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Aromatic side-chain interactions in proteins. II. Near- and far-sequence Phe-X pairs.

Authors
  • Thomas, Annick1
  • Meurisse, Rita
  • Brasseur, Robert
  • 1 Institut National de la Santé et de la Recherche Médicale Unité 410, Paris Cedex, France. [email protected]
Type
Published Article
Journal
Proteins Structure Function and Bioinformatics
Publisher
Wiley (John Wiley & Sons)
Publication Date
Sep 01, 2002
Volume
48
Issue
4
Pages
635–644
Identifiers
PMID: 12211031
Source
Medline
License
Unknown

Abstract

We have collected all aromatic pairs (3152) involving an N-phenyl partner in a dataset of 593 proteins of the PDB: 728 of these pairs involve a partner residue less than 6 apart in the sequence. These near-sequence Phe-X pairs correspond to specific conformations that stabilize secondary structures, mainly alpha-helices when the residues are 1, 3, and 4 apart, and beta-strands when they are 2 apart in the sequence. These conformations are not spatially random and have been examined in detail. The remaining phenylalanine pairs (2424) are between partners more than 5 apart in the sequence. Of these far-sequence pairs, 34% of occurrences are in sheets. Next in frequencies are pairs that bridge a beta-strand to a helix (24%), followed by pairs that bridge a beta-strand to a random coiled structure (15%). Helix to helix pairs only constitute 12% of these far-sequence pairs. Analysis of the pairing frequency supports the hypothesis that aromatic interactions are late events of protein folding.

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