TYPICAL INTERACTION PATTERNS IN ALPHA-BETA-TURN AND BETA-ALPHA-TURN MOTIFS

A fully automatic classification procedure of short protein fragments is applied to identify connections between alpha-helices and beta-stra nds in a dataset of 141 protein chains. It yields 15 structural famili es of alpha beta turns and 15 families of beta alpha turns with at lea st five members. The sequence and structural features of these turn mo tifs are analysed with the focus on the local interactions located at alpha-helix and beta-strand ends, This analysis reveals specific inter action patterns that occur frequently among the members of many of the identified turn motifs. For the beta-strands, novel patterns are iden tified at the strands' entry and exit; they involve side chain/side ch ain contacts and beta-turns, generally of type I or II. For the alpha- helices, the interaction patterns consist of several backbone/backbone or backbone/side chain hydrogen bonds and of hydrophobic contacts; th ey generalize the well known N-terminal capping and C-terminal Schellm an motifs, The interaction patterns at both ends of alpha-helices and beta-strands are found to constitute favourable structure motifs with low amino acid sequence specificity; their possible stabilizing role i s discussed. Finally, the robustness of our classification procedure a nd of the description of N- and C-cap interaction patterns is validate d by repeating our analysis on a, larger dataset of 381 protein chains and showing that the results are maintained.