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Protein Contact Maps

By Benjamin Rafferty1, Zachary Carl Flohr1, Ashlie Martini1

1. Purdue University

Create and view protein contact maps and distance maps.

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Version 1.2 - published on 15 Aug 2014

doi:10.4231/D35M62761 cite this

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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 A PDB id should be four characters long, and begin with a numeral. See 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 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


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 (2014), "Protein Contact Maps," (DOI: 10.4231/D35M62761).

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Tags, a resource for nanoscience and nanotechnology, is supported by the National Science Foundation and other funding agencies. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.