The Contact Map plugin provides an easy-to-use interface for viewing residue-residue contacts between two sets of selected atoms from molecules loaded into VMD. The contact distances are displayed as a color-coded matrix where darker colors indicate residues which are close to each other and lighter colors indicate residue pairs which are distant from each other.

The controls allow selection of the molecules used for the calculation, with a separate atom selection for each molecule. The graphical display of residue contacts can be scrolled and zoomed as necessary to see results for large structures.

Image of Contact Map Plugin

Brief Tutorial Example:

  1. Start VMD
  2. Load two molecules, or one molecule with two parts you want to compare.
    • Note: If you have no molecules handy to compare, use the below to load two identical, but slightly unaligned proteins as Molecule 0 and Molecule 1. Enter this into the VMD console:

      mol pdbload 1tit; mol pdbload 1tit
      set sel [atomselect 1 "all"]; $sel move [transaxis x 4 deg]

  3. Select Extensions:contactmap from "VMD Main" window.
  4. In the left hand column, select molecule numbers for Molecule A and Molecule B. Select the parts of the molecules which wish to compare.
  5. Select "fit all", then "Calculate: Calc res-res Dists".
    The vertical axis lists MoleculeA resiudes, the horizontal axis list MoleculeB residues.
  6. Contact distance coloring: The alpha-Carbon to alpha-Carbon distance for each pair is plotted. A graph sqaure is colored black at 0.0 Angstrom distance, to a linear gray scale between 0.0 and 10.0 Angstroms, and white when equal to or greater than 10.0 Angstroms.
  7. Pair scanning: move over contact map with button 2 (middle button) pressed to see pair selected. The vertical axis residue appears in green, the horizontal axis residue appears in brown. Scrubbing over the horizontal or vertical direction provides a "walk" along the molecule.
  8. Change selection: After you change either molecule selection text, or molecule number for MoleculeB, you must re-select the "MoleculeA" molecule number. (This is slightly broken, you must Re-select "Molecule A" molecule number even if you have changed the information for MoleculeB. To change both, change selection for B, then for A,)
  9. Graph zooming: Control the residue numbering as for the Sequence Viewer [link to section]. The top left horizontal slider sets the scale for the horizontal axis. The horizontal slider below it sets the scale for both axes simultaneously axis. "Fit all" will fit both the vertical and horizontal graphs into the window.