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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| Affiliation: | 1 Biology Department, and
4 Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA,
2 Laboratory of Kinetics and Catalysis, Chair of Physical Chemistry, Chemistry Department, Moscow State University, Moscow 119899, Russia |
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| Abstract: | Empirical criteria for identification of hydrogen bonds wereanalyzed to produce a set of geometrically consistent criteria.For a data set of 30 structures, application of a set of purelygeometrical criteria, along with exclusion of abnormal backboneconformations, also excluded a common interaction of Ser/Thrside chains with Asp/Glu side chains (ST]/DE] pairs). Theseinteractions were termed `bifurcated hydrogen bonds/', whichimplies delocalization of a positively charged hydrogen of hydroxylbetween the two acceptor atoms of the carboxylic group. These`bifurcated/' interactions are among the most common packingpatterns for ST]/DE] pairs of side chains. Therefore, theidentification of hydrogen bonds cannot be based on geometricalcriteria only and requires introduction of some physico-chemicalcriteria. |
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