Main-chain conformational features at different conformations of the side-chains in proteins

1To whom correspondence should be addressed An analysis of the known protein structures has shown that the main-chain torsion angles, f and y of a residue can be affected by the side-chain torsion angle, c1. The (c1, y) plot of all residues (except Gly, Ala and Pro) show six distinct regions where points are concentrated—although some of these regions are nearly absent in specific cases. The mean of these clusters can show a shift along the y axis by as much as 30 ° as c1 is changed from around 180 to –60 to 60°. Because of the lesser steric constraint points are more diffused along the y axis when c1 is approximately –60°. Although points are more spread out along the f axis in the (c1, f) plot, the dependence of f on c1 shows up in a shortened f range (by about 30°) when c1 is around –60°, and a distinct tendency of clustering of points into two regions when c1 µ 60°, especially for the aromatic residues. Based on the dependence of the back-bone conformation on its side-chain the 17 amino acids can be grouped into five classes: (i) aliphatic residues branched at the Cb position (although Thr is atypical), (ii) Leu (branched at the Cg position), (iii) aromatic residues (Trp can show some deviations), (iv) short polar residues (Asp and Asn), and (v) the remaining linear-chain residues, mainly polar. Ser and Thr have the highest inclination to occur with two different orientations of the side-chain that can be located through crystallography. Such residues exhibiting two c1 angles have their f and y angles in a region that is common to the Ramachandran plots at the two different c1 angles. The dependence of f and y angles on c1 can be used to understand the helical propensities of some residues. Moreover, the average f, y values in the a-helices vary with the side-chain conformation