Abundance and arrangement of single, double and bifurcated hydrogen bonds in protein α-helices: Statistical analysis of PDB-select

Abstract

Statistics are collected and analyzed for the possibility of hydrogen bonding in the secondary structures of globular proteins, based on geometric criteria. Double and bifurcated bonds are considered as pairs of admissible H-bonds with two proton donors or two proton acceptors, respectively. Most of such bonds belong to peptide groups in α-helices, with Oi…Ni + 3 nearly as frequent as Oi…Ni + 4; in contrast, most of the 3/10-helical segments are too short to have any. Alternating double and bifurcated bonds in α-helices form an apparently cooperative network structure. A typical α-helical segment perhaps carries two stretches of the H-bond network broken in the middle. The constituent H-bonds are nonlinear: the hydrogen atom is off the straight line connecting the proton donor and proton acceptor atoms. This deflection is larger for Hi + 3 vs. bond line Oi−Ni + 3 than for Hi + 4 vs. Oi−Ni + 4, and though the two kinds of bond have about the same length (exceeding those typical of low-molecular compounds), Oi…Ni + 4 must be stronger than Oi…Ni + 3. Double/bifurcated bonds are also not coplanar, i.e., hydrogen atoms are beyond the N…O…N (or O…N…O) plane.