[Systematic analysis of buried polar side chains and their interactions in alpha-helical proteins].
Examination of 80 alpha-helical proteins and domains demonstrates that they contain from 1 to more than 20 completely buried (water-inaccessible) polar side chains. As a rule the latter have partners for H-bonding but the resulting H-bond system is often not exhaustive. Basing on statistical analysis, we determined the optimal number of H-bonds for every type of polar side chain, and discuss the structural role of vacant donors and acceptors. About half of the H-bonds formed by buried side chains pertain to interhelix contacts of the (side chain)-(side chain) and (side chain)-(main chain) types. Such interactions appear to be a most important factor determining the mutual arrangement of alpha-helices in proteins. Analysis of the frequency of occurrence of various interacting pairs reveals that these interactions are selective.
Kondratova
M S
MS
Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia.
Efimov
A V
AV
D030562:Databases, Protein; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
D011506:Proteins