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Ramachandran Plot

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This page was featured in the Journal of Biochemistry and Molecular Biology Education as it appeared on November 30, 2010.

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OTHER ENTRIES IN PROTEOPEDIA

Interactive Ramachandran plots can be generated for any entry in Proteopedia with the use of a typed Jmol command[7]:

  1. For example, in a new browser window open the entry in Proteopedia for 1bhl
  2. In the Jmol applet showing the 3D structure on the page, click on the Jmol logo (or frank) in the bottom right corner.
  3. When the menu comes up, select Console
  4. Click in the lower text window of the console that comes up and type the command Ramachandran, followed by the return key.
  5. After some processing the Ramachandran plot will be visible and you can hover over and click on the points in the plot just as you can with atoms in a Jmol scene window. (To return to the model, an easy solution is to reload the page or open a new browser instance of that page, or enter into the console 'model 1.1' without the quotes.) With the console window open, the values will be listed as you click on the spheres.
  6. To limit the plot to displaying certain residues or portions of the structure, you can issue commands in the console, such as 'display helix' or 'display gly'. The latter command will limit the plotted display to just glycine residues. In order to return to showing all values on the plot, issue the command 'display all' in the Jmol console.
This method to generate interactive Ramachandran plots will also work for other instances of the Jmol applet elsewhere on the web as long as the version of the Jmol is 11.4 or greater.
If you just need to report φ and ψ values for a few residues, use the Scene Authoring Tools to select the residues of interest and enter the command draw RAMACHANDRAN in the console.

Notes

  1. RAMACHANDRAN GN, RAMAKRISHNAN C, SASISEKHARAN V (July 1963). "Stereochemistry of polypeptide chain configurations". J. Mol. Biol. 7: 95–9. PMID 13990617
  2. Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003 Feb 15;50(3):437-50. PMID:12557186 doi:10.1002/prot.10286
  3. Laskowski,RA, MacArthur,MW, Moss,DS and Thornton,JM (1993) PROCHECK - a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 26, 283–291
  4. Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003 Feb 15;50(3):437-50. PMID:12557186 doi:10.1002/prot.10286
  5. Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lutteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH. A new generation of crystallographic validation tools for the protein data bank. Structure. 2011 Oct 12;19(10):1395-412. PMID:22000512 doi:10.1016/j.str.2011.08.006
  6. Ting D, Wang G, Shapovalov M, Mitra R, Jordan MI, Dunbrack RL Jr. Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model. PLoS Comput Biol. 2010 Apr 29;6(4):e1000763. PMID:20442867 doi:10.1371/journal.pcbi.1000763
  7. Command defined at site for official Jmol documentation

External Resources

Proteopedia Page Contributors and Editors (what is this?)

Karl Oberholser, Wayne Decatur, Eran Hodis, Jane S. Richardson, Alexander Berchansky, Jaime Prilusky, Shelly Livne, Joel L. Sussman

DOI: http://dx.doi.org/10.14576/381225.1772128 (?)
Citation: Oberholser K, Sussman J L, Hodis E, Decatur W, Livne S, Prilusky J, Richardson J S, Berchansky A, 2013, "Ramachandran Plot", Proteopedia, DOI: http://dx.doi.org/10.14576/381225.1772128
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