Analyzing the Crystallography of the SH2 Domain and Its Residue Contact Map

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Analyze the crystallography of a protein and produce a residue contact map in order to study interactions among atoms.

Contributed by: Luca Zammataro (March 2011)
Open content licensed under CC BY-NC-SA


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This Demonstration provides an easy way to analyze the crystallographic data of a protein.

When you are in "crystallography" view, you can rotate to look at the protein; you can check and uncheck the lateral chains checkbox to remove lateral chains of all residues, permitting a better visualization of the protein backbone. You can also light the backbone using the gray level bar, which only acts on the color of lateral chain atoms.

You can browse the primary sequence with the slider bar, or jump to a specific residue, using buttons.

When you choose the "contact map" view, a residue contact map is shown. The program calculates RMSD, which is the measure of the average distance between atoms. The function starts from a selected threshold and size of the plotting area, by means of corresponding sliders controls.

Use the two red bars to localize a specific dot inside the map. Each black dot represents an RMSD value less than the RMSD threshold. Pushing the two red bars across the map by means of the two sliders, a plot label will show the exact positions of atoms and amino acids pointed to by the bars. For example, C79, I9 - O53, F6 means that the dot represents a distance less than the RMSD threshold for these two atoms, Carbon 79 and Oxygen 53, of two residues: ILE in position 9 and PHE in position 6.

After you have chosen contacts that you would study, see the two neighboring atoms in the crystallography view. They will appear in red.

http://www.rcsb.org

G. Waksman, D. Kominos, S. R. Robertson, N. Pant, D. Baltimore, R. B. Birge, D. Cowburn, H. Hanafusa, B.J . Mayer, M. Overduin, M. D. Resh, C. B. Rios, L. Silverman, and J. Kuriyan, "Crystal Structure of the Phosphotyrosine Recognition Domain SH2 of V-SRC Complexed with Tyrosine-Phosphorylated Peptides," Nature, 358, 1992 pp. 646–653.

http://en.wikipedia.org/wiki/Root_mean_square _deviation



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