Evaluation of packing

The Occluded Surface Packing Value (OSP) is calculated for each residue. This value is 0.0 for completely exposed residues and is 1.0 for the impossible case where 100% of molecular surface is in contact with other van der Waals surface. The average for a protein is dependent on the molecular weight of the protein.

For each atom that has occluded surface, the value of (os*[1-raylength]) is calculated. Here raylength is the fractional length of the extended normal. (A fractional length of 1.0 is equivalent to the diameter of a water molecule, 2.8 Ang.) These values are summed for each residue to give the parameter listed in column four of the output file below. This parameter is divided by the total surface area for that amino acid type to give a normalized occluded surface packing value listed under "OSP" in the output file.

Thus, if the complete residue surface is occluded, and all rays have a length of zero, the packing value is the same as the total residue surface area and OSP = 1.0.


Output is in the file, prot.pak

    Resnum  Resname       OS     os*[1-raylen]   OSP
       74     THR       36.93       27.61       0.263
       75      ?         0.0         0.0        0.0
       76     ILE       41.35       20.30       0.178
       77     ILE       41.15       24.81       0.219
       78     PHE       56.07       38.81       0.269
       79     GLY       46.99       35.25       0.659
       80     VAL       55.52       38.29       0.397
        ...

Note: If a residue has zero occluded surface the residue name will not be listed as for residue 75, above.


The output file, pak.plt, contains columns 1 and 5 from the above file without the column labels for plotting residue number versus OSP.

Note for ligands in OS: To calculate the ligand/protein OS and os*[1-raylen] change the name of the ligand to UNK in the prot.srf file. The program respak will not calculate parameters for unrecognized residue names.


Revised: Wednesday, 29-Nov-2000 16:38:18 EST