Before you start
Estimated time 15–20 minutes.
Prerequisites Basic familiarity with amino acids and peptide chains. Use the table on this page or the downloadable code CSV as a reference.
Learning objectives
- Translate a short sequence between three-letter and one-letter amino acid codes.
- Record a terminal group, a site-specific modification and an unknown residue without losing their locations.
- Explain how P2 and P4 differ from P1 even when one property, such as the base sequence or intact mass, agrees.
Look up a residue
Read the examples from the N-terminus to the C-terminus, left to right. Preserve the source notation. A composition count summarizes the base sequence; record terminal groups, residue modifications and any specified stereochemistry alongside it.
| One letter | Three letters | Amino acid |
|---|---|---|
| A | Ala | Alanine |
| C | Cys | Cysteine |
| D | Asp | Aspartic acid |
| E | Glu | Glutamic acid |
| F | Phe | Phenylalanine |
| G | Gly | Glycine |
| H | His | Histidine |
| I | Ile | Isoleucine |
| K | Lys | Lysine |
| L | Leu | Leucine |
| M | Met | Methionine |
| N | Asn | Asparagine |
| P | Pro | Proline |
| Q | Gln | Glutamine |
| R | Arg | Arginine |
| S | Ser | Serine |
| T | Thr | Threonine |
| V | Val | Valine |
| W | Trp | Tryptophan |
| Y | Tyr | Tyrosine |
Practice: read the whole record
| Case | Record | Question |
|---|---|---|
| P1 | Gly–Ala–Gly–Lys–Leu–Val; both termini stated free | What is the base sequence and composition? |
| P2 | Ac–Gly–Ala–Gly–Lys–Leu–Val–NH₂ | What does each end annotation describe? Can the two records be treated as the same form? |
| P3 | GAM[Oxidation]KLV | Which residue is annotated? What string would a base-sequence counter take? |
| P4 | GAGKIV instead of GAGKLV | Which residue differs? Can intact monoisotopic mass alone settle which of these two is present? |
| P5 | GAXKLV | Can this be fully counted using only the 20-code set? How should you preserve the unresolved position? |
- Translate each residue from left to right. Write a base sequence for every case with an assigned residue at each position.
- Record any terminal group, residue modification or unknown position alongside the source notation.
- Compare P1 with P2 and P4. State what each record can tell you about the form or sequence.
- Count the residues in P1 and check your notes against the worked answers.
Worked answer key
- P1.
GAGKLV. Six residues, five distinct codes: G × 2; A, K, L and V × 1 each. - P2. The base sequence is still
GAGKLV. In this conventional display, Ac– marks N-terminal acetylation and –NH₂ marks C-terminal amidation. These are changes to the termini, not extra residues. Preserve those labels; the record describes a different form from P1. - P3. The ProForma 2.0 notation puts the modification after methionine at position 3. Use
GAMKLVfor the base count and keep the full original string plus the site annotation. The basic reader accepts the letters only. - P4. Position 5 changes from L (Leu) to I (Ile). These residues are structural isomers with the same elemental composition. If the remainder of the molecule is identical, intact monoisotopic mass alone cannot distinguish these two sequences.
- P5. X marks an unspecified residue in common sequence notation and falls outside this tool’s 20-letter input. Record X at position 3 and ask for the assignment. Deleting X would misstate the length and shift later positions.
Scope of the table. These are the 20 codes accepted by the companion reader. The reader converts lowercase input to uppercase. Keep any D-amino acid annotations in the source record alongside the base sequence.
Instructor notes
- Ask learners to keep a column for the source record and another for the base sequence. Compare the two columns for P2 and P3.
- Check that learners keep X in position 3 of P5 and use the term ‘unknown’ for that position.