Close Contact Map Analysis
Analysis of residue-residue close contacts can help in identifying residues in protein that are making contact with each other during the simulation. This can give hints about the residues which are more likely to interact with each other during the protein folding process. A residue-residue close contact map for each of the systems was generated (Figure 2 ) using the gmx mdmat, with 1.5 nm cutoff distance, which calculates the inter-residue distance matrix and provides the average close contacts between the residues.