Basics: what are we plotting?

The first output from ConAn!

This contact map shows inter-residue distances of a protein. The distance is defined (here) as the shortest distance between any two heavy atoms from the two residues. Both the x and the y-axes show the sequence of the protein. The main diagonal contains "trivial cases" (any residue is at d=0 from itself), the off-diagonal elements show the secondary, or tertiary, structure of the protein. If you are very familiar with contact maps, perhaps you have already identified that we are working with ubiquitin here (as we will always do unless otherwise mentioned). Any distance longer to 1nm is truncated to this value for clarity (and all the statistical analyses that follow will use this truncated value). Here it is in all its glory (PDB ID: 1UB1):

This contact map can tell a good structural biologist more than a simple 3D structure. For example, by combining sequence data with the contacts, you can identify probable physical interactions (this is also obtained by ConAn):

In the following, we will show further analyses with ConAn (all on ubiquitin), first the "cooler" case of unfolding simulations, and then more subtle analyses on equilibrium simulations.