NOTE:

Upload query structure in the three-dimensional coordinate set format of the protein data bank. The filename should be a four letter code with a .pdb or .ent or .atm or .txt extensions. e.g.,: 1EJG.pdb




INTRAPROTEIN INTERACTIONS

              * This option can accept a monomeric or a multichain protein file.


Upload a file in PDB format:      



                 Hydrophobic Interactions   Enter the interaction cut-off value    (Default 5A)

                 Disulphide Bridges

                 Main Chain-Main Chain Hydrogen Bonds

                 Main Chain-Side Chain Hydrogen Bonds

                 Side Chain-Side Chain Hydrogen Bonds

                 Ionic Interactions   Enter the interaction cut-off value    (Default 6A)

                 Aromatic-Aromatic Interaction : cut-off value  to  (Default 4.5A to 7A)

                 Aromatic-Sulphur Interactions   Enter the interaction cut-off value    (Default 5.3A)

                 Cation-Pi Interactions   Enter the interaction cut-off value    (Default 6A)


To E-mail the results enter a valid e-mail address:     (Optional)




PROTEIN-PROTEIN INTERACTIONS

               * This option can accept only a multichain protein file.


Upload a file in PDB format:  



                 Hydrophobic Interactions   Enter the interaction cut-off value    (Default 5A)

                 Disulphide Bridges

                 Main Chain-Main Chain Hydrogen Bonds

                 Main Chain-Side Chain Hydrogen Bonds

                 Side Chain-Side Chain Hydrogen Bonds

                 Ionic Interactions  Enter the interaction cut-off value    (Default 6A)

                 Aromatic-Aromatic Interactions  : cut-off value   to  (Default 4.5A to 7A)

                 Aromatic-Sulphur Interactions  Enter the interaction cut-off value    (Default 5.3A)

                 Cation-Pi Interactions  Enter the interaction cut-off value    (Default 6A)


To E-mail the results enter a valid e-mail address:    (Optional)






  Solvent accessibilty is calculated using NACCESS.Residues that has all atoms relative accessibility value greater than 7 are considered as exposed.  Residues that has all atoms relative accessibility value less than or equal to 7 are considered as buried.


SOLVENT ACCESSIBILITY BASED CALCULATIONS


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Calculation of Intraprotein Interactions based on solvent accessibility


* This option can accept a monomeric or a multichain protein file.

       Interactions between buried residues
       Interactions between exposed residues
   

Calculation of Protein-Protein Interactions based on solvent accessibility


* This option can accept only a multichain protein file.

       Interactions between buried residues
       Interactions between exposed residues

To E-mail the results enter a valid e-mail address:    (Optional)




DEPTH CALCULATION

           Under Revampment!!


  *  Please ensure that the ATOM records in the input file terminates with "TER". This format is required for the proper running of the depth program


                "Caution:   This calculation is time consuming!"

Upload a file in PDB format:


     Interaction between residues which have depth less than 5 Angstrom

     Interaction between residues which have depth greater than 5 Angstrom

     Enter number of iteration:


To E-mail the results enter a valid e-mail address before submitting:



PLEASE CITE:    K. G. Tina, R. Bhadra and N. Srinivasan, PIC: Protein Interactions Calculator, Nucleic Acids Research, 2007, Vol. 35, Web Server issue W473–W476. Click here for PDF


Server developed by:
 K.G.Tina in association with R.Bhadra and Prof.N.Srinivasan (ns@mbu.iisc.ernet.in).
Webpage developed by:
Dinesh D.C.

Maintained by:
Naveen Kumar .N (nkumar@mbu.iisc.ernet.in)