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An automated method for consistent helix assignment using turn information
Author(s) -
Koch Oliver,
Cole Jason
Publication year - 2011
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22968
Subject(s) - helix (gastropod) , turn (biochemistry) , hydrogen bond , alpha helix , crystallography , helix turn helix , chemistry , computer science , biology , circular dichroism , biochemistry , dna binding protein , molecule , gene , ecology , organic chemistry , snail , transcription factor
A new automated helix assignment method is presented that leads to a more consistent definition of the helix termini, especially of the helix C‐terminus. The method assigns a helix to segments of protein chain where adjacent helical turn structures are observed, capped by specific distorted turn types (e.g., open helical turns without a hydrogen bond) or capping motifs (e.g., the Schellman motif). Helix termini are detected by observing the behavior of the NH group in N‐termini and the CO group in C‐termini; in each case, the respective group must be free to interact with hydrogen bonding partners outside of the putative helix for a helix terminus to be assigned. The presented assignment method and SHAFT‐assigned helices are part of Secbase and are made available with Relibase+ 3.0 and the free web version of Relibase 3.0. The method can also be used for the helix assignments of additional protein structures. Proteins 2011; © 2011 Wiley‐Liss, Inc.