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.

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).

  BibTex | EndNote

1. contact map 1
2. distance map 1
3. nano/bio 1
4. open source tool 1
5. Protein Structure 1