Computation of the sterically allowed conformations of peptides

Abstract The sterically permitted conformations for various di‐ and tripeptides have been described using mathematical and computer methods outlined in an earlier paper. The effects of variations in the size and shape of the side‐chain groups on the allowed conformations have been assessed. Steric restrictions, due to the backbone atoms alone, permit the peptide groups adjacent to glycyl residues to assume only about 50% of all conceivable conformations. An alanine side chain limits these to 16% and, with further side chain complexity, restrictions increase so that the backbone adjacent to valyl or isoleucyl side chains can take up only about 5% of all possible conformations. The results of the computations are therefore consistent with what is known of the ability of various residues to fit into α‐helical polypeptide chains, and of the comparative stabilities of the α‐helical forms of poly‐ L ‐alanine and polyglyeine. The rigid ring structures in prolyl peptides provide such severe steric restrictions that, a trans polyprolyl chain can exist only in a left‐handed helical form of the type observed experimentally for collagen II. Other factors which have been investigated are the effects of possible variations in the geometry of the planar amide backbone and in van der Waals' contact distances between atoms on the sterically permitted backbone conformations. The evaluation of steric restrictions emphasizes their important role as a determinant in protein conformation, and the results will lie useful in applying the computer techniques to the determination of the conformation of longer polypeptide chains.