb ala 44} P 30.579 10.298 3.287 {hb3 ala 44} 30.161 10.337 4.195 
@labellist {atom labels} color=yellowtint off nobutton master= {atom labels}
{ O n-1} P  30.374 13.253 2.64 <o ala 44>


@group {Phe  n} dominant
@subgroup {mc n H}   master= {H}

@vectorlist {mc H} color=brown nobutton
{n phe 45}P 28.153 12.815 2.58 {h phe 45}27.398 12.157 2.411
@labellist {mc H} color=yellowtint off nobutton master= {atom labels}
{ H}27.398 12.157 2.411 <h phe 45>
@vectorlist {dummy} color= sea nobutton 0bondrot  0.0 

@subgroup {mainchain} 
@vectorlist {mc} color=white
{n phe 45} P 28.153 12.815 2.58
{ca phe 45}27.732 14.188 2.696
{c phe 45}26.649 14.315 3.805

@labellist {atom labels} color=yellowtint off nobutton master= {atom labels}
{ N}28.153 12.815 2.58 <n phe 45>
{ Ca}27.732 14.188 2.696 <ca phe 45>
{ C}26.649 14.315 3.805 <c phe 45>
@labellist {angle labels} color=pinktint nobutton master= {angle label}
{ PHI} 27.943 13.501 2.638
{ PSI} 27.33 14.24 3.11
@vectorlist {mc N} color= blue  nobutton
{n phe 45}P U 28.053 12.815 2.58 {n phe 45}U 28.253 12.815 2.58
P U 28.153 12.715 2.58 {n phe 45}U 28.153 12.915 2.58
P U 28.153 12.815 2.48 {n phe 45}U 28.153 12.815 2.68

@subgroup {mc H}  master= {H}
@vectorlist {mc H} color=brown nobutton 
{ca phe 45}P 27.732 14.188 2.696 {ha phe 45}28.527 14.889 2.741
@labellist {atom labels} color=yellowtint off nobutton master= {atom labels}
{ Ha}28.527 14.889 2.741 <ha phe 45>

@subgroup {ca-cb}   master= {ca-cb}
@labellist {atom labels} color=yellowtint off nobutton master= {atom labels}
{ Cb}27.054 14.595 1.345

@vectorlist {CHI1 ca-cb} color= sea 1bondrot  -58.6 
{ca phe 45}P 27.732 14.188 2.696 {cb phe 45}27.054 14.595 1.345

@subgroup {sidechain} master= {side ch}

@vectorlist {sc H} color=brown nobutton master= {H}
{cb phe 45}P 27.054 14.595 1.345 {1hb phe 45}26.35 13.759 1.326
{cb phe 45}P 27.054 14.595 1.345 {2hb phe 45}26.487 15.501 1.444
@labellist {angle labels} color= cyan  nobutton master= {angle label}
{ Chi 1} 27.393 14.392 2.021


@vectorlist {CHI2 cb-cg} color=cyan master= {side ch} 2bondrot  90.6 
{cb phe 45} P 27.054 14.595 1.345 {cg phe 45}27.916 14.462 0.14


@vectorlist {sc} color= cyan 
{cg phe 45} P 27.916 14.462 0.14
{cd1 phe 45}27.953 13.294 -0.602
{cg phe 45}P 27.916 14.462 0.14
{cd2 phe 45}28.752 15.525 -0.138
{cd1 phe 45}P 27.953 13.294 -0.602
{ce1 phe 45}28.783 13.173 -1.704
{cd2 phe 45}P 28.752 15.525 -0.138
{ce2 phe 45}29.615 15.424 -1.25
{ce1 phe 45}P 28.783 13.173 -1.704
{cz phe 45}29.599 14.241 -1.99
{ce2 phe 45}P 29.615 15.424 -1.25
{cz phe 45}29.599 14.241 -1.99

@vectorlist {sc H} color=brown nobutton master= {H}
{cd1 phe 45}P 27.953 13.294 -0.602 {hd1 phe 45}27.341 12.513 -0.316
{cd2 phe 45}P 28.752 15.525 -0.138 {hd2 phe 45}28.699 16.44 0.415
{ce1 phe 45}P 28.783 13.173 -1.704 {he1 phe 45}28.84 12.308 -2.293
{ce2 phe 45}P 29.615 15.424 -1.25 {he2 phe 45}30.188 16.207 -1.556
{cz phe 45}P 29.599 14.241 -1.99 {hz phe 45}30.224 14.157 -2.851

