Amino Acid Reference Table: Properties, Structures, and Classification

The 20 standard (proteinogenic) amino acids are the building blocks of peptides and proteins, encoded by the universal genetic code. Each amino acid consists of a central alpha-carbon bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom, and a variable side chain (R group) that determines its chemical properties. The table below lists all 20 standard amino acids with their codes, molecular weights, and key properties.

• Glycine (Gly, G) — MW: 75.03 Da — Residue mass: 57.02 Da — Nonpolar, achiral. The smallest amino acid with no side chain (R = H). Provides backbone flexibility due to minimal steric constraints. The only amino acid without a chiral center.
• Alanine (Ala, A) — MW: 89.09 Da — Residue mass: 71.04 Da — Nonpolar, aliphatic. Simple methyl side chain. High helix-forming propensity. One of the most abundant amino acids in proteins.
• Valine (Val, V) — MW: 117.15 Da — Residue mass: 99.07 Da — Nonpolar, aliphatic, branched-chain. Isopropyl side chain. Beta-branched, which restricts backbone conformations and favors beta-sheet structures.
• Leucine (Leu, L) — MW: 131.17 Da — Residue mass: 113.08 Da — Nonpolar, aliphatic, branched-chain. Isobutyl side chain. The most abundant amino acid in proteins. Strong helix-forming tendency.
• Isoleucine (Ile, I) — MW: 131.17 Da — Residue mass: 113.08 Da — Nonpolar, aliphatic, branched-chain. Has two chiral centers (C-alpha and C-beta). Same molecular weight as leucine but different structure (isomers).
• Proline (Pro, P) — MW: 115.13 Da — Residue mass: 97.05 Da — Nonpolar, cyclic. Unique cyclic side chain bonded to both the alpha-carbon and the nitrogen atom, forming a pyrrolidine ring. Introduces rigid kinks in the peptide backbone. Acts as a structural disruptor of alpha-helices and beta-sheets.
• Phenylalanine (Phe, F) — MW: 165.19 Da — Residue mass: 147.07 Da — Nonpolar, aromatic. Benzyl side chain. Absorbs UV at 257 nm (weak). Contributes to hydrophobic core packing in folded structures.
• Tryptophan (Trp, W) — MW: 204.23 Da — Residue mass: 186.08 Da — Nonpolar, aromatic. Indole side chain — the largest standard amino acid. Strong UV absorption at 280 nm (molar extinction coefficient ~5,500 M⁻¹cm⁻¹). Susceptible to oxidation under UV light.
• Methionine (Met, M) — MW: 149.21 Da — Residue mass: 131.04 Da — Nonpolar, sulfur-containing. Thioether side chain. Susceptible to oxidation (+16 Da → methionine sulfoxide). Often the initiating residue in protein translation (start codon AUG).
• Serine (Ser, S) — MW: 105.09 Da — Residue mass: 87.03 Da — Polar, uncharged. Hydroxymethyl side chain. Common site of phosphorylation. The hydroxyl group participates in hydrogen bonding and enzymatic catalysis.
• Threonine (Thr, T) — MW: 119.12 Da — Residue mass: 101.05 Da — Polar, uncharged. Has a hydroxyl group and a methyl group on the beta-carbon. Beta-branched with two chiral centers. Site of O-linked glycosylation and phosphorylation.
• Cysteine (Cys, C) — MW: 121.16 Da — Residue mass: 103.01 Da — Polar, sulfur-containing. Thiol (–SH) side chain. Forms disulfide bonds (–S–S–) with other cysteine residues under oxidizing conditions. pKa of thiol group: ~8.3. Highly susceptible to oxidation.
• Tyrosine (Tyr, Y) — MW: 181.19 Da — Residue mass: 163.06 Da — Polar, aromatic. Phenol side chain (hydroxylated phenylalanine). UV absorption at 274 nm. pKa of phenol hydroxyl: ~10.1. Site of phosphorylation, sulfation, and iodination.
• Asparagine (Asn, N) — MW: 132.12 Da — Residue mass: 114.04 Da — Polar, uncharged. Amide side chain. Susceptible to deamidation (Asn → Asp, +1 Da), especially in Asn-Gly sequences. Common site of N-linked glycosylation (Asn-X-Ser/Thr motifs).
• Glutamine (Gln, Q) — MW: 146.15 Da — Residue mass: 128.06 Da — Polar, uncharged. Longer amide side chain than asparagine. Also susceptible to deamidation (Gln → Glu) but at slower rates than asparagine. Important in nitrogen metabolism.
• Aspartic acid (Asp, D) — MW: 133.10 Da — Residue mass: 115.03 Da — Negatively charged at physiological pH. Carboxylate side chain with pKa ~3.65. Participates in metal ion coordination and enzymatic catalysis. Asp-Pro bonds are susceptible to acid-catalyzed hydrolysis.
• Glutamic acid (Glu, E) — MW: 147.13 Da — Residue mass: 129.04 Da — Negatively charged at physiological pH. Longer carboxylate side chain than aspartate, pKa ~4.25. Neurotransmitter precursor. Strong helix-forming propensity.
• Lysine (Lys, K) — MW: 146.19 Da — Residue mass: 128.09 Da — Positively charged at physiological pH. Amino-butyl side chain with epsilon-amino group, pKa ~10.5. Common site of post-translational modifications (acetylation, methylation, ubiquitination). Contributes to TFA counter-ion content in synthetic peptides.
• Arginine (Arg, R) — MW: 174.20 Da — Residue mass: 156.10 Da — Positively charged at physiological pH. Guanidinium side chain with pKa ~12.5 — remains protonated under virtually all physiological and laboratory conditions. Forms extensive hydrogen bonds. Highest contributor to TFA salt content in synthetic peptides.
• Histidine (His, H) — MW: 155.16 Da — Residue mass: 137.06 Da — Charged or uncharged depending on pH. Imidazole side chain with pKa ~6.0. The only amino acid whose charge state changes near physiological pH, making it critical for enzyme catalysis and buffering. Coordinates metal ions (Zn²⁺, Cu²⁺, Fe²⁺).

