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Proteins. 2009 Feb 1;74(2):353-67. doi: 10.1002/prot.22185.

Turns revisited: a uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions.

Author information

1
Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany.

Abstract

Turns are irregular secondary structure elements with a hydrogen bond or a specific Calpha-Calpha distance between the first and the last residue. They are up to six residues in length. Here, we present a uniform classification for all normal (CO(i) - NH(i+n) hydrogen bond), open (a Calpha(i)-Calpha(i+n) distance up to 10 A), and reverse (NH(i) - CO(i+i) hydrogen bond) turn families based on current structural data. Considering the large amount of data evaluated, this classification likely covers quite comprehensively most of the possible conformations of turns. All turn structures of a nonredundant dataset of 1903 protein chains were retrieved using Relibase and clustered using emergent self-organizing maps. This leads to three normal, four open, and five reverse turn families with several new turn-types. Based on the amino acid propensities, the achieved separation into normal, open, and reverse turn families seems convincing. In combination with beta-sheet and helix classification on average 96% of the given protein chain can now be successfully classified.

PMID:
18704930
DOI:
10.1002/prot.22185
[Indexed for MEDLINE]

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