Investigation of a physical basis for conformational similarity in proteins

Amino acid residues in a globular protein fold against one another into a compact structure. We have sought common physical factors within similarly folded backbone structures in such proteins which might influence the folding and which could be used in predicting the backbone structure. The physical factors examined are the 10 orthogonal ones identified by Kidera et al. (1985a). Comparison of the smoothed physical factor profiles between sequences, which have similar backbone structures, shows that there is good agreement among the profiles of helical stretches, but not for other backbone structures that have been examined. This is ascribed to the fact that helical structures involve local interactions, which then require similar physical profiles to form, but that other structures are not so strongly locally determined in the native structure.