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

[Steve Darnell]

Rodrigo,

This is just to expand on Peter's comment.  Your original question implicitly mentioned two types of angles: bond and dihedral angles.  A bond angle can be calculated with three atoms, two vectors, and a dot product (the first type mentioned).  When you use the term phi and psi angles, you are mentioning dihedral (or torsion) angles (the angle betweeen two planes where the intersection is along the bond of interest).  It's more complicated to calculate, but relatively straight forward:

http://en.wikipedia.org/wiki/Dihedral_angle

Were you originally asking about how to calculate the torsion angles in the side chain?  These are known as the chi angles and are used for defining rotational conformations (rotomers).  I'll stop here since I'm guessing I misunderstood your original question.

Regards,
Steve

--
Steve Darnell
DNASTAR, Inc.
Madison, WI USA


-----Original Message-----
From: biopython-bounces at lists.open-bio.org [mailto:biopython-bounces at lists.open-bio.org] On Behalf Of Peter Cock
Sent: Monday, September 21, 2009 4:19 AM
To: Rodrigo faccioli
Cc: biopython
Subject: Re: [Biopython] Protein side-chain angles from a PDB file

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

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