Alpha-alpha linking motifs and interhelical orientations

Proteins. 2005 Nov 1;61(2):325-37. doi: 10.1002/prot.20522.


While the geometry and sequence preferences of turns that link two beta-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 phi/psi 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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs*
  • Amino Acids / chemistry
  • Computational Biology
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Structure
  • Protein Structure, Secondary*
  • Proteins / chemistry


  • Amino Acids
  • Proteins