APPENDIX
Additional descriptions and color figures can be seen on the Journal of Computational Chemistry Web site
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Figure 1. Superimposed conformations of 9 structures where the value of all psi(i) and phi(i+1) have been incremented by 40 degrees, and follow the rule psi(i) = -phi(i+1) starting from the right
hand alpha helix conformation with torsion angle values of -40/-60 (psi(i)/phi(i+1). In this and
subsequent figures, the following color scheme is used, nitrogen(blue), oxygen(red) and
carbon(green). This figure is the same as Fig. 2 in the paper.
Figure 2.
The four conformational groups shown in Fig. 2, Group 1 (top left), Group 2 (bottom left),
Group 3 (top right) and Group 4 (bottom right), were organized such that the peptide planes,
CA(i), C(i), O(i), N(i+1) and C(i+1) in each group were superimposed. All of the groups shown
in Fig. 2 are orientated so that the peptide plane carbonyl bond direction is into the plane of the
paper. The direction of the amide (NH) bond of the peptide plane is out of the plane of the paper.
All CB bonds are in the plane of the paper. It can be seen that the Group 1 (top left in Fig. 2) and
Group 2 (bottom left in Fig. 2) conformations are similar except that the N-terminal bond
direction of Group 1 is rotated 180 degrees from that in Group 2. Similarly, the N-terminal bond
direction of Group 3 (top right in Fig. 2) is rotated 180 degrees from that in Group 4 (bottom
right in Fig.2).
Figure 3. All dipeptide structures generated with a restricted conformation dataset of 6 conformations per residue, superimposed into two groups. The top figure represents 18
superimposed structures from Groups 1 and 3 (Table 2). The bottom figure represents 18
superimposed structures from Groups 2 and 4 (Table 2). The N-terminal atoms are to the left
the paper, the peptide plane carbonyl/nitrogen and N-terminal nitrogen atoms point into and out
of the plane of the paper. In the top figure, the peptide plane carbonyls of Group 1 and Group 3
point out of and into the plane of the paper respectively. In the bottom figure, the peptide plane
carbonyls of Group 2 and Group 4 point out of and into the plane of the paper respectively. This
figure is the same as Fig. 3 in the paper.
Figure 4.
A view down the CA-CA axis of these same structures from Fig. 3 is shown in Fig. 4. It
can be seen that while the C-terminal bond directions (CA(i+1)-C(i+1)) are aligned, the
N-terminal bond directions (N(i)-CA(i)) for the top figure (Group 1 and 3) are rotated 180 degrees
from that for the bottom figure (Group 2 and 4). In the top figure, the peptide plane carbonyls
pointing to the left are from Group 1 while the peptide plane carbonyls pointing right are from
Group 3. Similarly, in the bottom figure, the peptide plane carbonyls pointing to the left are from
Group 2 while the peptide plane carbonyls pointing right are from Group 4. The N-terminal bond
directions for Groups 1 and 3 (top figure) are to the left. The N-terminal bond directions for
Groups 2 and 4 (bottom figure) are to the right. In both groups the N-terminal bond directions,
span a range of approximately 40-80 degrees. It is interesting to note that the conformation with
torsion values of 140/-65 (psi(i), phi(i+1) lies in the middle of the N-terminal bond direction range
of values in the group of conformations in the top of Fig. 4. The conformation with torsion
values of -40/-65 (psi(i),phi(i+1) lies in the middle of the N-terminal bond direction range of
values in the group of conformations in the bottom of Fig. 4. This suggests that the psi(i) value of
these two conformations (+/- 45 degrees) are representative of all 36 Rooman dipeptide
conformations.
Figure 5.
Conformations using the frame shifted angles for Group 1 and 3 are shown in the top of Fig 5,
superimposed structures using the first 18 torsion values listed in Table 3. The bottom figure
represents superimposed structures using the last 18 torsion values listed in Table 3. The
N-terminal nitrogen is to the left and the C-N-terminal atoms are to the right. The CA atoms and the
C-terminal CO atoms are in the plane of the paper. Since phi(i+1) was fixed to -60 degrees, the
heavy atoms CA(i), C(i), O(i), N(i+1), CA(I+1), C(i+1), O(i+1) and CB(i+1) are all
superimposed.
Figure 6.
An end on view of these structures in Fig. 5 is shown in Fig. 6. The CA(i+1) and CA(i)
atoms are perpendicular to the plane of the paper. The C-terminal bond directions point to the
top of the figure. All carbonyl bond directions point to the left. The N-terminal bond directions
for the first 18 structures using the torsion values listed in Table 3 (top figure) are to the left. The
N-terminal bond directions for the last 18 structures using the torsion values in Table 3 (bottom
figure) are to the right. It can be seen that the N-terminal bond direction of N(i)-CA(i) for Group
1 and 3 is rotated by approximately 180 degrees to the N-terminal bond direction in Groups 2 and
4.
Figure 7. Rooman and Frame shifted superimposed structures. The first 12 structures using the torsion values listed in Table 3 (1-12, second column) for the Rooman conformations are
superimposed onto the first 12 structures using the frame shifted torsion values listed in Table 3
(1-12, third column). The N-terminal nitrogens are to the left and the C-terminal atoms are to the
right. The CA atoms and the C-terminal CO atoms are in the plane of the paper. The N-terminal
bond directions and the peptide plane carbonyl atoms point out of the plane of the paper.
Figure 8. Rooman and Frame shifted superimposed structures. The 6 structures using the torsion values listed in Table 3 (13-18, second column) for the Rooman conformations are
third column). The N-terminal nitrogens are to the left and the C-terminal atoms are to the right.
The CA atoms and the C-terminal CO atoms are in the plane of the paper. The peptide plane
carbonyl atoms for the frame shifted structures point out of the plane of the paper. The peptide
plane carbonyl atoms for the Rooman structures point into the plane of the paper. The N-terminal
bond directions point out of the plane of the paper.
Figure 9. Rooman and Frame shifted superimposed structures. The 12 structures using the torsion values listed in Table 3 (19-30, second column) for the Rooman conformations are
superimposed onto the 12 structures using the frame shifted torsion values listed in Table 3
(19-30, third column). The N-terminal nitrogens are to the left and the C-terminal atoms are to the
right. The CA atoms and the C-terminal CO atoms are in the plane of the paper. The peptide
plane carbonyl atoms for the Rooman and frame shifted structures point out of the plane of the
paper. The N-terminal bond directions point into the plane of the paper.
Figure 10. Rooman and Frame shifted superimposed structures. The 6 structures using the torsion values listed in Table 3 (31-36, second column) for the Rooman conformations are
superimposed onto the 6 structures using the frame shifted torsion values listed in Table 3 (31-36,
third column). The N-terminal nitrogens are to the left and the C-terminal atoms are to the right.
The CA atoms and the C-terminal CO atoms are in the plane of the paper. The peptide plane
carbonyl atoms for the frame shifted structures point out of the plane of the paper. The peptide
plane carbonyl atoms for the Rooman structures point into the plane of the paper. The N-terminal
