Answers.Body: <p>There is some confusion in the question.</p>
  
  <p>Solvent accessibility of a residue, i.e. the area accessible to the solvent (water), depends on the 3D structure of the protein. It's not a property of  an amino-acid (chemical compound such as alanine, leucine, ...).</p>
  
  <p>There may be a correlation -- amino-acids with hydrophobic side chains are more likely to be buried, but in general amino-acids (chemical compounds) cannot be classified as buried or exposed.</p>
  
  <p>I don't have access to the first article, but I tried running the prediction server described in the second linked article, and I got a result</p>
  
  <pre><code>GSGMQIFVKTFRDRLRNLLPQTITLEVEPSDTIENVKAKIQDKEGIPPDQQVLIFSRKRL
  CCCCEEEEEECEEEEEECCCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEECCEEC
  EEEBeBbBebbEbEbEebEEeEbeBEBeeEeeBeeBbEeBeEeEEbEeEeBeBbbEEeeb
  
  ...
  
  Porter (Secondary Structure):
  H = Helix   (DSSP classes H, G and I)
  E = Strand  (DSSP classes E and B)
  C = Coil    (DSSP classes S, T and .)
  
  PaleAle (Relative Solvent Accessibility):
  B = very buried      (&lt;=4% accessible)
  b = somewhat buried  (&gt;4% and &lt;=25% accessible)
  e = somewhat exposed (&gt;25% and &lt;=50% accessible)
  E = very exposed     (&gt;50% accessible)
  </code></pre>
  
  <p>In one place in the sequence you can see <code>QQ</code>, predicted as <code>eB</code>.
  So clearly glutamine is NOT assigned to a particular RSA class.</p>
  
  <p>Dividing RSA (relative solvent accessibility, 0-100%) into categories is arbitrary, I don't think there is any widely used convention. The easiest way would be to just use numeric values.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-07-23T13:30:32.503Z
Answers.LastActivityDate: 2018-07-23T13:30:32.503Z
Answers.UserDisplayName: marcin
Body: <p>I came across an <a href="https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty155/4934942?redirectedFrom=fulltext" rel="nofollow noreferrer">article</a> which has defined 3 categories: Buried [A, L, F, C, G, I, V, W], Exposed [ R, K, Q, E, N, D] and Intermediate [M, S, P, T, H, Y] when analyzing the solvent accessibility of a protein. But I could not find any reference validating the claim. </p>
  
  <p>Another <a href="https://academic.oup.com/bioinformatics/article/29/16/2056/204670" rel="nofollow noreferrer">article</a> has come up with 4 divisions:</p>
  
  <p>B=completely buried (0-4% exposed)<br>
  b=partly buried (4-25% exposed)<br>
  e=partly exposed (25-50% exposed)<br>
  E=completely exposed (50+% exposed)   </p>
  
  <p>Which is authentic when dealing with solvent accessibility, and which should be used? Also for the second article [B,b,e,E], which amino acid corresponds to which class?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-23T10:50:23.527Z
Comments.Text: "All models are wrong but some are useful" is usually used in statistics, in this case, what do you want to solve? Can't you use both of them? If it is not explained in the 2nd article or in the supplementary information it will be hard to know by us to which amino acids are in each 4 categories. Did you looked there?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-23T11:02:47.720Z
Comments.Text: @Llopis yes I looked, no mention of anything. Since it wasn't mentioned. I thought it was probably a well known fact which is why they did not cite the source, hence I asked
Comments.UserDisplayName: girl101
Tags: <proteins><protein-structure><3d-structure><computation><secondary-structure>
Title: Which is the amino acids classification when analyzing the solvent accessibility of a protein?
ThreadText: # Which is the amino acids classification when analyzing the solvent accessibility of a protein?
  
  (Asked by: username_0 on 2018-07-22)
  
  I came across an [article](https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty155/4934942?redirectedFrom=fulltext) which has defined 3 categories: Buried [A, L, F, C, G, I, V, W], Exposed [ R, K, Q, E, N, D] and Intermediate [M, S, P, T, H, Y] when analyzing the solvent accessibility of a protein. But I could not find any reference validating the claim.
  
  Another [article](https://academic.oup.com/bioinformatics/article/29/16/2056/204670) has come up with 4 divisions:
  
  B=completely buried (0-4% exposed)  
  b=partly buried (4-25% exposed)  
  e=partly exposed (25-50% exposed)  
  E=completely exposed (50+% exposed)
  
  Which is authentic when dealing with solvent accessibility, and which should be used? Also for the second article [B,b,e,E], which amino acid corresponds to which class?
  
  **Tags:** proteins, protein-structure, 3d-structure, computation, secondary-structure
  
  > **Comments:**
  > **username_1**: "All models are wrong but some are useful" is usually used in statistics, in this case, what do you want to solve? Can't you use both of them? If it is not explained in the 2nd article or in the supplementary information it will be hard to know by us to which amino acids are in each 4 categories. Did you looked there?  
  > **username_0**: @Llopis yes I looked, no mention of anything. Since it wasn't mentioned. I thought it was probably a well known fact which is why they did not cite the source, hence I asked  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-07-23. Score: 2 | Accepted answer
  
  There is some confusion in the question.
  
  Solvent accessibility of a residue, i.e. the area accessible to the solvent (water), depends on the 3D structure of the protein. It's not a property of an amino-acid (chemical compound such as alanine, leucine, ...).
  
  There may be a correlation -- amino-acids with hydrophobic side chains are more likely to be buried, but in general amino-acids (chemical compounds) cannot be classified as buried or exposed.
  
  I don't have access to the first article, but I tried running the prediction server described in the second linked article, and I got a result
  
  ```
  GSGMQIFVKTFRDRLRNLLPQTITLEVEPSDTIENVKAKIQDKEGIPPDQQVLIFSRKRL
  CCCCEEEEEECEEEEEECCCCEEEEEECCCCCHHHHHHHHHHHHCCCHHHEEEEECCEEC
  EEEBeBbBebbEbEbEebEEeEbeBEBeeEeeBeeBbEeBeEeEEbEeEeBeBbbEEeeb
  
  ...
  
  Porter (Secondary Structure):
  H = Helix   (DSSP classes H, G and I)
  E = Strand  (DSSP classes E and B)
  C = Coil    (DSSP classes S, T and .)
  
  PaleAle (Relative Solvent Accessibility):
  B = very buried      (<=4% accessible)
  b = somewhat buried  (>4% and <=25% accessible)
  e = somewhat exposed (>25% and <=50% accessible)
  E = very exposed     (>50% accessible)
  
  ```
  
  In one place in the sequence you can see `QQ`, predicted as `eB`.
  So clearly glutamine is NOT assigned to a particular RSA class.
  
  Dividing RSA (relative solvent accessibility, 0-100%) into categories is arbitrary, I don't think there is any widely used convention. The easiest way would be to just use numeric values.
  
  
  ---
  
  