How to see conserved regions

From Proteopedia

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 Proteopedia

Right click here to 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, such as 2hhd.

• Click the orange load full button to load all atoms in the model (rather than the initial simplified model, which loads only alpha carbon atoms).

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  Look for the section Evolutionary Conservation and check a checkbox there to color the molecule according to ConSurfDB.

Not all pages titled with a PDB code have an Evolutionary Conservation section (example: 4d7b). If your does not, please see the instructions below.

My Molecule Has No Evolutionary Conservation Section in Proteopedia

If, in Proteopedia, the molecule of interest has no Evolutionary Conservation Section, 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. FirstGlance has many conveniences and advantages over other viewers.

Conservation in Green Links in Proteopedia

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

Conservation in FirstGlance

Exploring conservation in FirstGlance has many advantages. You can easily hide portions of the molecule, locate sequence numbers of interest, examine the conservation of the amino acids that bind a ligand, etc. See this List of Advantages. In order to visualize/analyze your ConSurf result in FirstGlance, you must process your PDB file at the ConSurf Server following these instructions. Unfortunately, PDB files from the ConSurf Database (ConSurfDB) had their interface to FirstGlance removed in 2022, so these PDB files no longer work in FirstGlance.

You can only color one chain at a time by evolutionary conservation when using FirstGlance. Here is the reason.

See Also

• ConSurf/Index, a list of all articles in Proteopedia providing guidance to using ConSurf.