beta- and gamma-turns in proteins revisited: A new set of amino acid turn-type dependent positional preferences and potentials

The number of beta-turns in a representative set of 426 protein three-dimen sional crystal structures selected from the recent Protein Data Bank has ne arly doubled and the number of gamma-turns in a representative set of 320 p roteins has increased over seven times since the previous analysis. beta-tu rns (7153) and gamma-turns (911) extracted from these proteins were used to derive a revised set of type-dependent amino acid positional preferences a nd potentials. Compared with previous results, the preference for proline, methionine and tryptophan has increased and the preference for glutamine, v aline, glutamic acid and alanine has decreased for beta-turns. certain new amino acid preferences were observed for both turn types and individual ami no acids showed turn-type dependent positional preferences. The rationale f or new amino acid preferences are discussed in the light of hydrogen bonds and other interactions involving the turns. Where main-chain hydrogen bonds of the type NH(i + 3) --> CO(i) were not observed for some beta-turns, oth er main-chain hydrogen bonds or solvent interactions were observed that pos sibly stabilize such beta-turns. A number of unexpected isolated beta-turns with proline at i + 2 position were also observed. The NH(i + 2) --> CO(i) hydrogen bond was observed for almost all gamma-turns. Nearly 20% classic gamma-turns and 43% inverse gamma-turns are isolated turns.