Relative Accessible Surface Area Calculation With Naccess

Question

[agarwa]

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!!

Answer 1

[Neilfws]

1. Yes, REL is the percent relative accessibility. It is defined in the Naccess README, which also explains why the value may be > 100.

2. 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.

[agarwa]

Thank you for your explanation.