• Nonpolar, aliphatic: Gly (G), Ala (A), Val (V), Leu (L), Ile (I), Pro (P)
• Nonpolar, aromatic: Phe (F), Trp (W)
• Polar, uncharged: Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), Gln (Q)
• Sulfur-containing: Cys (C), Met (M)
• Positively charged (basic): Lys (K), Arg (R), His (H — at pH < 6)
• Negatively charged (acidic): Asp (D), Glu (E)
• Aromatic (UV-absorbing): Phe (F) at 257 nm, Tyr (Y) at 274 nm, Trp (W) at 280 nm
• Beta-branched (conformationally restricted): Val (V), Ile (I), Thr (T)

The molecular weight of a free amino acid includes the full backbone (NH₂-CHR-COOH). When incorporated into a peptide, one water molecule (18.015 Da) is lost per peptide bond formed. The residue mass is the mass contribution of each amino acid within the peptide chain (free amino acid MW minus 18.015 Da). To calculate the molecular weight of a peptide, sum all residue masses and add 18.015 Da for the terminal water.

The pKa values of ionizable groups determine the charge state of a peptide at any given pH. The alpha-amino group (N-terminus) has a typical pKa of 7.5-8.5, and the alpha-carboxyl group (C-terminus) has a pKa of 3.0-3.5. Ionizable side chains have characteristic pKa values that influence peptide solubility, HPLC behavior, and biological interactions.

• Asp (D) side chain: pKa ~3.65
• Glu (E) side chain: pKa ~4.25
• His (H) side chain: pKa ~6.0
• Cys (C) side chain: pKa ~8.3
• Tyr (Y) side chain: pKa ~10.1
• Lys (K) side chain: pKa ~10.5
• Arg (R) side chain: pKa ~12.5
• N-terminus (alpha-NH₃⁺): pKa ~8.0
• C-terminus (alpha-COO⁻): pKa ~3.1

These pKa values are averages for isolated amino acids. In peptides, actual pKa values may shift by ±1-2 units depending on neighboring residues, local electrostatic environment, and hydrogen bonding interactions.

Hydrophobicity scales rank amino acids by their tendency to partition into nonpolar environments. Multiple scales exist, each based on different experimental measurements. The Kyte-Doolittle scale (1982) is the most widely used, based on water-to-vapor transfer free energies and interior-vs-surface residue distributions. Positive values indicate hydrophobic character, negative values indicate hydrophilic character.

• Most hydrophobic: Ile (+4.5), Val (+4.2), Leu (+3.8), Phe (+2.8), Cys (+2.5), Met (+1.9), Ala (+1.8)
• Intermediate: Gly (-0.4), Thr (-0.7), Ser (-0.8), Trp (-0.9), Tyr (-1.3), Pro (-1.6)
• Most hydrophilic: His (-3.2), Glu (-3.5), Gln (-3.5), Asp (-3.5), Asn (-3.5), Lys (-3.9), Arg (-4.5)

Hydrophobicity influences HPLC retention time (more hydrophobic peptides elute later in RP-HPLC), solubility in aqueous buffers, membrane permeability, and aggregation propensity. The grand average of hydropathy (GRAVY) score for an entire peptide is calculated as the sum of all residue hydropathy values divided by the number of residues.

