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 inte ractions in 131 proteins, In antiparallel beta -sheets, the geometry of the NH . . .O bond is: median N . . .O distances, 2.9 Angstrom, C=O . . .N ang les 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 alphaH . . .O and NH . . .O could cooperate to sheet stabilit y, In cw-helices, the main chain C=O interact with the NH of their n + 4 ne ighbor on one side, and with a C betaH or C gammaH on the other side. The m edian O . . .N distance (3.0 Angstrom) and C=O . . .N angle (147 degrees) s uggest a canonical H-bond, but the C alpha -C=C . . .H dihedral angle inval idates 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 no ncanonical, In many instances, the C gammaH or the C betaH of the n + 4 res idue stands opposite to the NH with respect to the oxygen, Therefore, we pr opose that, in alpha -helices, the C gammaH or C betaH and the MH of the n + 4 residue hold the oxygen like an electrostatic pincher. Proteins 2001;43 :37-44. (C) 2001 Wiley-Liss, Inc.