Here, the and indicate partial charges on the atoms and the dashed line between the H and Y is the
axis of the lone pair. Any deviation from the ideal geometry of these hydrogen bonds results in higher energy.
Thus, the detailed geometry of a protein–nucleic acid complex is a crucial aspect of its stability.
Hydrogen bonds between proteins and nucleic acids are mediated by donor and acceptor groups from the
bases of DNA and the side chains of most of the polar amino acids. For example, arginine and asparagine side
chains frequently make bidentate hydrogen bonds with G and A residues (Figure 10.4a). Such interactions
388 Chapter 10
Figure 10.4 Representative interactions between side chains, water molecules and nucleic acids. (a) The arginine
and asparagine (or glutamine) side chains can make bidentate hydrogen-bonding interactions with G
and A, respectively (PDB: 1AO2). Hydrogen-bonding interactions are indicated by the dashed black
lines. (b) Water molecules provide a non-covalent extension of the surface of the DNA-binding protein;
here water (red) bridges between the hydroxyl group of a threonine side chain and the major-groove
amino groups of a C/A base step in the trp repressor/operator complex (PDB: 1TR0). (c) Salt bridge and
hydrogen-bonding interaction with the non-esterified phosphate oxygen atoms (PDB: 1OCT). (d)
Recognition from contacts of non-polar atoms. Two alanine residues contact the 5-methyl carbon of a T in
the HincII/DNA complex (PDB: 1CKT). The atoms are in space-filling representation, where carbon atoms
are cyan, nitrogen atoms blue, oxygen red and phosphorus yellow. (e) Another intercalationinteraction,
where a glutamine side chain stacks onto a G base in the HincII restriction enzyme/DNA complex
(PDB: 1KC6). The interaction may align favourably the permanent dipoles, indicated by the black
arrows. (f) The intercalation of an aromatic residue between unstacked bases in the A domain of
HMGB/DNA structure (PDB: 1KC6). Only the phenylalanine side chain of the protein is shown for clarity