Amino acid reference for peptide research
A reference to the 20 standard amino acids, with three-letter and one-letter codes, side-chain chemistry and groupings, plus the non-standard residues most often found in research peptides, such as Aib, norleucine, D-isomers, pyroglutamate and ornithine.
Why residue chemistry matters
Every amino acid in a peptide shares the same backbone unit: an amino group, a central alpha carbon and a carboxyl group. What differs is the side chain attached to the alpha carbon, and it is the side chains that give a sequence its charge, hydrophobicity, reactivity and tendency to fold or aggregate. Reading a sequence residue by residue is therefore the quickest way to anticipate how a peptide will behave in solution and in analysis.
Side-chain chemistry also determines practical risks. Some residues oxidize, some deamidate, some form disulfide bonds and some make a sequence hard to dissolve. The sequence analyzer summarizes composition, charge and hydrophobicity from a sequence, and the sections below explain what lies behind those numbers.
The 20 standard amino acids
The ribosomally encoded amino acids are listed below with their three-letter and one-letter codes and a short description of the side chain. All except glycine are chiral, and in proteins they occur as the L-isomer. Two further residues, selenocysteine (Sec, U) and pyrrolysine (Pyl, O), are genetically encoded in some organisms but are rare in research peptides.
- Ala (A): small, hydrophobic, non-polar; a methyl side chain that favors helices
- Arg (R): basic, positively charged at physiological pH; guanidinium group, strongly hydrophilic
- Asn (N): polar, uncharged amide; prone to deamidation, especially before Gly or Ser
- Asp (D): acidic, negatively charged at neutral pH; prone to aspartimide formation
- Cys (C): polar thiol; forms disulfide bonds and oxidizes readily
- Gln (Q): polar, uncharged amide; can deamidate slowly and cyclize to pyroglutamate at the N-terminus
- Glu (E): acidic, negatively charged at neutral pH; carboxylic acid side chain
- Gly (G): no side chain, achiral; highly flexible, common in turns
- His (H): imidazole side chain, only partly charged near neutral pH; binds metals such as copper and zinc
- Ile (I): hydrophobic, branched aliphatic; favors beta-sheet structure
- Leu (L): hydrophobic, branched aliphatic; common in helices and hydrophobic cores
- Lys (K): basic, positively charged at physiological pH; primary amine used for conjugation and lipidation
- Met (M): hydrophobic thioether; oxidizes to the sulfoxide (+16 Da)
- Phe (F): hydrophobic aromatic; contributes little UV absorbance at 280 nm
- Pro (P): cyclic secondary amine; rigid, breaks helices and introduces kinks
- Ser (S): small, polar hydroxyl; site of phosphorylation in biology
- Thr (T): polar hydroxyl, beta-branched; site of phosphorylation and glycosylation
- Trp (W): large hydrophobic aromatic indole; strong UV absorber at 280 nm and light-sensitive
- Tyr (Y): aromatic phenol, mildly polar; absorbs at 280 nm and can be phosphorylated or iodinated
- Val (V): hydrophobic, beta-branched aliphatic; favors beta-sheet structure
Grouping by side-chain chemistry
Textbooks group the standard residues in slightly different ways, but the most useful practical grouping follows charge and polarity. These groups map directly onto solubility, retention in reversed-phase HPLC and susceptibility to particular degradation reactions.
Some residues fit more than one group. Tyrosine is aromatic but also polar enough to sit at protein surfaces; histidine is aromatic and ionizable; glycine and proline are often considered separately because their effects on backbone flexibility outweigh their side-chain chemistry. Cysteine behaves as a hydrophobic residue in some scales and as a reactive polar group in others.
- Hydrophobic aliphatic: Ala, Val, Leu, Ile, Met
- Aromatic: Phe, Tyr, Trp, and His in some schemes
- Polar uncharged: Ser, Thr, Asn, Gln, Cys
- Acidic (negative at neutral pH): Asp, Glu
- Basic (positive at neutral pH): Lys, Arg, and His when protonated
- Conformationally special: Gly (flexible) and Pro (rigid)
Ionizable groups and net charge
Net charge at a given pH comes from the free N-terminal amine, the free C-terminal carboxyl and the ionizable side chains of Asp, Glu, His, Cys, Tyr, Lys and Arg. At neutral pH, Asp and Glu are essentially fully deprotonated and negative, Lys and Arg are fully protonated and positive, and histidine is partly protonated. Cysteine and tyrosine are largely neutral at neutral pH and become negative only under basic conditions.
