The dependence of amino acid pair correlations on structural environment.
A statistical analysis was performed to determine to what extent an amino acid determines the identity of its neighbors and to what extent this is determined by the structural environment. Log-linear analysis was used to discriminate chance occurrence from statistically meaningful correlations. The classification of structures was arbitrary, but was also tested for significance. A list of statistically significant interaction types was selected and then ranked according to apparent importance for applications such as protein design. This showed that, in general, nonlocal, through-space interactions were more important than those between residues near in the protein sequence. The highest ranked nonlocal interactions involved residues in beta-sheet structures. Of the local interactions, those between residues i and i + 2 were the most important in both alpha-helices and beta-strands. Some surprisingly strong correlations were discovered within beta-sheets between residues and sites sequentially near to their bridging partners. The results have a clear bearing on protein engineering studies, but also have implications for the construction of knowledge-based force fields.
Cootes
A P
AP
Research School of Chemistry, The Australian National University, Canberra, ACT.
Curmi
P M
PM
Cunningham
R
R
Donnelly
C
C
Torda
A E
AE
D000596:Amino Acids / Q000737:chemistry* / Q000378:metabolism*; D016208:Databases, Factual; D006860:Hydrogen Bonding; D015202:Protein Engineering; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013223:Statistics as Topic
D000596:Amino Acids