Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?

We investigate the suggestion that aromatic rings can act as hydrogen-bond acceptors in proteins, by an analysis of 55 non-homologous high-resolution protein chain structures. Approximately 10% of interactions between sp2 hybridized nitrogen atoms, from either side-chains or main-chains, and phenylalanine or tyrosine rings have the nitrogen atom positioned above the ring. In these instances, however, the sp2 nitrogen atoms tend to form stacked interactions with the aromatic rings, these geometries outnumbering amino/aromatic hydrogen bonds by around 2.5:1. The statistically expected distribution, in contrast, would have only a few stacked structures and many more with larger interplanar angles, corresponding to amino/aromatic hydrogen bonds. Thus, although we do find some of these unconventional hydrogen bonds, they are clearly disfavoured relative to stacked geometries. In stacked geometries, the nitrogen-bearing groups are observed to fulfil their hydrogen-bonding potential by forming conventional, energetically stronger, hydrogen bonds with other groups in protein or solvent. This may explain the favourability of stacking. Thus, although ab initio calculations of the gas phase interaction energies for three model systems generally favour the amino/aromatic hydrogen-bonded over the stacked geometries, the differences are small enough to be outweighed easily by the additional conventional hydrogen bonding in stacked structures.