Table 1.
Correlation between the ASA values obtained for three representative Cα-only structures for various probe radii and accessibility values obtained for full-atom models and a probe radius of 1.4Å.
Figure 1.
Selecting large enough probe radius for Cα-only structures.
Plotted on Y-axis is the number of structures (Cα-only) showing the value of quantity “per” (as defined in the text) less than or equal to 20% at different probe radii values plotted on X-axis.
Figure 2.
Correlation between ASA and accessibility values for Cysteine.
Accessible surface area values were calculated for full-atom structures using 1.4Å probe radius and for Cα-only structures at 3.5Å probe radius. The average ASA values (obtained in case of Cα-only structures) for every residue type in each structure was then plotted against accessibility values for the same residues in each structure (as obtained using full-atom structures). Shown here are the values obtained for cysteines. The ASA values corresponding to 7% and 10% accessibility values were then computed from the regression line.
Table 2.
The ASA values of Cα atoms for each residue type as obtained from Cα-only structures, corresponding to the 7% and 10% accessibility values from full-atom structures.
Table 3.
The average values of the validation parameters calculated for the dataset of 1100 structures.
Table 4.
Comparison of performance of recognition of exposed and buried residues using proposed Cα-based approach, all-atom models generated starting from Cα positions in relation to all-atom crystal structures.
Table 5.
The average values of the validation parameters calculated for the dataset of protein-protein complexes in the recognition of interface residues solely from Cα positions.
Figure 3.
Visual validation of the interface residues determined using Cα-only records.
Visual graphics tool Pymol was used to visualize the interface residues as determined in case of Default structures as well as Cα-only structures. Shown here in Figure 3a is the PDB structure of 1l7a (Cephalosporin C deacetylase) and in Figure 3b 2fef (Protein PA2201 from Pseudomonas aeruginosa), wherein the interface residues are shown in sticks while the remaining structure as cartoon. The interface residues determined using whole ATOM record are shown in green color while those determined using Cα-only records are shown in blue/cyan color. The residues in orange are the common residues between the two.
Table 6.
Comparison of interface recognition using the proposed approach (Cα), solvent accessibility calculations on all-atom crystal structures (ASA) and inter-subunit distance calculation using crystal structures (Distance).
Table 7.
List of low resolution structures used with only Cα positions available.