FIGURE 1.

Scatter maps (a) and ellipsoidal functions (b–d) representing the distributions of water oxygens and amino acid atoms in contact with adenine and thymine in B-DNA (b and c) and protein-DNA structures (d). Ligand-binding ellipsoids around the ideal A·T basepairs in b and d are generated by local Fourier averaging and those in c by local clustering. The contour surfaces correspond to an energy level of 2, where the lengths along the principal axes are equal to twice the variance in these directions. Donor ligands in the vicinity of proton acceptor atoms on the bases are illustrated in blue and acceptor ligands in contact with proton donor atoms on the bases are shown in red.