Hi,
I would like to find the relative ASA of residues in percentage. I used naccess to find it. The output of naccess(.rsa file) is shown below.
REM Relative accessibilites read from external file "standard.data"
REM File of summed (Sum) and % (per.) accessibilities for
REM RES _ NUM All-atoms Total-Side Main-Chain Non-polar All polar
REM ABS REL ABS REL ABS REL ABS REL ABS REL
RES ILE A 189 186.83 106.7 142.62 103.4 44.21 119.0 142.62 102.5 44.21 122.9
RES ALA A 190 110.69 102.5 76.79 110.6 33.89 87.9 77.24 108.2 33.45 91.4
RES LYS A 191 177.09 88.2 158.77 97.2 18.33 48.9 111.91 96.0 65.18 77.4
RES GLU A 193 82.74 48.0 80.51 59.8 2.23 5.9 43.73 72.5 39.01 34.8
RES THR A 197 152.77 109.7 97.50 95.9 55.27 147.1 98.21 129.7 54.56 85.9
I think, column name "REL" represents the percentage of relative accessible surface area. I would like to know whether my opinion correct or not... I would also like to know, which cut off value is suitable to retrieve interface and surface residues??
Your suggestions would be appreciated!!
1 answer
Yes, REL is the percent relative accessibility. It is defined in the Naccess README, which also explains why the value may be > 100.
Choice of cutoff is arbitrary - there is no "good" value. You're trying to map a continuous variable (RSA) onto a categorical variable (buried/exposed). I suggest you search the literature with terms such as "amino acid relative solvent accessibility cutoff buried exposed" to see how other people approach this problem. For example in this figure, cutoff values of 0, 5 and 25% RSA are employed.
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