Reference

Amino acid table: codes, masses, pKa and hydropathy

The 20 standard amino acids in one place: one- and three-letter codes, residue formulas and masses, side-chain pKa, charge at pH 7, hydropathy, and the mass shifts of common peptide modifications. Every number here is the same constant the peptide calculators use.

Codes, formulas and masses

Code	3-letter	Amino acid	Class	Residue formula	Residue avg (Da)	Residue mono (Da)	Free amino acid (g/mol)
G	Gly	Glycine	Nonpolar	C₂H₃NO	57.0513	57.0215	75.07
A	Ala	Alanine	Nonpolar	C₃H₅NO	71.0779	71.0371	89.09
S	Ser	Serine	Polar	C₃H₅NO₂	87.0773	87.0320	105.09
P	Pro	Proline	Nonpolar	C₅H₇NO	97.1152	97.0528	115.13
V	Val	Valine	Nonpolar	C₅H₉NO	99.1311	99.0684	117.15
T	Thr	Threonine	Polar	C₄H₇NO₂	101.1039	101.0477	119.12
C	Cys	Cysteine	Polar	C₃H₅NOS	103.1429	103.0092	121.16
L	Leu	Leucine	Nonpolar	C₆H₁₁NO	113.1576	113.0841	131.17
I	Ile	Isoleucine	Nonpolar	C₆H₁₁NO	113.1576	113.0841	131.17
N	Asn	Asparagine	Polar	C₄H₆N₂O₂	114.1026	114.0429	132.12
D	Asp	Aspartic acid	Acidic	C₄H₅NO₃	115.0874	115.0269	133.10
Q	Gln	Glutamine	Polar	C₅H₈N₂O₂	128.1292	128.0586	146.14
K	Lys	Lysine	Basic	C₆H₁₂N₂O	128.1723	128.0950	146.19
E	Glu	Glutamic acid	Acidic	C₅H₇NO₃	129.1140	129.0426	147.13
M	Met	Methionine	Nonpolar	C₅H₉NOS	131.1961	131.0405	149.21
H	His	Histidine	Basic	C₆H₇N₃O	137.1393	137.0589	155.15
F	Phe	Phenylalanine	Aromatic	C₉H₉NO	147.1739	147.0684	165.19
R	Arg	Arginine	Basic	C₆H₁₂N₄O	156.1857	156.1011	174.20
Y	Tyr	Tyrosine	Aromatic	C₉H₉NO₂	163.1733	163.0633	181.19
W	Trp	Tryptophan	Aromatic	C₁₁H₁₀N₂O	186.2099	186.0793	204.23

Residue masses are the amino acid minus one water, which is what each position adds to a chain. Average masses use standard atomic weights and are the ones for weighing and molarity; monoisotopic masses use the most abundant isotope of each element and are the ones a mass spectrometer reports for small peptides. The molecular weight calculator adds these up for any sequence.

Charge and hydropathy

Code	Amino acid	Side-chain charge at pH 7	Hydropathy (Kyte-Doolittle)	Counted hydrophobic
G	Glycine	0	−0.4	No
A	Alanine	0	+1.8	Yes
S	Serine	0	−0.8	No
P	Proline	0	−1.6	No
V	Valine	0	+4.2	Yes
T	Threonine	0	−0.7	No
C	Cysteine	−0.03	+2.5	No
L	Leucine	0	+3.8	Yes
I	Isoleucine	0	+4.5	Yes
N	Asparagine	0	−3.5	No
D	Aspartic acid	−1.00	−3.5	No
Q	Glutamine	0	−3.5	No
K	Lysine	+1.00	−3.9	No
E	Glutamic acid	−1.00	−3.5	No
M	Methionine	0	+1.9	Yes
H	Histidine	+0.24	−3.2	No
F	Phenylalanine	0	+2.8	Yes
R	Arginine	+1.00	−4.5	No
Y	Tyrosine	0	−1.3	Yes
W	Tryptophan	0	−0.9	Yes

