A protein’s distance matrix is the n by n symmetric matrix that gives the pairwise distances between a protein’s amino acid residues.
This page shows the binary contact map of a given protein by truncating the distance matrix at a length specified by the slider.
Because the distance matrix and contact map are calculated from a protein residue inter-relations, they can be thought of as a coordinate-free representation.
The principal eigenvektor of the contact map is shown above the matrix, and can be thought of as an “importance score” for a given residue, and correlates with residue depth.
This eigenvektor is calculated is JavaScript via the power method, a simple and fast iterative procedure.
You’ll have the best performance with a browser that has a fast JavaScript engine (Google Chrome).