Geometric criteria of hydrogen bonds in proteins and identification of "bifurcated" hydrogen bonds |
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Authors: | Torshin Ivan Y Weber Irene T Harrison Robert W |
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Institution: | Biology Department, Georgia State University, Atlanta, GA 30303, USA. biotiy@suez.cz.gsu.edu |
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Abstract: | 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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