CARBON
The ability of the protein polypeptide chain to adopt complex three dimensional conformations comes from double bond characteristics of the alpha carbon (which carries the amino acid side group). This allows the bonds in either direction of the alpha carbon to freely rotate. The angles formed at these bonds are designated phi and psi. The adjacent image shows two peptide planes and the connecting alpha carbon (red). The linked animation (0.8 Meg) shows this structure as phi and psi are taken through the range 180 to -180.
DIAGRAM
Of all possible combinations of phi and psi only a small subset can physically occur due to collisions of the peptide oxygen and hydrogen atoms. Of these allowable combinations some exhibit better stability than others.
The diagram shows a plot of all phi and psi angles. The diagram is divided into regions indicating whether a polypeptide chain with the given angles would form a left-handed or right-handed helix structures. Chains at the boundaries form linear structures. The green regions indicate the allowable and stable conformations. Alpha indicates the choice of phi and psi which produces the most stable right-handed helix chain. Beta indicates the choice which produces the beta-pleated sheet.
Clicking on a point within the diagram will submit a request to generate an animation of a short peptide chain adopting the conformation corresponding to the choice of angles. The animation is computed using the RenderMan(tm) system. This computation takes approximately 5 minutes. Requests are queued and the resulting animations are kept for several days.
