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I'm reading the papers linked below and all three of them mention a 20% cut-off for buried/exposed residues, by calculating a relative solvent accessibility (RSA) value.

I understand how the RSA is calculated, by dividing the calculated solvent accessibility against its total solvent accessibility values from paper 4 table 2.

RSA = calculated/total

e.g. if arginine is calculated to have a solvent accessibility of 55.43 and its total solvent accessibility is 241 then the RSA = 55.43/241 = 23%, so this arginine is considered exposed (see statement 1 below).

What leaves me confused is the definition or lack of the 20% method for defining an exposed or buried residue.

I am assuming it means one of the following:

  1. If an amino acids RSA is below 20% it is buried and above 20% it is exposed. So for an amino acid with an RSA of 21% is considered exposed, this value seems a little low for me. I think statement 2 would make for sense.

  2. If an amino acids RSA is below 20% it is buried and above 80% it is exposed.

Which statement if any is correct?

Paper 1 - see methods section first paragraph

Paper 2 - see figure 5 and table 3

Paper 3 - see abstract and dataset

Paper 4 - see table 2 for total values

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1 Answer 1

up vote 3 down vote accepted

Its 1. Below cutoff, buried, above cutoff accessible.

Paper 1: "A cutoff of 20% was used to define the two states, buried or exposed. With this definition, the dataset was, roughly, evenly split between the two states."

Only two states are possible: solvent accessible and buried.

Paper 2: "A given residue is defined as exposed (e) if its RSA is larger than the cutoff value, and otherwise it is defined as buried (b)."

Abstract for Paper 3: a cutoff of 20% for two-state definition of solvent accessibility.

If it were def #2 it would be a three state definition.

Paper 4: "On average, 15% of residues in small proteins and 32% in larger ones may be classed as “buried residues”, having less than 5% of their surface accessible to the solvent..."

This paper, by the dean of structural analysis Cyrus Chothia, uses a 5% cutoff, not 20%...

The abstract goes on to say... "The accessibilities of most other residues are evenly distributed in the range 5 to 50%."

This passage hints that SA doesn't even go up to 80%. Just considering that you often won't get more than say 60% with this calculation. I'm just guessing; but the thought being that unless you are at a terminus of the protein, which is often disordered and doesn't show up in a crystal structure, you will have two adjoining amino acids for each residue - just the solvent accesible area taken up by the contact with neighbors could easily be 20% of total.

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1  
thanks for clearing this up for me –  harpalss Feb 20 '13 at 10:51
    
y welcome! papers are like a wall of words. This belies the fact that the methods are often the simplest method you can think of. –  shigeta Feb 20 '13 at 17:46

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