Geometric criteria of hydrogen bonds in proteins and identification of "bifurcated" hydrogen bonds.
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.
Torshin
Ivan Y
IY
Biology Department, Georgia State University, Atlanta, GA 30303, USA. biotiy@suez.cz.gsu.edu
Weber
Irene T
IT
Harrison
Robert W
RW
D000596:Amino Acids / Q000737:chemistry*; D006860:Hydrogen Bonding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins