ConSurf Quick Analysis Procedure

From Proteopedia

Updated July, 2024.

Here is a quick procedure for coloring a protein molecule by evolutionary conservation. (This page is a supplement to How to see conserved regions.)

1. Go to the ConSurf Server.
2. Enter your PDB code (or upload your PDB file).
3. Choose one chain from the pull-down Select chain identifier menu. (ConSurf can analyze only one chain at a time. Get chain IDs by examining the model in FirstGlance in Jmol.)
   You will likely be offered a pre-calculated result in the ConSurf DataBase ConSurfDB, but it cannot be used in FirstGlance in Jmol, which has many powerful conveniences for visualizing conservation patterns. Continue with the steps below to get a FirstGlance-compatible result.
4. Enter a job title, which should include the PDB code or protein name.
5. Enter your email address.
6. If this is your first try with this protein, click Submit with default parameters. If the default result needs improvement (see Interpreting ConSurf Results and Limiting ConSurf Analysis to Proteins of a Single Function), you can click Select run parameters manually to try improving the result.
7. Processing may take a few minutes or a few hours. After FINISHED appears at the top of the ConSurf Job Status Page, click Go To The Results.

Why FirstGlance in Jmol? Because it has many advantages. It has shortcut tools making it easy to see conservation of salt bridges, cation-pi interactions, the residues binding ligands/substrates/inhibitors, the residues engaging in protein crosslinks, or any residues that you specify. For a tour of these tools, see FirstGlance/Visualizing Conservation.

Want to make sure your ConSurf result is optimal for answering your questions? See Interpreting ConSurf Results.

Two methods for viewing your results in FirstGlance:

• At the ConSurf results page, open High Resolution Figures and PDB Files, and then click Download ConSurf PDB File for FirstGlance in Jmol. Then at FirstGlance.Jmol.Org, proceed to upload the downloaded file.

• Right click the link Download ConSurf PDB File for FirstGlance in Jmol, and select Copy Link. Then at FirstGlance.Jmol.Org, click enter a molecule's URL and paste the link into the slot. This requires that the ConSurf job be recent, since the results will remain on the server for a limited time.