compute-new1.html

Compute

PDBparam server computes different parameters from the three dimensional structure of the protein.To calculate the properties, mark the checkboxes and enter the PDB code below.

The features are classified into four catagories namely, Inter-residue interactions, Propensities, Physicochemical properties, Identification of binding sites.

The results are shown residue-wise or protein-wise whichever is applicable or both.

Please enter the following

PDB-ID Chain name (optional)

Upload PDB File Chain name (optional)

Identification of binding site

Protein-Protein

Protein-Ligand

Protein-DNA/RNA

Chain Name (optional) Distance threshold

Inter-residue interactions

Short range interactions

Medium range interactions

Long range interactions

Contact order

Long range order LRO

Total contact distance

No. of Contacts (8A, CA atoms)

No. of Contacts (14A, CA atoms)

No. of Contacts (8A, CB atoms)

No. of Contacts (14A, CB atoms)

Multiple contact index for 2 state proteins

Multiple contact index for 3 state proteins

All

Secondary structure propensities

Amino acid compositions in high B-value regions	Frequency of occurance in beta-bends	Normalised frequency of turn	Normalised frequency of N-Helix	Normalised frequency of C-Helix	Normalised frequency of middle-Helix
Propensity to form MCI for 2 state proteins	Propensity to form MCI for 3 state proteins	Alpha-helical tendency	Beta-sheet tendency	Coil tendency	All

Physicochemical properties
Centre of mass	Radius of gyration ROG	Disulphide interactions	Ionic Interactions	Hydrophobic interactions	Aromatic-Aromatic interactions
Aromatic-sulphur interactions	Cation- pi interactions	Accessible surface area for the native protein	Surrounding hydrophobicity	Surface hydrophobicity	ASA of Hydrophobic residues
Hydrophobic free energy	Free energy due to Disulphide interactions	Main chain Main chain Hydrogen bond interactions	Main chain side chain hydrogen bond interactions	Side chain side chain Hydrogen bond interactions	Average gain in surrounding hydrophobicity or hydrophobic enrichment
Average gain ratio in surrounding hydrophobicity	Br Buriedness	Ra Solvent accessible reduction ratio or Mean fractional area loss	Mean area buried on transfer	Ns Average number of surrounding residues	Normalized flexibility parameters (B-values), average
Normalized flexibility parameters (B-values) for each residue surrounded by none rigid neighbours			Normalized flexibility parameters (B-values) for each residue surrounded by one rigid neighbours
Normalized flexibility parameters (B-values) for each residue surrounded by two rigid neighbours
All