I am a software engineer with little knowledge of molecular biology. However I am trying to understand some bioinformatics computer code where the protein alphabet appears to be represented as the following string, with each of the twenty amino acid constituents of protein:


The code appears to define a second string in which the first is reordered as:


I am not sure of the biological significance of this. Does this reordering represent some specific interaction between these molecules?

  • 2
    $\begingroup$ Welcome to Biology.SE. Have you looked at a table of amino acid properties? There are many ways of grouping amino acids, so if it isn't documented why that order is being used I doubt anyone can give you a definitive answer beyond the trivial 'ordered by physicochemical properties'. $\endgroup$
    – tyersome
    Nov 20 '21 at 17:56
  • $\begingroup$ @tyersome But the mapping given by the OP doesn't appear to be based on physicochemical properties at all? $\endgroup$
    – user338907
    Nov 20 '21 at 19:30
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    $\begingroup$ What is the context? HPLC? Mass spectrometry? 2D gels? Sucrose gradients? Protein folding? What kind of analysis? $\endgroup$ Nov 21 '21 at 4:09
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    $\begingroup$ OP is probably referring to this. $\endgroup$
    – Voile
    Nov 22 '21 at 4:25
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    $\begingroup$ @Luca — Strange. I'll have a look at it myself perhaps. I am having to work on someone else's Django code at the moment, so I might as well try to suss out the Python. If it beats me I have friends I can lean on. This whole thing would have probably been better on SE Bioinformatics, although I don't go there much. $\endgroup$
    – David
    Nov 22 '21 at 22:49

As suggested by tyersome's comment, the amino acids are grouped by their physiochemical properties. Let's add some commas:

  • aspartic acid (D) and glutamic acid (E) are acidic
  • lysine (K), arginine (R), and histidine (H) are basic
  • asparagine (N) and glutamine (Q) are amidic
  • serine (S) and threonine (T) are hydroxylic
  • proline (P), glycine (G), alanine (A), valine (V), isoleucine (I), and leucine (L) are aliphatic
  • methionine (M) and cysteine (C) are sulfur-containing
  • phenylalanine (F), tyrosine (Y), and tryptophan (W) are aromatic

My source is this graphic.

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    $\begingroup$ Thank you! Lots to take in! $\endgroup$
    – Luca
    Nov 20 '21 at 18:31
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    $\begingroup$ I am the person who came up with that reordering and I can confirm that acvill is correct. Specifically, the hope was that in heat maps relating the sequence to other properties like colours would show up in clusters. It actually does not work that great but it's the best you can do arranging them in one dimension. $\endgroup$
    – Deipatrous
    Nov 21 '21 at 8:44
  • $\begingroup$ I have deleted my previous comment about strings as it transpires, to my surprise, that the computer code contains the two 20 amino acid sequences as strings. So your answer might be modified to say that "the second string contains the 20 amino acids arranged so that those of similar physiochemical properties are grouped together". The reason for constructing such strings can only be discerned from an understanding of the computer algorithm. $\endgroup$
    – David
    Nov 22 '21 at 15:26
  • $\begingroup$ @David I will contact the authors and update the thread. $\endgroup$
    – Luca
    Nov 22 '21 at 15:29

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