TUTORIAL
Analysing an active
site
Building Loops
Building a functionnal unit
from a monomer
Crystal
Symmetries
Electron Density Maps
Energy minimisation
Fitting Residues into
Electron Density
Homology modelling
Making Phi/Psi
statistics
Superposing Proteins
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Last
modified
31 March 98
by N.Guex
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Tutorial :
Making Phi/Psi Statistics
In this example, we will display a
Ramachandran plot, learn how to detect CIS amino-acids, and
collect some backbone torsion angles.
Step by Step
- First of all, open the pdb file 1ldm (this file is
included in the tutorial
package).
- Choose the "non-trans" item of the "Select" menu and
click OK.
- Choose the "Show Ramachandran Plot" item of the
"Display" menu.
- Choose the "Colour by Type" item of the "Display"
menu.
At this stage, you should see
something like this.
Now, you can move the dot over
any point to know which residue it is.
- Now, select the "Save" item of the "File" menu. This
will write a tab-tabulated text file containing the
omega/phi/psi angles of the currently selected
amino-acids (see below).
entry secondary
name aa struct omega phi psi
--------------------------------------------
1ldm THR -174.042 -113.455 150.350
1ldm GLU -173.445 -67.249 143.847
1ldm LYS -173.490 -95.261 137.654
1ldm ILE H 174.125 -43.002 -49.334
1ldm ASP 174.025 -93.739 -2.536
1ldm PHE -171.111 -98.524 27.250
1ldm LEU -174.899 -148.073 -174.787
1ldm ALA -170.314 -68.300 -23.500
1ldm LYS S -173.173 -142.321 123.422
1ldm TYR H -173.366 -63.933 11.001
1ldm SER 174.528 -75.204 144.844
Obviously, there are too many
non-trans residues. By having selected the default value of
175° in the dialog, you have selected all slightly
distorted residues.
- So, choose the "non-trans" item of the "Select" menu
type 90 and click OK. This will select only residues with
an omega torsion angle inferior to 90° (In the case
of 1ldm, only Pro139).
- Hit the "return" key, and then the "=" key of the
keypad (right mouse button for PC users). Now select the
"torsion tool" of the main display window and click on
any atom. You will have a numerical feedback of omega,
phi psi angles for this residue.
- If your "Caps-lock" key is down, hit "esc" to exit
from this repeated torsion angles measurement mode.
- An other interesting option is the one allowing to
automatically select residues with bad backbone
conformations. You can do so with the "Select AA with
Phi/Psi out of Allowed regions" item of the "Select"
menu. In the case of 1ldm, only three residues other than
Gly have unusual backbone angles (Asp220, Asp276, Gln222)
the two first being very close to allowed regions.
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