[BiO BB] how to calculate the atom distance between antigen and antibody

[Xue Li]

Thank you guys for replying my email.

I think that I did not make myself clear enough.

My problem is I do not even know from a pdb file which atoms belongs to
antigen and which belongs to antibody.

For example, for 1JPS.pdb. There are three chains: chain L, chain H and
chain T.

Part of the pdb is :

----------------------
HEADER    IMMUNE SYSTEM                           03-AUG-01
1JPS
TITLE     CRYSTAL STRUCTURE OF TISSUE FACTOR IN COMPLEX
WITH
TITLE    2 HUMANIZED FAB
D3H44
COMPND    MOL_ID:
1;
COMPND   2 MOLECULE: IMMUNOGLOBULIN FAB D3H44, LIGHT
CHAIN;
COMPND   3 CHAIN:
L;
COMPND   4 FRAGMENT: FAB
FRAGMENT;
COMPND   5 ENGINEERED:
YES;
COMPND   6 MOL_ID:
2;
COMPND   7 MOLECULE: IMMUNOGLOBULIN FAB D3H44, HEAVY
CHAIN;
COMPND   8 CHAIN:
H;
COMPND   9 FRAGMENT: FAB
FRAGMENT;
COMPND  10 ENGINEERED:
YES;
COMPND  11 MOL_ID:
3;
COMPND  12 MOLECULE: TISSUE
FACTOR;
COMPND  13 CHAIN:
T;
COMPND  14 FRAGMENT: EXTRACELLULAR
DOMAIN;
COMPND  15 ENGINEERED: YES

-----------------------------------

Is chain T antigen, because chain L and chain  H are denoted as LIGHT CHAIN
and HEAVY CHAIN?

Is this a general rule to tell which chain corresponds to antigen?

Thank you very much!

Li


On Tue, Jul 15, 2008 at 11:34 AM, Kalidas Yeturu <ykalidas at gmail.com> wrote:

> Hi Mr.Li
>  You may use my program 'get_list_of_all_pair_distances.c' to obtain all
> pair distances between atoms in a given PDB file. The program will output
> <line-1> <line-2> <distance>
> where lines correspond to corresonponding lines in PDB file that have
> ATOM/HETATM cards; and <distance>es are in ascending order.
>
> You can select that pair of lines which correspond to the pair of atoms
> from chains you want to find distance. I checked '1jps.pdb' and noticed
> that
> there are 3 chains L, H and T.
>
> You may need to tailor the above program to tune the output to your
> specific
> need.
>
> With Regards
> Kalidas. Y
>
> On Tue, Jul 15, 2008 at 4:27 AM, Xue Li <me.lixue at gmail.com> wrote:
>
> > hello all,
> >
> > I am new in this.
> >
> > If I have 1JPS.pdb, would someone please tell me how to calculate the
> atom
> > distance between antigen and antibody?
> >
> > Thank you.
> >
> > Li
> > _______________________________________________
> > BBB mailing list
> > BBB at bioinformatics.org
> > http://www.bioinformatics.org/mailman/listinfo/bbb
> >
>
>
>
> --
> Kalidas Y
> http://ssl.serc.iisc.ernet.in/~kalidas<http://ssl.serc.iisc.ernet.in/%7Ekalidas>
>
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb
>
>


-- 
Xue, Li
Bioinformatics and Computational Biology program
Material Science
Iowa State University
Ames, IA 50010
515-450-7183