Pex, Analytical Tools For Pdb Files. II. H-Pex: Noncanonical H-Bonds In Alpha-Helices

We use the H-Pex (Thomas et al., this issue) to analyze the main chain
interactions in 131 proteins. In antiparallel beta-sheets, the geometry of the
N...O bond is: median N...O distances, 2.9 SA, C==O...N angles at 154 degrees and
the C alpha--C==O...H angles are dispersed around 3 degrees. In some instances,
the other side of the C==O axis is occupied by a HC alpha. As recently supported
by Vargas et al. (J Am Chem Soc 2000;122:4750-4755) C alpha H...O and NH...O
could cooperate to sheet stability. In alpha-helices, the main chain C==O
interact with the NH of their n + 4 neighbor on one side, and with a C beta H or
C gamma H on the other side. The median O...N distance (3.0 A) and C==N angle
(147 degrees) suggest a canonical H-bond, but the C alpha--C==O...H dihedral
angle invalidates this option, since the hydrogen attacks the oxygen at 122
degrees, i.e., between the sp(2) and pi orbitals. This supports that the H-bond
is noncanonical. In many instances, the C gamma H or the C beta H of the n + 4
residue stands opposite to the NH with respect to the oxygen. Therefore, we
propose that, in alpha-helices, the C gamma H or C beta H and the NH of the n + 4
residue hold the oxygen like an electrostatic pincher.