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Protein Engineering, Vol. 15, No. 5, 359-363, May 2002
© 2002 Oxford University Press

Geometric criteria of hydrogen bonds in proteins and identification of `bifurcated' hydrogen bonds

Ivan Y. Torshin1,2,3, Irene T. Weber1 and Robert W. Harrison1,4

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

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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