Cation-pi interactions play an important role to the stability of protein structures. In this work, we have analyzed the influence of cation-pi interactions in RNA binding proteins. We observed cation-pi interactions in 32 out of 51 RNA binding proteins and there is a strong correlation between the number of amino acid residues and number of cation-pi interactions. The analysis on the influence of short (< +/- 3 residues), medium (+/- 3 or +/- 4 residues) and long range contacts (> +/- 4 residues) showed that the cation-pi interactions are mainly formed by long-range contacts. The cation-pi interaction energy for Arg-Trp is found to be the strongest among all interacting pairs. Analysis on the preferred secondary structural conformation of the residues involved in cation-pi interaction indicates that the cationic Lys and Arg prefer to be in alpha-helices and beta-strands, respectively, whereas the aromatic residues prefer to be in strand and coil regions. Most of the cation-pi, interactions forming residues in RNA binding proteins are conserved among homologous sequences. Further, the cation-pi interactions have distinct roles to the stability of RNA binding proteins in addition to other conventional non-covalent interactions. The results observed in the present study will be useful in understanding the contribution of cation-pi interactions to the stability of RNA binding proteins. (c) 2005 Elsevier Ltd. All rights reserved.