Visualize a Protein Contact Map from a Residue Distance Matrix

A protein contact map is a simplified representation of protein structure that records which pairs of residues are close to each other in space. Here, a residue means one amino-acid unit of the protein chain, and two residues are treated as being in contact when the distance between them is below a chosen cutoff. In this example, we use myoglobin to compute a residue distance matrix, convert it into a binary contact map, and visualize the result alongside the protein's 3D structure.

Show the protein structure used in the example:

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BioMoleculePlot3Dmol=BioMolecule

PDB structure

1MBN

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Use a cutoff of 8 to threshold the residue distance matrix and display the resulting contact map:

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ArrayPlot[UnitStep[QuantityMagnitude[mol["ResidueDistanceMatrix"]]-8],FrameTicksAll]

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Plot the full residue distance matrix:

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MatrixPlot[mol["ResidueDistanceMatrix"]]

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View the residue distance matrix as a 3D surface:

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ListPlot3D[mol["ResidueDistanceMatrix"]]

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Wolfram Language Example Repository

Visualize a Protein Contact Map from a Residue Distance Matrix

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Visualize a Protein Contact Map from a Residue Distance Matrix

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