[BiO BB] how to calculate the atom distance between antigen and antibody
me.lixue at gmail.com
Wed Jul 16 16:20:08 EDT 2008
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
Part of the pdb is :
HEADER IMMUNE SYSTEM 03-AUG-01
TITLE CRYSTAL STRUCTURE OF TISSUE FACTOR IN COMPLEX
TITLE 2 HUMANIZED FAB
COMPND 2 MOLECULE: IMMUNOGLOBULIN FAB D3H44, LIGHT
COMPND 3 CHAIN:
COMPND 4 FRAGMENT: FAB
COMPND 5 ENGINEERED:
COMPND 6 MOL_ID:
COMPND 7 MOLECULE: IMMUNOGLOBULIN FAB D3H44, HEAVY
COMPND 8 CHAIN:
COMPND 9 FRAGMENT: FAB
COMPND 10 ENGINEERED:
COMPND 11 MOL_ID:
COMPND 12 MOLECULE: TISSUE
COMPND 13 CHAIN:
COMPND 14 FRAGMENT: EXTRACELLULAR
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!
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
> there are 3 chains L, H and T.
> You may need to tailor the above program to tune the output to your
> 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
> > distance between antigen and antibody?
> > Thank you.
> > Li
> > _______________________________________________
> > BBB mailing list
> > BBB at bioinformatics.org
> > http://www.bioinformatics.org/mailman/listinfo/bbb
> Kalidas Y
> BBB mailing list
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