Table of Contents
CMView is a software tool for visualizing and analyzing the network of contacts between amino acid residues in a protein structure. Formally, this network is a graph where each residue corresponds to a node and two nodes are connected by an edge if and only if the two residues are in contact. Two residues are considered to be in contact if they are spacially close in the three dimensional structure. The exact definition of contact depends on two parameters which can be chosen interactively in the program: the contact type and the distance cutoff. The contact type defines a subset of atoms of the residue. Two residues i and j are then in contact if two atoms out of this subset, one from i and one from j, are not further apart than the distance cutoff. The depiction of the contact network as a matrix is often called a contact map. CMView shows the contact map of a single polypeptide chain in its main window.
The supported contact types are:
AL | All atoms |
BB | All backbone atoms |
SC | All side-chain atoms |
C | The C atom of the backbone |
Ca | The C-alpha atom of the backbone |
Cb | The C-beta atom of the side-chain (C-alpha for glycine) |
CMView shows the contact map of a single polypeptide chain in its main window. A position (i,j) in the contact map corresponds to residues i and j in the sequence of the displayed chain. In the lower left corner information is displayed about the current residue pair (or pairs in compare mode):
The residue numbers of i and j in the sequence
The residue types (in three letter notation)
The secondary structure types (alpha, beta or none)
The PDB residue numbers. These are shown only if a tertiary structure file was loaded. By default, CMView numbers residues by their position in the sequence. This does not necessarily match the numbers assigned to residues in the ATOM lines of PDB files. To compare with other data where the PDB residue numbering is used, the residue numbers as found in the PDB file are printed here.
The rulers shown above and to the left of the contact map are used for:
Displaying secondary structure elements
Selecting residues (see selection modes)
Selecting secondary structure elements (see selection modes)
The color scheme for secondary structure elements is:
Blue: Alpha-helix
Red: Beta-sheet
Green: Turn