Have a look at our site. The interface area measured the extent of contact between the protein and nucleic acid. As judged by its chemical and amino acid composition, the average protein surface in contact with the DNA is more polar than the solvent accessible surface or the typical protein-protein interface. An equivalent number of polar interactions involved water molecules, which are generally abundant at protein-DNA interfaces. Calculations of Voronoi atomic volumes, performed in presence and absence of water molecules, showed that protein atoms buried at the interface with DNA are on average as closely packed as in the protein interior.
Water molecules contribute to the close packing, thereby mediating shape complementarily.
Finally, conformational changes accompanying association were analyzed in 24 of the complexes for which the structure of the free protein was also available. On the DNA side the extent of deformation showed some correlation with the size of the interface area. On the protein side the type and size of the structural changes spanned a large spectrum. No clear correlation could be found between the extent of conformational adjustments in the protein and nucleic acid moieties. Structural features of protein-nucleic acid recognition sites.