title: Typical interaction patterns in alphabeta and betaalpha turn motifs.
abstract: A fully automatic classification procedure of short protein fragments is applied to identify connections between alpha-helices and beta-strands in a dataset of 141 protein chains. It yields 15 structural families of alphabeta turns and 15 families of betaalpha turns with at least five members. The sequence and structural features of these turn motifs are analysed with the focus on the local interactions located at alpha-helix and beta-strand ends. This analysis reveals specific interaction patterns that occur frequently among the members of many of the identified turn motifs. For the beta-strands, novel patterns are identified at the strands' entry and exit; they involve side chain/side chain 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; they generalize the well known N-terminal capping and C-terminal Schellman 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 is discussed. Finally, the robustness of our classification procedure and of the description of N- and C-cap interaction patterns is validated by repeating our analysis on a larger dataset of 381 protein chains and showing that the results are maintained.
authors.affiliation: Unité de Conformation des Macromolécules Biologiques, Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: R
authors.initials: R
authors.lastname: Wintjens
authors.forename: S J
authors.initials: SJ
authors.lastname: Wodak
authors.forename: M
authors.initials: M
authors.lastname: Rooman
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D016208:Databases, Factual; D006801:Humans; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry* / Q000235:genetics*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D017421:Sequence Analysis
chemical_list: D010446:Peptide Fragments; D011506:Proteins