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Amino acids are often denoted using either a 3-letter abbreviation or a 1-letter notation, e.g. Glutamine is denoted via $\mathrm{Gln}$ or $\mathrm{Q}$.

When one notation should be preferred over the other and what are the reasons behind?

P. S. This is a follow-up to my question on Chemistry.SE Proper common notation for a ligand, where the problem of distinction between $\mathrm{L}$ notation for "ligand" and for "leucine" occured.

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In my experience neither is preferred.

When simply presenting a protein sequence, e.g. in the context of a database of proteins encoded by a genome, then the one-letter code tends to be used.

When showing an alignment of a DNA sequence with the encoded protein sequence both can be used, although personally I prefer the one-letter code for this too because I don't like squished-together text like LysAlaTrpLeu.

In papers referring to an individual residue in a protein I would say that the three-letter code would be more likely to be used.

When referring to a mutation (or, rather, an amino acid substitution) you might see Leu129Gln or L129Q.

And, by the way, I use L for ligand and have never found it to be confusing. If the reader of your text is sophisticated enough to know that L is leucine then I think they would be able to tell from the context that you were using L for ligand.

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