Methyl group conformation and hydrogen bonds in proteins determined by neutron protein crystallography

Using ‘Hydrogen and Hydration in Proteins Data Base’ (HHDB) that catalogs all H atom positions in biological macromolecules and in hydration water molecules that have been determined thus far by neutron macromolecular crystallography, methyl group conformation and hydrogen bonds (H.B.) in proteins are explored. It is found that most of the methyl groups belong to the stable staggered conformation but 11% of them seemed to be close to the eclipsed conformation. And geometrical consideration has been done for H.B. involved in α-helices. 125 H.B. were identified as donors for acceptor CO in the main chain α-helix. For these H.B., it is found that co-linear H.B. were rare, that hydrogen atoms seen from acceptors CO can localize upon certain arrangements, that H.B. are not parallel to the helix axis but rather inclined to C-terminal direction, and that hydrogen atoms except water are located inside, not outside of cylinders which the backbones of α-helices form.