Journal of Physical Chemistry B, Vol.111, No.30, 8680-8683, 2007
Close contacts between carbonyl oxygen atoms and aromatic centers in protein structures: pi center dot center dot center dot pi or lone-pair center dot center dot center dot pi interactions?
Lone-pair center dot center dot center dot pi and, more recently, pi center dot center dot center dot pi interactions have been studied in small molecule crystal structures, and they are the focus of attention in some biomolecules. In this study, we have systematically analyzed 500 high-resolution protein structures (resolution <= 1.8 A) and identified 286 examples in which carbonyl oxygen atoms approach the aromatic centers within a distance of 3.5 A. Contacts involving backbone carbonyl oxygens are frequently observed in helices and, to some extent, in strands. Geometrical characterization indicates that these contacts have geometry in between that of an ideal pi center dot center dot center dot pi and a lone-pair center dot center dot center dot pi interaction. Quantum mechanical calculations using 6-311++G** basis sets reveal that these contacts give rise to energetically favorable interactions and, along with MD simulations, indicate that such interactions could stabilize secondary structures.