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Keywords:

  • secondary structure elements;
  • helix;
  • automated helix assignment;
  • turn;
  • Relibase

Abstract

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.