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: CG2   28.374 es    2.792 os   31.166 ts    0.527 Rln THR   13
INF THR   13@CG2_>LEU  14@O___     7 pts   1.412 A2    0.175 Rlen  3.74 Dxx
INF THR   13@CG2_>ILE  15@CG1_     5 pts   0.858 A2    0.840 Rlen  5.94 Dxx
INF THR   13@CG2_>MET  26@CE__     1 pts   0.299 A2    0.991 Rlen  6.52 Dxx
INF THR   13@CG2_>ILE  15@CA__     1 pts   0.223 A2    0.964 Rlen  6.11 Dxx
    ES_Total      :   57.962                                       THR   13
    ES_Backbone   :   10.702                                       THR   13
    ES_Side Chain :   47.260                                       THR   13
    OS_Total      :   32.587                                       THR   13
    OS_Backbone   :   25.113                                       THR   13
    OS_Side Chain :    7.474                                       THR   13
    Ave_Raylength :    0.430                                       THR   13
    MC_RAYLENGTH  :    0.426                                       THR   13
    SC_RAYLENGTH  :    0.438                                       THR   13
...

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 first INF line means the following:
The CG2 atom of THR 13 is occluded by the O atom of LEU 14;
seven (6) surface points (pts) with a total surface area of 1.412 square Angstoms (A2) is occluded;
the mean fractional raylength (Rlen) for this occluded patch is 0.175;
the distance between the CG2 and O atom centers is 3.74 Angstroms (Dxx).

In the residue summary section:

ES_Total is the total exposed surface area for THR 13
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
Ave_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 THR 13; equals 0.0 if 100% of the molecular surface of THR 13 were in contact with van der Waals surface of other atoms.)
MC_RAYLENGTH and SC_RAYLENGTH break down the raylength averages to main chain and side chain components.