ConSurf Quick Analysis Procedure
Here is a quick procedure for coloring a protein molecule by evolutionary conservation. This procedure does not necessarily give the highest quality result, but will give you a preliminary result that is often sufficient. (This page is a supplement to How to see conserved regions.)
- Go to the ConSurf Server.
- Check Amino Acids.
- Check Yes there is a known protein structure.
- Enter your PDB code (or upload your PDB file) and click the Next button.
- Choose one chain from the pull-down Chain Identifier menu. (ConSurf can only analyze one chain at a time. Get chain IDs by examining the model in
FirstGlance in Jmol.
- Check No you do not have a Multiple Sequence Alignment (MSA) to upload.
- Don't worry, you can leave all the settings that appear now at their defaults.
- Check automatically for "Select homologs".
- Leaving everything else at the defaults, enter a job title (optional).
- Enter your email address in the bottom slot! This avoids losing the result and having to do it over.
- Click the Submit button.
- Processing may take a few minutes or a few hours. After FINISHED appears at the top of the Job Status Page, scroll down to Final Results and click View ConSurf Results with FirstGlance in Jmol.
Why FirstGlance in Jmol? Because 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.