@labellist {angle labels} color= cyan  nobutton master= {angle label}
{ Chi 2} 27.485 14.528 0.743

@subgroup {mainchain} 

@vectorlist {dummy} color= sea nobutton 0bondrot  0.0 
@vectorlist {PSI ca-c} color=white 1bondrot  153.3 
{ca phe 45} P 27.732 14.188 2.696 {c phe 45}26.649 14.315 3.805 
@labellist {atom labels} color=yellowtint off nobutton master= {atom labels}
{ O}25.856 13.419 4.021 <o phe 45>
@vectorlist {mc} color=white
{c phe 45}P 26.649 14.315 3.805 {o phe 45}25.856 13.419 4.021
{c phe 45}P 26.649 14.315 3.805 {n lys 46}26.654 15.523 4.326
@vectorlist {mc O} color= red  nobutton
{o phe 45}P U 25.756 13.419 4.021 {o phe 45}U 25.956 13.419 4.021
P U 25.856 13.319 4.021 {o phe 45}U 25.856 13.519 4.021
P U 25.856 13.419 3.921 {o phe 45}U 25.856 13.419 4.121

@group {Ala  n+1} dominant
@subgroup {mainchain} 
@vectorlist {mc} color=white
{n ala 46} P 26.654 15.523 4.326
{ca ala 46}25.67 15.81 5.399
{c ala 46}24.36 16.291 4.876
{o ala 46}23.386 16.226 5.649
{c ala 46}P 24.36 16.291 4.876
{n ser 47}24.337 16.734 3.622
@labellist {angle labels} color=gray nobutton master= {angle label}
{ Omega} 26.65 14.77 4.0
@vectorlist {ca-cb} color= sea master= {ca-cb}
{ca ala 46}P 25.67 15.81 5.399
{cb ala 46}26.188 16.72 6.512
@vectorlist {mc N} color= blue  nobutton
{n ala 46}P U 26.554 15.523 4.326 {n ala 46}U 26.754 15.523 4.326
P U 26.654 15.423 4.326 {n ala 46}U 26.654 15.623 4.326
P U 26.654 15.523 4.226 {n ala 46}U 26.654 15.523 4.426
@vectorlist {mc O} color= red  nobutton
{o ala 46}P U 23.286 16.226 5.649 {o ala 46}U 23.486 16.226 5.649
P U 23.386 16.126 5.649 {o ala 46}U 23.386 16.326 5.649
P U 23.386 16.226 5.549 {o ala 46}U 23.386 16.226 5.749
@subgroup {H}  master= {H}
@vectorlist {H} color=brown nobutton 
{n ala 46}P 26.654 15.523 4.326 {d ala 46}27.344 16.221 4.047
{ca ala 46}P 25.67 15.81 5.399 {ha ala 46}25.458 14.851 5.822
{cb ala 46} P 26.188 16.72 6.512 {hb1 ala 46} 26.459 17.602 6.126 
{cb ala 46} P 26.188 16.72 6.512 {hb2 ala 46} 26.979 16.295 6.952 
{cb ala 46} P 26.188 16.72 6.512 {hb3 ala 46} 25.468 16.863 7.191 
@labellist {atom labels} color=yellowtint off nobutton master= {atom labels}
{ H n+1}27.344 16.221 4.047 <d ala 46>

@group {to n+2} dominant
@subgroup {mainchain} 
@vectorlist {mc} color=white
{n ser 47} P 24.337 16.734 3.622
{ca ser 47}23.068 17.191 3.061
@vectorlist {mc H} color=brown nobutton master= {H}
{n ser 47}P 24.337 16.734 3.622 {d ser 47}25.18 16.751 3.053
@vectorlist {mc N} color= blue  nobutton
{n ser 47} P U 24.237 16.734 3.622 U 24.437 16.734 3.622
P U 24.337 16.634 3.622 U 24.337 16.834 3.622
P U 24.337 16.734 3.522 U 24.337 16.734 3.722

@vectorlist {dummy} color= sea nobutton 0bondrot  0.0