How to see conserved regions

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

Contents

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).
  • 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:

  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 Proteopedia

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

Conservation 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. (Examples)

  • Enter your PDB code at the ConSurf Database (ConSurfDB). In some cases, once you choose a single protein chain, there will be a link to view a pre-calculated evolutionary conservation pattern in FirstGlance. If not,
  • You will need to calculate the evolutionary conservation pattern following these instructions.

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

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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