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Tutorial: Identifying Distorted Residues

When you are modelling a protein, or solving a structure, it is always helpful to identify bad regions. Swiss-PdbViewer provides some tools for that purpose.

Identifying Backbone Problems:

The best way to have a quick glance at the global problems is to color the protein by "backbone problems". This will highlight disconnected regions of the backbone, which is very useful during homology modelling, to help you loacte and modify where the insrtions/deletions should be placed. In addition, residues with a bad phi/psi conformation are also readily identified; which might be useful during refinement of your structure.

 

FASL
example of preliminary model analysis. Spots where insertions and deletions will be needed appear in cyan; whereas residues with bad phi/psi conformation appear in yellow (red for Prolines).

 

Identifying Distorted Residues.

The best way to illustrate this is to give a practical example. Load the protein 1CRN.pdb (which is included in the tutorial package), and color it by Force Field Energy (but do only compute bond and angles energies; and do not show the energy report). Overall, the protein topology is correct, the residue with the highest energy (the more bond distortion) beeing Proline 5.

 

1crnE

 

Now Select the Arg17 only (which was blue, meaning that its bond length and angles are quite good). Use the tool menu to "Shake the Selected Groups". Apply a 0.2Å random displacement of any atom of Arg17. This means that if you measure the RMS deviation between the unshaked residue and the shaked residue, you will obtain a RMSd of 0.2. Indeed, by inspecting your protein, it is hard to say that this Arg. is distorted.
Now color your protein by force field energy. The distorted Arginie will shine in bright red, whereas the rest of the protein is dark blue (except Pro 5, which is blue).

 

1crnE2