Role of cation-pi interactions in single chain 'all-alpha' proteins.

Cation-pi interactions are known to be important contributors to protein stability and ligand-protein interactions. In this study, we have analyzed the influence of cation-pi interactions in single chain 'all-alpha' proteins. We observed 135 cation-pi interactions in a data set of 75 proteins. No significant correlation was observed between the total number of amino acid residues and number of cation-pi interactions. These interactions are mainly formed by long-range contacts and there is preference of Arg over Lys in these interactions. Arg-Phe interactions are predominant among the various pairs analyzed. Despite the scarcity of interactions involving Trp, the average energy for Trp-cation interactions, was quite high. This information implies that the cation-pi interactions involving Trp, maybe of high relevance to the proteins. Secondary structure analysis reveals that cation-pi interactions are formed preferably between residues, in which at least one of them, is in the secondary structure of alpha-helical segments. Among the various types of folds of 'all-alpha' proteins considered for the analysis, proteins belonging to alpha-alpha superhelix fold have the highest number of cation-pi interaction forming residues.