Protein Amino Acid Contact Graphs can reveal key residues.

A protein structure is a complex 3D object, defined by the coordinates in 3D space of its atoms. Traditionally, protein structures have been analyzed by the secondary structure and fold arrangements of residues. Methods to identify crucial residues in a PDB structure are very welcome to improve the understanding of the protein’s function. These methods are usually based on the structure itself and based on energy calculations like alanine scanning or molecular dynamic simulations, and sometimes require long-running times.

A network representation of proteins as protein contact Graphs(PCG) provide a systems approach to topological analysis of complex three-dimensional structures irrespective of secondary structure and fold type and would also provide insights into structure-function relationship and would be complementary to any of the methods listed above. PCG is a powerful tool for comparison and visualization of structural features and helps in elucidating long range interactions in proteins.

A PCG is an unweighted graph where nodes are the amino acids of the protein and an edge which connects two nodes i and j only if the Euclidean distance between them has a value included in the interval: 2.7 Angstrom (threshold for only non-covalent interactions like including h-bond interactions) and 8 Angstrom (threshold for only significant interactions).

Cα atom of an amino acid residue is considered as a node and an edge is drawn if the Cα–Cα distance between a pair…