Fig 1.
Overview of dataset construction.
The flowchart showing steps in the construction of various datasets.
Fig 2.
Plots of the best interface matches for Domain-CC-2 dataset.
Scatter plot of the interfacial RMSD versus (A) fraction of aligned residues (fres) and (B) fraction of aligned contacts (fcon) for the closest match of 1511 domain-domain interfaces extracted from proteins having only two CATH classified structural domains. Each point is represented using color gradient based on IS-score. Histogram and density plots of RMSD, fres, fcon and IS-score are shown surrounding main scatter plot.
Table 1.
Summary statistics of the best similar interfaces for datasets.
Fig 3.
Examples of similar intra-chain domain-domain interface pairs.
Two domains of template protein are shown in cyan and blue colors, while target protein domains are shown in orange and red colors. The aligned C-alpha residues are shown in green and yellow for target and template structures respectively. A) Periplasmic receptor CeuE (domains 1 and 2 of 4inoA) and manganese transport regulator (MNTR) protein (domains 1 and 2 of 2f5fB), PDB identifier is followed by the chain identifier. B) RhoA-dependent invasion protein (domains 1 and 2 of 4ldrB) and Peroxiredoxin protein (domains 1 and 2 of 2v2gA). C) Pullulanase enzyme (domains 3 and 4 of 2fh8A) and DNA polymerase sliding clamp (domains 1 and 2 of 4tr8B). D) Hyaluronate lyase enzyme (domains 1 and 3 of 1n7oA) and serum albumin (domains 5 and 6 of 4f5uA). E) Thermolysin (domains 1 and 2 of 4n4eE) and tetrahydropicolinate succinyltransferase (domains 1 and 2 of 3r8yB). The coordinates of structures were obtained from the PDB. In superposed structures, the interface and non-interface regions are shown in solid and transparent color respectively. Molecular images are generated using VMD [52].
Fig 4.
Scatter plot of the best interface matches for domain-CU-M dataset.
Scatter plot of interfacial RMSD versus (A) fraction of aligned residues (fres) and (B) fraction of aligned contacts (fcon) for the closest match of 1046 domain-domain interfaces extracted from proteins having > 2 CATH structural domains. Distribution of IS-score is shown as histogram.
Fig 5.
Structural comparison of inter-chain domain and intra-chain domain interfaces.
Scatter plot of interfacial RMSD versus (A) fraction of aligned residues (fres) and (B) fraction of aligned contacts (fcon) for the closest match of 1464 protein-protein interfaces with intra-chain domain interfaces. Distribution of IS-score is shown as histogram.
Fig 6.
Examples of similar domain-domain and protein-protein interfaces.
Two domains of template (domain-domain interface) protein are shown in blue and sky blue colors, while two interacting proteins are shown in pink and cyan colors. The aligned C-alpha residues are shown in green and yellow for target and template structures respectively. A) Two domains of outer surface protein A (domains 1 and 2 of 1ospO) is aligned with human major histocompatability complex with T-cell receptor (4pjeC (domain C02/ 4pjeE (domain E01). B) Structural interface alignment of protein of unknown function (domains 1 and 2 of 2o62A) is complexed with antibody fragments (3qnzB (domain B02)/3qnzA (domain A02). The coordinates of structures were obtained from the PDB. In superposed structures, the interface and non-interface regions are shown in solid and transparent color respectively. Molecular images are generated using VMD.