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α‐α linking motifs and interhelical orientations
Author(s) -
Engel Donald E.,
DeGrado William F.
Publication year - 2005
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.20522
Subject(s) - link (geometry) , sequence (biology) , chemistry , crystallography , protein structure , mathematics , combinatorics , biochemistry
While the geometry and sequence preferences of turns that link two β‐strands have been exhaustively explored, the corresponding preferences for sequences that link helical structures have been less well studied. Here we examine the interhelical geometry of two connected helices as a function of their link's length. The interhelical geometry of a helical pair appears to be significantly influenced by the number of linking residues. Furthermore, for relatively short link lengths, a very limited number of predominant conformations are observed, which can be categorized by their ϕ/ψ angles. No more than two predominant linking backbone conformations are observed for a given link length, and some linking backbone conformations correlate strongly with distinctive interhelical geometric parameters. In this study, sequence and hydrogen‐bonding patterns were defined for predominant interhelical link motifs. These results should assist in both protein structure prediction and de novo protein design. Proteins 2005. © 2005 Wiley‐Liss, Inc.