jlangsdo Lv 1
In the Cartoon view, which shows sheets, each sheet is drawn from quadrilateral plates with donor and acceptor atoms on the 4 corners, with the sidechain coming out of the center. I think this is misleading.
The flex point in each amino acid is on the C-alpha that has the sidechain coming out of it. That's what is special about the peptide bond; the 3 bonds along the backbone between two C-alpha atoms are coplanar. This is why we can't draw bands between adjacent amino acids - the bands connect C-alpha atoms, and none of the bonds between them flex relative to one another. This stiffness is shown nicely in the Trace Tube view, where the joints are the C-alpha atoms with fixed length tubes between them.
So I suggest that the cartoon sheets be drawn differently, shifting the meaning of the plates.
The sheet should be built out of chevron shaped plates (see below) that are drawn from C-alpha to C-alpha, with a donor and acceptor on the side of the plate. As in the Trace Tube view, you would select the C-alpha and it would highlight as a joint along with and half of each of the two attached plates. At the ends of the sheet (where it connects to a loop), the sheet should be closed with a triangle, so selecting the last amino acid of the sheet would highlight the triangle and half of one plate.
That way the stiffness of the peptide bond and it planarity would be visualized in the Cartoon sheet. Bending of the sheet would be accurately represented as a rotation at a joint between two stiff plates, rather than like a flexing of the plates themselves.
Proposed:
|
—R ——-
/ / |
O==C |
\ \ Inflexible plate
\ N–H |
\/ \ |
R— —– Joint at C-alpha
\ \ |
C==O |
/ / Inflexible plate
H–N / |
/ \/ |
—R ——-
Present:
R
/
O==C O___
\ \
N–H N
/
R Flexible plate, joint in the center
\
C==O ___O
/ /
H–N N
\
R
