期刊
PROTEIN ENGINEERING
卷 15, 期 5, 页码 359-363出版社
OXFORD UNIV PRESS
DOI: 10.1093/protein/15.5.359
关键词
hydrogen-bonding criteria; protein tertiary structure; side chain-side chain packing
Empirical criteria for identification of hydrogen bonds were analyzed to produce a set of geometrically consistent criteria. For a data set of 30 structures, application of a set of purely geometrical criteria, along with exclusion of abnormal backbone conformations, also excluded a common interaction of Ser/Thr side chains with Asp/Glu side chains ([ST]/[DE] pairs). These interactions were termed `bifurcated hydrogen bonds/', which implies delocalization of a positively charged hydrogen of hydroxyl between the two acceptor atoms of the carboxylic group. These `bifurcated/' interactions are among the most common packing patterns for [ST]/[DE] pairs of side chains. Therefore, the identification of hydrogen bonds cannot be based on geometrical criteria only and requires introduction of some physico-chemical criteria.
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