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Protein Contact Maps

Create and view protein contact maps and distance maps.

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Version 1.1 - published on 06 Apr 2012

doi:10.4231/D3VT1GP47 cite this

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Abstract

This tool allows the user to easily generate contact maps and distance maps for protein molecules. Input may be given in one of two ways:

PDB ID: If an RCSB Protein Data Bank identifier is given, the tool will automatically retrieve the structure from www.pdb.org. A PDB id should be four characters long, and begin with a numeral. See www.pdb.org for more information.

File upload: The user may also upload their own .pdb file. A properly formed pdb file must be given, and may be obtained directly from www.pdb.org or as a result from a simulation tool. If a file is given which contains multiple models representing a trajectory, then the results will be shown as a sequence of plots.

If the selected structure contains multiple chains, the first chain is implicitly selected.

Other input parameters are available:

Distance map options:

  • Title: An optional title may be given, which will be displayed on the distance map.
  • Color: If enabled, the distance map will use a color (blue->red) scale. If disabled, the result will be grayscale.
  • Contour lines: If enabled, contour lines will be displayed on the result.
  • Interpolation: If enabled, the distance matrix will be interpolated, resulting in a smoother appearance. If disabled, each position in the distance matrix will be a discrete color value.

Contact map options:

  • Title: An optional title may be given, which will be displayed on the contact map.
  • Threshold: Threshold distance that determines how close two atoms must be to be deemed “in contact”

Outputs:

  • Distance map: Presents the Cα-Cα distance between every pair of amino acids as a two dimensional matrix. A single image is produced if only one model is present, or a sequence of images if multiple models exist.
  • Contact map: Similar to the distance map, except the data is a binary two dimensional matrix representing which amino acid pairs closer than a given threshold.
  • Molecule viewer: Provides an interactive 3 dimensional view of the complete atomic coordinates for comparison with the distance and contact maps. A cartoon style representation can be useful for comparison. To select a molecule representation style, open the view settings panel by clicking on the wrench icon on the right hand side of the molecule viewer.

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Rappture, Python, Biopython, matplotlib

References

H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.

Cite this work

Researchers should cite this work as follows:

  • Benjamin Rafferty; Zachary Carl Flohr; Ashlie Martini (2012), "Protein Contact Maps," http://nanohub.org/resources/contactmaps. (DOI: 10.4231/D3VT1GP47).

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