Dihedral angle preferences of DNA and RNA binding amino acid residues in proteins Ponnuraj K and Saravanan KM* Centre for Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai – 600025, Tamilnadu India. Abstract A protein can interact with DNA or RNA molecules to perform various cellular processes. Identifying or analyzing DNA/RNA binding site amino acid residues is important to understand molecular recognition process. It is quite possible to accurately model DNA/RNA binding amino acid residues in experimental protein-DNA/RNA complex by using the electron density map whereas, locating/modeling the binding site amino acid residues in the predicted three dimensional structures of DNA/RNA binding proteins is still a difficult task. Considering the above facts, in the present work, we have carried out a comprehensive analysis of dihedral angle preferences of DNA and RNA binding site amino acid residues by using a classical Ramachandran map. We have computed backbone dihedral angles of non-DNA/RNA binding residues and used as control dataset to make a comparative study. The dihedral angle preference of DNA and RNA binding site residues of twenty amino acid type is presented. Our analysis clearly revealed that the dihedral angles (φ, ψ) of DNA/RNA binding amino acid residues prefer to occupy (−89° to −60°, −59° to −30°) bins. The results presented here will help to model/locate DNA/RNA binding amino acid residues with better accuracy. Amino acid composition of DNA and RNA binding residues Positional preferences of DNA and RNA binding residues along the sequence Percentage of occurrences of φ and ψ angles in twelve different 30° bins Ramachandran map of DNA (A), RNA (B) and nonbinding (C) amino acid residues