Systematic analysis of possible hydrogen bonds between amino acid side chains and B-form DNA.

The ways in which amino acid side chains could make a pair of hydrogen bonds within the major groove of B DNA are systematically analyzed. Hydrogen bond donors within the major groove are characterized by determining the idealized position of the hydrogen bond acceptors that they might bond with. It appears that an amino acid side chain could, at most, contact a pair of base pairs. The ten possible pairs of base pairs are analyzed to determine how they could be recognized by the amino acid side chains.