prot.srf file

The prot.srf file contains all the information from the calculation of occluded surface and extension of surface normals. The additional programs in this package analyze the data in this file.

A sample of a typical prot.srf file is explained below: 

...
AVG for ATOM:  CZ    2.352 es   16.002 os   18.354 ts    0.400 Rln PHE  112
INF PHE  112@CZ__>ILE 147@CG1_     9 pts   1.578 A2    0.076 Rlen  3.75 Dxx
INF PHE  112@CZ__>LYS 110@CD__     7 pts   1.446 A2    0.194 Rlen  4.09 Dxx
INF PHE  112@CZ__>LYS 110@CG__     7 pts   1.947 A2    0.194 Rlen  4.02 Dxx
INF PHE  112@CZ__>LYS 110@CB__     6 pts   0.855 A2    0.480 Rlen  4.78 Dxx
    ES_Total      :   43.966                                       PHE  112
    ES_Backbone   :   17.743                                       PHE  112
    ES_Side Chain :   26.223                                       PHE  112
    OS_Total      :   98.547                                       PHE  112
    OS_Backbone   :   19.673                                       PHE  112
    OS_Side Chain :   78.874                                       PHE  112
    Raylength     :    0.418                                       PHE  112
...

where,

For the AVG line:
es is the exposed surface area in Angstroms for that atom
os is the occluded surface area in Angstroms for that atom
ts is the total surface area in Angstroms for that atom
Rln is the mean raylength for that atom

The last INF line means the following:

The CZ atom of PHE 112 is occluded by the CB atom of LYS 110; six (6) surface points (pts) with a total surface area of 0.855 square Angstoms (A2) is occluded and the mean fractional raylength (Rlen) for this occluded patch is 0.480; the distance between the CZ and CB atom centers is 4.78 Angstroms (Dxx).

In the residue summary section:

ES_Total is the total exposed surface area for PHE 112
ES_Backbone is the exposed surface area of the N, CA, C, O atoms
ES_Side Chain is the exposed surface area of the side chain atoms
OS_Total is the total exposed surface area
OS_Backbone is the exposed surface area of the N, CA, C, O atoms
OS_Side Chain is the exposed surface area of the side chain atoms
Raylength is the mean fractional raylength for the residue (Equals 1.0 if there is no occluding van der Waals surface within 2.8 Angstroms of the molecular surface of TYR 21; equals 0.0 if 100% of the molecular surface of PHE 112 is in contact with van der Waals surface of other atoms).