Cation-π interactions play an important role in the stability of protein structures. In this work, we have analyzed the influence of cation-π interactions in DNA binding proteins. We observed cation-π interactions in 45 out of 62 DNA binding proteins and there is no significant correlation between the number of amino acid residues and number of cation-π interactions. These interactions are mainly formed by long-range contacts, and the role of short and medium-range contacts is minimal. The preference of Arg is higher than Lys to form cation-π interactions. The pair-wise cation-π interaction energy between aromatic and positively charged residues shows that Arg-Tyr energy is the strongest among the possible six pairs. The structural analysis of cation-π interaction forming residues shows that Lys, Trp, and Tyr prefer to be in the binding site of protein-DNA complexes. Further, the accessible surface areas of cation-π interaction forming cationic residues are significantly less than that of other residues. The preference of cation-π interaction forming residues in different secondary structures shows that Lys prefers to be in strand and Phe prefers to be in turn regions. The results obtained in the present study will be useful in understanding the contribution of cation-π interactions to the stability and specificity of protein-DNA complexes. © 2004 Elsevier B.V. All rights reserved.