Amino Acid Notation

You aren’t expected to know all of the standardized notation in biochemical and biological research. However, it is helpful and at times vital to know the basic notation encountered in these fields. This module will walk you through all of the amino acid notation that you might encounter and present problems involving each.

Learning Objectives

  • Translate standard amino acid notation into plain English
  • Read amino acid mutation or variant notation
  • Learn to use the different notations in the context of problems

Peptides and Sequences

Amino acids are referred to in three different ways: by their full name (ex: Aspartate), by their three letter abbreviation (ex: Asp), or by their one letter abbreviation (ex: D).  You should know all three as the AAMC loves to ask questions and interchanges the different forms frequently. 

Within passages, you will most often encounter the one and three letter abbreviations. The abbreviations can be strung together to indicate a peptide or amino acid sequence. Below are two shorter examples.

One Letter String
This notation indicates the amino acid sequence starting with the N-Terminus on the left ending with the C-terminus on the right. Peptide bonds are implied and present between each letter in the sequence.

Three Letter String
As with the one letter notation, the N-terminus is on the right and the C-terminus is on the left. Here dashes indicate peptide bonds between the amino acid residues.

By convention, the Amino-terminus or N-terminus will always be shown first, and the Carboxy-terminus or C-terminus will be shown last. This carries forward for each of the amino acids present as well. For example, Tyrosine (Y) is attached to Histidine (H) on its amino end and Glutamate (E) on its carboxy-end.

Concept Check: Peptides

Specific Position

Some amino acid sequences or peptides are much too large to display. In these cases, the passage might only talk about a few key residues and will list their identity followed by their location as shown below.

One Letter with a #
Here the letter indicates the identity of the amino acid
with the number identifying its location in a larger sequence.
This represents glutamate at the 567th position.

Mutations and Substitutions

Lastly and most importantly, is mutation and substitution notation. This notation most commonly appears when the function of a particular amino acid in a larger sequence is being studied or when the impact of an amino acid mutation is being investigated.

Original # Replacement
This notation tells us the original amino acid residue first and its position just like above.
The additional amino acid residue that follows the number lets us know what it
changed to. In this, which represents the mutation in sickle cell anemia,
the 6th glutamate is mutated to valine.

This notation is extremely important because questions often reference these variants or mutants. In order to answer them, you will need to decode this notation and determine what differences the mutation introduced.

In sickle cell anemia the E6V mutation changes a charged glutamate into a hydrophobic valine. This causes the newly hydrophobic residue to get caught in an adjacent hydrophobic pocket distorting the red blood cell’s shape into a sickle. Go ahead and give the question below a shot to see how this notation can come up in questions.