Table 3. Protein interface properties for datasets of protein–RNA, protein–ssDNA and protein–dsDNA complexes.

	Protein–RNA	Protein–ssDNA	Protein–dsDNA
Number of examples	20	3	26
ΔASA	1128.9 (554.3)	906.7 (106.4)	1586.3 (499.4)
Segments	8.5 (5.4)	7.3 (0.6)	7.31 (3.5)
Gap volume index	3.3 (1.8)	2.9 (1.3)	2.6 (0.87)
Hydrogen bonds	1.2 (0.5)	0.6 (0.4)	1.4 (0.4)
Bridging waters	0.3 (0.4)	0.1 (0.1)	0.6 (0.6)
% Polarity	45.7 (7.1)	45.1 (4.2)	48.1 (9.1)

The data for the protein–dsDNA complexes is taken from our previous analysis (25).

The parameter definitions are as follows:

ΔASA: for the protein–DNA complexes this is the ASA of the protein that is buried on complex formation with the DNA. For the protein–protein complexes this is the ASA of one protomer that is buried on complex formation. For hetero-complexes the mean ASA buried by each protomer was calculated. The ASAs were calculated with Naccess (http://wolf.bms umist.ac.uk/naccess).

Segments: the number of sequence segments in the protein interface was defined such that interface residues separated by more than five residues in sequence were defined in different segments.

Gap volume index: the gap volume between protein and DNA, or two protein protomers was calculated using the algorithm SURFNET (http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html). The index is defined as Gap Index (Å) = gap volume between molecules (ų)/interface ASA (Ų) per complex.

Hydrogen bonds: the number of intermolecular hydrogen bonds per 100Ų ΔASA were calculated using HBPLUS (29), in which hydrogen bonds are defined according to standard geometric criteria.

Bridging waters: the number of water molecules that form hydrogen bonds with both parts of a complex were calculated using HBPLUS (29).

% Polarity: this is defined as [ΔASA(polar)/ΔASA(p)] × 100 where ΔASA(polar) is the ASA of polar atoms buried on complexation and ΔASA(p) is the ASA of protein buried on complexation with DNA.