How to see conserved regions

Conserved regions on the surface of a folded protein molecule identify functional sites. For an explanation with examples, please see Introduction to Evolutionary Conservation.

Conservation in ProteopediaConservation in Proteopedia

Open a duplicate of this page in a separate tab or window so you can keep this page visible.

Enter your PDB code in the upper search slot at the left side of the either tab/window. This should take you to a page titled with your PDB code.

Most molecules in Proteopedia, on pages titled with a PDB code, have an Evolutionary Conservation line below the molecule. Clicking on [show] in this line will color the molecule by evolutionary conservation, as calculated by ConSurfDB.

If the molecule of interest lacks the Evolutionary Conservation line below the molecule, please see the instructions below.

My Molecule Has No Evolutionary Conservation Line in ProteopediaMy Molecule Has No Evolutionary Conservation Line in Proteopedia

If, in Proteopedia, the molecule of interest lacks the Evolutionary Conservation line below the molecule:

1. Try looking directly in ConSurfDB. If it has no results for your molecule, or if you wish to obtain better results, try the next step.
2. Calculate the conservation pattern yourself at the ConSurf Server. Here are instructions. When you get the result, there will be a link for showing that result in FirstGlance in Jmol.

Conservation in Green Links in ProteopediaConservation in Green Links in Proteopedia

You can show ConSurf-colored molecules with green links in Proteopedia.

Conservation in FirstGlanceConservation in FirstGlance

You might wish to explore a conservation-colored molecule in FirstGlance so you can hide portions of it, locate sequence numbers of interest, or examine the conservation of the amino acids that bind a ligand, or for other reasons.

1. Enter the PDB code in the search slot in Proteopedia.
2. At the page title with the PDB code, click on [show] in the line labeled Evolutionary Conservation beneath the molecule. (If there is no such line, see below.)
3. The Evolutionary Conservation section is now expanded. Click on the link Complete Results at ConSurfDB.
4. At ConSurfDB, click on the button for the chain of interest under View 3D structure colored by conservation in FirstGlance in Jmol. (You can only see one chain at a time at ConSurfDB. Here is the reason.)