Questions for Plaxco et al. paper

For every protein, you can define its residue-residue contact map, which is simply a matrix A with entries a[i][j] equal to 1 if residues (amino acids) i and j touch each other and 0 otherwise. Amino acids are labeled sequentially in the polypeptide chain.

If you want to know more about contact maps and are curious what a contact map of a real protein from the PDB site looks like, you may download the Macromolecular Contact tool and play with it. It is Java-based and should be pretty much plug-and-play.

Note. No rigorous proofs are required, just good, qualitative logic.