Shadow Contact Map
Click here to make your own Shadow contact map
A contact map is an important component of a structure-based model. It is a symmetric matrix that encodes the tertiary structure of the molecule by defining the interactions that stabilize the native state. A common method of choosing these interactions is to choose a cut-off distance and define all atoms within the cut-off distance in the native state as the stabilizing interactions. The cut-off distance needs to be long enough to include all relevant short range interactions, for proteins ~6Å should be sufficient. With a cut-off definition for contacts, in order to include the contacts between 5-6Å, several "unphysical" contacts will be introduced. The unphysical contacts being those that are acting through another atom. To avoid this situation we introduce the Shadow contact map (SCM).
![](/SCM/shadow.jpg)
The SCM algorithm is described in the above figure. It is a cut-off contact map with a screening term S introduced. All atoms are given a radius S. To determine the atoms contacting atom i, all atoms within a cutoff distance C of atom i are considered possible contacts. Those contacts which have an intervening atom are considered screened out and are discarded. The algorithm is simply stated: a light source is located at the center of atom i, any atoms within C which have no shadow cast upon them are considered contacts. One can change S to scale the amount of shadowing. S=1Å works well with proteins. The figure below highlights SCM in action. The upper figure shows an RNA double helix. With a cut-off of 4Å the blue atom is in contact with the orange and green atoms. With a shadowing radius of 1Å, only the green atoms are in contact with the blue. The lower figure shows the interior of chymotrypsin inhibitor 2 (PDB code 2CI2). The blue atoms are contacting with a 4Å cut-off map, but with S>0.5Å the orange atom shadows and throws out the contact.
Details are described in the following reference:
Noel JK, Whitford PC, Onuchic JN. (2012) "The shadow map: A general contact definition for capturing the dynamics of biomolecular folding and function" J. Phys. Chem. B DOI:10.1021/jp300852d
Shadow (SCM.jar) software
SCM.jar is distributed as part of the SMOG 2 software bundle, available here. See SMOG 2 user manual for usage details.User Manual: PDF
HOW SCM WORKS:
- Determines which atoms are in contact using the following algorithm:
- Checks if two atoms are within cutoff (-c) angstroms.
- Checks if two atoms are greater than the specified number of residues apart or in separate chains.
- If so then checks to see if any atoms are between the two. This is determined by putting a light bulb at the center of each of the atoms and seeing if any of the other atoms cast a shadow on the potential contacting atom. If so then the contact is thrown out.
- The size of the atoms is determined by size (-s).
- A
potentially shadowing atom is given a size of 0.5 angstrom when it is
bonded to the shadowee. This is because the C-C bond length
is 1.5
angstrom and bonded neighbors should not shadow.
This resource is provided by the Center for Theoretical Biological Physics.
Please direct questions and comments to info@smog-server.org.
Page created and maintained by Jeff Noel and Paul Whitford