Analysis of dom-face Properties
We found that 98.8% of the interaction sites studied are contained within corresponding ranges of SCOP domains. This suggests that the analysis of interaction sites based on structural domains (i.e. dom-face) does not lose interaction information.
Average values of diverse dom-face properties for different PPI types are shown in Table 2. The distribution of df-ASA for different types is presented in Supplementary Figure One [see Additional file 2]. It is possible to observe a distinct difference in the distribution of non-obligate (i.e., ENZ and nonENZ) and obligate (i.e., HET and HOM) complexes. The distribution patterns of dom-face area for ENZ are similar to those of nonENZ and the same trend occurs between HET and HOM. In the distribution of the area of interaction sites, obligate PPI types exhibit a greater variance and in general tend to have larger interaction sites than non-obligate complexes.
Table 2  Average values of the properties
Type  ASA(Å2)  HH  inPro  nAtom  nAA  nSSE  LCS  nFrag
ENZ  860.42  0.40  0.596  121.73  33.71  11.22  3.3  12.32
nonENZ  823.06  0.37  0.530  106.89  29.59  12.91  2.5  12.91
HET  2237.92  0.41  0.982  344.26  82.56  21.35  3.5  21.35
HOM  1306.37  0.42  0.262  184.55  48.14  13.00  2.9  16.78 The average hydrophobicity (HH) values for ENZ, nonENZ, HET and HOM are respectively 0.40, 0.37, 0.41, and 0.42. Even though average HH values are similar for different PPI types, the histogram distributions of hydrophobicity (see Supplementary Figure Two [see Additional file 2]) exhibit distinctive separation patterns between non-obligate and obligate interactions. The distribution of HH for ENZ is similar to nonENZ and that of HET is similar to HOM.
We note that Arg, His, Tyr, Gln and Trp exhibit higher propensities than other amino acids, while Gly has a low propensity in our analysis. Average residue propensities are shown in Table 2. HET has the highest residue propensity and HOM the lowest. We also analyzed the top four frequent residues for each interaction type calculating the sum of ASA for each amino acid (results in Supplementary Figure Three [see Additional file 2]). Hydrophobic residues including Leu, Ala, and Val frequently occur in types HET and HOM. The charged residue Glu also appears frequently in HET. In nonENZ, charged residues including Asp, Glu, Lys, and Arg are present in the top four frequent residues.
ENZ includes not only some polar residues Ser and Tyr but also the charged residue Glu. We observed that the charged residues occur very frequently in all interaction types and appear dominantly in HET. Trp, Cys, and Met rarely occurred in interface area through all types.
The average values of the size ratio between dom-face area and domain area for ENZ, nonENZ, HET, and HOM are 27.03, 20.67, 31.94, and 23.26 respectively as shown in Table 2. The distribution of size ratio is shown in Supplementary Figure Four [see Additional file 2]. We observed that 92% of dom-faces are smaller than a half of their domain sizes based on the calculation of ASA values. The average length of consecutive residues (LCS) are 3.3, 2.5, 3.5 and 2.9 for ENZ, nonENZ, HET, and HOM respectively as shown in Table 2.
The average distribution of SSE elements (helix, strand and non-regular regions) for different PPI types is shown in Figure 1. We have seen that interaction sites are mostly composed of non-regular regions followed by helix and strand regions. ENZ contains 64.15% of non-regular regions, which is the highest percentage. Helix content are greater than 36% in types nonENZ, HET and HOM but are less than 17% in ENZ. Strand content for all types are less than 20% and HET exhibits the lowest value (13.72%).
Figure 1  Distribution of SSE content. The average distribution of SSE content is distinctive among different PPI types. More than 40% of atoms in interaction sites for all PPI types are positioned in non-regular regions. Interaction sites contain higher portion of non-regular regions than those of helix and strand regions. Especially, less than 20% of interaction sites are composed of strands. The variation in the number of amino acids (nAA) is similar to that for the number of atoms (nAtom). Average values for nAtom, nAA, nSSE and nFrag are shown in Table 2. We found that values for Types HET and HOM are higher than for Types ENZ and nonENZ in all these categories. The distribution of these properties (results shown in Supplementary Figure Seven [see Additional file 2]) for ENZ is similar to nonENZ.