Defining an Essence of Structure Determining Residue Contacts in Proteins
Figure 5
Deriving the structural essence from cone-peeling strategy.
A The contact map visualization of the common neighbourhoods. The cone shaped landscape of the CNbs is resultant of low CNb edges occupying the base of the cone, while the high CNb edges occupying the summits. The colour-bar shows the range of the CNb sizes. B The cone-peeling strategy characterizes the structural essence better than random selection. The algorithm selects a subset of native contacts that have high CNb and are also in the long sequence-range and removes all the local contacts. It can be seen that in all the proteins, the subsets selected from cone-peeling (blue) reconstruct better than a similar sized random subset (red) achieving a PI>1 consistently in all the cases. For every protein, the ensemble average Ca RMSD is reported. The sizes of the final subsets and the PIs of the individual proteins are given in Table 1. C The essential contacts (blue) obtained from cone-peeling are highlighted in the native structure of 1e6k (red) using Pymol [29]. With 4.3% of Ca-Ca and 9% of Cb-Cb contacts, the subsets achieve a PI of 1.74. D The overlay of the best reconstructed models onto native structure (1e6k). The models reconstructed from the essential subsets obtained from the cone-peeling algorithm are superposed to the native structure for comparison. The best models selected (in terms of Ca RMSD) are shown in ribbon representation (orange). The native structure is shown in cartoon (blue). The overlaid models show an average Ca RMSD of 4.5 Å to the native structure. In the reconstructed models, only with the essential subsets of contacts, the secondary structural regions are well distinguished from the inter-secondary structural regions.