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

[Rodrigo faccioli]

Steve Darnell and Peter Cock,

I apologize your answers. I have complicated my question because I have not
understood very well about these angles. However, I have understood more.

Thus, I'll retype my original question: How can I calculate the rotational
conformations (rotamers) when I have a PDB file?

Therefore, if I understood better, I need to know which amino acid I'm
working because the number of chi angles vary according to each amino acids.


Thanks in advance,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218


On Mon, Sep 21, 2009 at 12:03 PM, Steve Darnell <darnells at dnastar.com>wrote:

> 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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