Each group has a characteristic pKa, but the published values differ between reference sets and shift with the local environment in a peptide. That is why calculated net charges and isoelectric points are estimates rather than exact values. Terminal modifications matter too: N-terminal acetylation removes a positive charge and C-terminal amidation removes a negative one. The solubility by sequence guide shows how these estimates guide solvent choice.
Residues with handling implications
A handful of residues account for most stability problems. Methionine, cysteine and tryptophan oxidize; asparagine and, more slowly, glutamine deamidate; aspartic acid forms aspartimide and makes Asp-Pro bonds acid-labile; and an N-terminal glutamine or glutamate can cyclize to pyroglutamate. Stretches of Val, Ile, Leu, Phe and Tyr raise the risk of beta-sheet aggregation, discussed in peptide aggregation.
Composition also affects analysis. Only Trp and Tyr, and to a small extent cystine, absorb usefully at 280 nm, so peptides without them cannot be quantified by A280. Basic residues bind counter-ions, lowering net peptide content. Histidine, cysteine and the N-terminal amine coordinate metal ions, which is central to copper peptides such as GHK-Cu. See peptide storage and stability for the degradation chemistry in more detail.
Common non-standard residues
Synthetic and natural peptides often contain residues outside the standard twenty. They are introduced to resist proteases, fix a conformation, remove an oxidation-prone side chain or mimic a natural post-translational modification. Each has its own mass, so identity testing must use the modified structure.
- Aib (alpha-aminoisobutyric acid): an alpha-carbon with two methyl groups; achiral, strongly favors helical turns and blocks cleavage by some peptidases, as at position 2 of semaglutide
- Nle (norleucine): an unbranched four-carbon side chain that is roughly isosteric with methionine but cannot oxidize; used in PT-141 and melanotan II
- D-amino acids: mirror-image forms of the standard residues, written with a D- prefix; they change backbone geometry and resist many proteases, as in triptorelin; see D-amino acids and retro-inverso peptides
- pGlu (pyroglutamate): a cyclic lactam formed from N-terminal Gln or Glu; it removes the free N-terminal amine and is found in natural hormones such as gonadotropin-releasing hormone, the basis of gonadorelin
- Orn (ornithine): a basic residue with a side chain one methylene shorter than lysine; not ribosomally encoded but common in antimicrobial and cyclic peptides
- Others: sarcosine (N-methylglycine), hydroxyproline, citrulline and 2-naphthylalanine (2-Nal), the last appearing in ipamorelin
Using this reference
When reviewing a new sequence, a quick pass through the residues answers several practical questions at once: whether the peptide is acidic, basic or neutral; whether it is likely to dissolve in water; which degradation pathways to expect; whether it can be quantified by UV absorbance; and whether a certificate of analysis should mention modifications such as amidation or non-standard residues.
Notation for these residues and modifications is covered in peptide nomenclature and modifications. For a full calculation of mass, charge and hydrophobicity, enter the sequence into the sequence analyzer, taking care to specify any non-standard residues and terminal groups so the computed values describe the actual molecule.
Frequently asked questions
What is the difference between three-letter and one-letter amino acid codes?
They are two notations for the same residues. Three-letter codes such as Gly-His-Lys are easier to read and handle modifications clearly, while one-letter codes such as GHK are compact and standard in databases and sequence tools. Both are written from the N-terminus to the C-terminus. Non-standard residues usually need three-letter or bracketed abbreviations.
Which amino acids make a peptide hydrophobic?
Leucine, isoleucine, valine, phenylalanine, methionine, tryptophan and, to a lesser extent, alanine and tyrosine contribute most to hydrophobicity. A sequence rich in these residues and with little net charge is likely to be poorly soluble in water and prone to aggregation. Hydrophobicity scales such as GRAVY summarize the overall tendency as a single number.
Why do research peptides contain non-standard amino acids?
Non-standard residues are introduced to change properties that matter in experimental systems: resistance to proteases, a preferred conformation, removal of an oxidation-prone side chain, or mimicry of a natural modification. Examples include Aib, norleucine, D-amino acids and pyroglutamate. Each changes the molecular formula, so analytical data must match the modified sequence.
Compounds mentioned
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