Atoms are need not to be in sequence the coordinates itself would let you know which is where...

if you use visualization tools like pymol, rasmol,vmd etc. they calculate the bonding using nearest neighbor strategy from the 3D coordinates.

for details go to :

http://deposit.rcsb.org/adit/docs/pdb_atom_format.html

http://www.ccbb.pitt.edu/bbsi/2007/lectures/VMD.pdf

http://www.sci.ccny.cuny.edu/~gunner/Pages-422/PDF/IntroPyMOL.pdf

Atoms are need not to be in sequence the coordinates itself would let you know which is where...

if you use visualization tools like pymol, rasmol,vmd etc. they calculate the bonding using nearest neighbor strategy from the 3D coordinates.

for details go to :

http://deposit.rcsb.org/adit/docs/pdb_atom_format.html

http://www.ccbb.pitt.edu/bbsi/2007/lectures/VMD.pdf

http://www.sci.ccny.cuny.edu/~gunner/Pages-422/PDF/IntroPyMOL.pdf

In a pdb file the single entities forming the structure are bases or amino acid residues. For those, the topology is well known, the atoms have unique names that constitute their position within the molecular scaffold.

The order of the atoms within the residue is not relevant, the position is given via their xyz coordinates.

Thus, a 'bond' is known to exist between the known molecular species.

However, visualization programs like pymol or VMD use a distance measure to decide, whether to draw a bond or not. (This does not mean, that there is a bond or not in reality.)

I´m agree with Anselm Horn and Debasish Mukherjee, I would also like to add that depending on the visualization programs that you use you will get different results. For example, the PyMol accepts bond lengths for hydrogen bonds are between 2.8–3.0 Å.

Just to state it explicitely: PDB format does NOT have any information about the bonds. This is quite easy to understand, since it's mostly used for biological systems and if there's experimental info (e.g. x-ray) it is only about positions of atoms, not existence of bonds.

Obviously the bonds can be easily guessed from the atom positions using chemical knowledge.

Ankit: if you want to know details of bonding between atoms in amino acids, the best source is the charmm topology file, available at: http://mackerell.umaryland.edu/CHARMM_ff_params.html .

The CONECT records at the end of a PDB file specify bonds within ligands and in non-standard residues (ligands, modified amino acids etc). For standard amino acids and nucleotides, it is assumed that the structure is sufficiently well characterised that defining bonds is not needed.

PYMOL uses these CONNECT records, if present, to display connectvity of non-standard residues. Rasmol on the other hand, shows a bond between any atoms which are close, whether or not it makes any chemical sense.

I have gone through all your answers. it has helped me a lot. Thank you Mr. Horn for explaining the PDB file.

Thank you Debashish. I have read all the PDF's which explains the programing.

and Thank You Mr. Trzaskowski, Your page helped me to understand chemistry behind the bonding.

You may use visualization programs to produce mol file (from pdb) that contains connectivity table

If neither connection information is present as it is for standard residues, nor having an explicit CONNECT information, the assignment of bonds and bond orders (single, double, triple) becomes difficult. If there is a bond at all can be assigned in terms of overlap between van der Waals radii. The hybridization state may be derived from the geometrical arrangment of the neighboring atoms. For the unambigous assignment of bond orders, however, the number of hydrogens must be known. For example carbonic acid vs. carboxylate. An approach in this direction is the NAOMI model

by Rarey and co-workers.

StruMM3D will recreate the molecular connectivity, and bond orders, from the coordinate data in a PDB file.

If you need informations about intramolecular COVALENT bonds, just use Avogadro (http://avogadro.cc/wiki/Main_Page), open your pdb file, and then use Visualize, Properties, Bond Properties, and you get a table of all the covalent bond (including bond order).

Thank you all for your answers. Its really Appreciable. Thank Mr. Mauro, It shows all the bond properties of a protein (Avagadro). and Thank you Mr Thomas. the link you have provided explains a lot.