• Glycine (G): The only achiral amino acid. Provides maximum backbone flexibility. Favors tight turns and loops. The Asn-Gly motif is the fastest-deamidating dipeptide sequence.
• Proline (P): The only amino acid with a cyclic side chain bonded to the backbone nitrogen (imino acid). Cannot donate an amide hydrogen bond. Introduces rigid kinks and breaks helices. The Asp-Pro bond is uniquely susceptible to acid-catalyzed hydrolysis.
• Cysteine (C): Forms disulfide bonds under oxidizing conditions. Critical for peptide tertiary structure. Free thiol groups are nucleophilic and reactive. Requires careful handling to prevent unwanted oxidation.
• Methionine (M): The most oxidation-prone standard amino acid. Methionine sulfoxide formation (+16 Da) is a common degradation product detectable by mass spectrometry.
• Tryptophan (W): The strongest UV absorber among standard amino acids (ε₂₈₀ ~5,500 M⁻¹cm⁻¹). Susceptible to photodegradation under UV light. The rarest amino acid in proteins (~1.1% frequency).
• Histidine (H): The only amino acid with a side chain pKa near physiological pH (~6.0), enabling it to function as a proton shuttle in enzyme active sites. Coordinates transition metal ions.

To calculate the molecular weight of a peptide from its amino acid sequence: (1) Look up the residue mass for each amino acid in the sequence. (2) Sum all residue masses. (3) Add 18.015 Da for the terminal water molecule (H at N-terminus + OH at C-terminus). (4) Add the mass of any modifications (acetylation at N-terminus: +42.04 Da; amidation at C-terminus: -0.98 Da; disulfide bond: -2.016 Da per bond; phosphorylation: +79.97 Da).

This calculation yields the monoisotopic molecular weight. For comparison with mass spectrometry data, use the same mass type (monoisotopic or average) as the instrument reports. High-resolution instruments (Orbitrap, FT-ICR) report monoisotopic masses; lower-resolution instruments (quadrupole, ion trap) may report average masses.

Beyond the 20 standard amino acids, synthetic peptides may incorporate non-standard residues for research purposes:

• D-amino acids: Mirror images of natural L-amino acids. Confer resistance to proteolytic degradation. Designated with lowercase letters (e.g., d-Ala) or D- prefix.
• Norleucine (Nle): An isosteric replacement for methionine that is resistant to oxidation. Used in peptides where methionine oxidation is problematic.
• Alpha-aminoisobutyric acid (Aib): A di-methylated glycine that strongly promotes helical structure. Used in peptide design to stabilize alpha-helices.
• Beta-alanine (β-Ala): An amino acid with the amino group on the beta-carbon rather than the alpha-carbon. Found naturally in carnosine. Alters backbone geometry.
• Selenocysteine (Sec, U): The 21st proteinogenic amino acid, encoded by UGA codon with a specific SECIS element. Contains selenium instead of sulfur.
• Pyroglutamic acid (pGlu): Cyclized form of glutamine or glutamic acid at the N-terminus. Can form spontaneously during storage.

Sum the residue masses (monoisotopic or average) of each amino acid in the sequence, then add 18.02 Da for the water molecule lost during peptide bond formation. For example, a tripeptide Ala-Gly-Val = 71.04 + 57.02 + 99.07 + 18.02 = 245.15 Da (monoisotopic). This calculated MW should match the mass spectrometry result on the CoA within ±1 Da.

Monoisotopic mass uses the most abundant isotope of each element (e.g., ¹²C = 12.000). Average mass uses the weighted average of all naturally occurring isotopes. For peptides under ~2000 Da, monoisotopic mass is preferred as instruments can resolve individual isotope peaks. For larger peptides, average mass is more practical as isotope envelopes become unresolved.

Proline introduces rigid kinks due to its cyclic side chain. Glycine provides maximum conformational flexibility as the smallest amino acid. Cysteine forms disulfide bonds critical for 3D structure. Methionine is highly susceptible to oxidation. These properties directly impact peptide synthesis difficulty, stability, solubility, and HPLC retention behavior.

Explore detailed chemical profiles and research guides for compounds discussed in this article:

• BPC-157: Complete Research Guide → /learn/bpc-157
• GHK-Cu: Complete Research Guide → /learn/ghk-cu
• TB-500: Complete Research Guide → /learn/tb-500

• Read more: Acetate vs Arginate Salt Forms in Peptides: Which Is Better? → https://www.chemverify.com/learn/acetate-vs-arginate-salt-peptides-comparison
• Read more: Peptide Sequence Notation: One-Letter Codes, Three-Letter Codes, and Modifications → https://www.chemverify.com/learn/peptide-sequence-notation
• Read more: Peptide Aggregation: Why Peptides Clump and How to Prevent It → https://www.chemverify.com/learn/peptide-aggregation-clumping-prevention
• Read more: Peptide Research Glossary: 60+ Terms Every Laboratory Researcher Should Know → https://www.chemverify.com/learn/peptide-research-glossary