[Biopython] Protein side-chain angles from a PDB file

[Peter Cock]

On Sun, Sep 20, 2009 at 8:24 PM, Rodrigo faccioli
<rodrigo_faccioli at uol.com.br> wrote:
> Hi,
>
> I have a doubt about how can I calculate the protein side-chain angles from
> a PDB file?
>
> I've read the Bio.PDB.Vector evaluates the angles from three atoms. However,
> my question is how can I  chose these atoms from a PDB file?
>
> I have based on peter cook web-site and I have calculated the phi-psi angles
> but I haven't seen about side-chain angles.

http://www.warwick.ac.uk/go/peter_cock/python/ramachandran/calculate/

Its "Cock", not "Cook", but its a common mistake ;)

> Sorry if my question is very basic. However, I'm a computer scientist novice
> in chemistry issue.

How are you defining the side chain angle? From memory (without
checking the details), you have the protein back bone which includes
the "alpha carbon" (CA in PDB files) to which the side chains are
attached. I guess you want to measure the angle of the side chain
to the C-alpha to (either of the) neighbouring backbone atoms.
The point here is off the top of my head there are at least two
possible angles you might be asking about.

But in terms of the code, you'll just need to get the coordinates
of the three atoms defining the angle (which probably will be the
C-alpha and two others), which defines two vectors, then take
their dot product and thus get the cosine of the angle. Looking
at the Psi-Phi code should help here.

Peter