Charge is the average side-chain charge at pH 7.0 on the EMBOSS pKa scale. Hydropathy is the Kyte-Doolittle value: positive is hydrophobic, negative is hydrophilic. "Counted hydrophobic" marks the residues the solubility calculator counts when it decides whether a sequence needs an organic co-solvent.

pKa values by scale

	EMBOSS	Lehninger	Solomon
N-terminal amine	8.60	9.69	9.60
C-terminal carboxyl	3.60	2.34	2.40
Asp (D) side chain	3.90	3.86	3.90
Glu (E) side chain	4.10	4.25	4.30
His (H) side chain	6.50	6.00	6.00
Cys (C) side chain	8.50	8.33	8.30
Tyr (Y) side chain	10.10	10.00	10.10
Lys (K) side chain	10.80	10.50	10.50
Arg (R) side chain	12.50	12.40	12.50

Published pKa sets disagree by a few tenths, which is why two isoelectric point tools can give different answers for the same peptide. The isoelectric point calculator lets you switch between these three scales and plots net charge across pH.

Modification mass shifts

Modification	Average (Da)	Monoisotopic (Da)
N-terminal acetylation Ac- on the free amine	+42.0367	+42.0106
C-terminal amidation -NH2 in place of -OH	−0.9848	−0.9840
Disulfide bond two Cys side chains joined	−2.0159	−2.0157
Methionine oxidation Met to Met sulfoxide	+15.9994	+15.9949
Deamidation Asn to Asp, Gln to Glu	+0.9848	+0.9840
Pyroglutamate from N-terminal Gln cyclization, loses ammonia	−17.0305	−17.0265
Pyroglutamate from N-terminal Glu cyclization, loses water	−18.0153	−18.0106
Phosphorylation on Ser, Thr or Tyr	+79.9799	+79.9663

Add these to the unmodified sequence mass. On a certificate of analysis, an observed mass about 16 Da high often points to methionine oxidation, and about 1 Da high to deamidation; the COA guide covers how to read the mass-spec line.

Non-standard and ambiguity codes

Code	3-letter	Meaning
B	Asx	Asparagine or aspartic acid (unresolved)
Z	Glx	Glutamine or glutamic acid (unresolved)
J	Xle	Leucine or isoleucine (same mass)
X	Xaa	Any or unknown residue
U	Sec	Selenocysteine
O	Pyl	Pyrrolysine

The calculators accept only the 20 standard codes. Peptides built with non-standard residues such as Aib or norleucine need their formula from PubChem; see the molecular weight reference. Salt forms change the weight per molecule too: net peptide content explains by how much.

Questions

What are the one-letter codes for the 20 amino acids?

G glycine, A alanine, V valine, L leucine, I isoleucine, P proline, M methionine, F phenylalanine, Y tyrosine, W tryptophan, S serine, T threonine, C cysteine, N asparagine, Q glutamine, D aspartic acid, E glutamic acid, K lysine, R arginine and H histidine.

Why is phenylalanine F and not P?

P was already proline, so phenylalanine took F ("Fenylalanine"). The same logic gives R for arginine ("aRginine"), Y for tyrosine ("tYrosine"), W for tryptophan, D for aspartic acid ("asparDic"), E for glutamic acid ("glutEmic"), N for asparagine ("asparagiNe"), Q for glutamine ("Q-tamine") and K for lysine, next to L.

What is the difference between residue mass and amino acid mass?

A residue is the amino acid minus one water (18.02 g/mol), the water lost when each peptide bond forms. Glycine is 75.07 g/mol as a free amino acid and 57.05 as a residue. A peptide's mass is the sum of its residue masses plus one water for the free ends.

Which amino acids are charged at pH 7?

Aspartic acid and glutamic acid carry a negative charge; lysine and arginine carry a positive charge. Histidine (side-chain pKa near 6) is only partly protonated at pH 7, and cysteine and tyrosine are almost fully neutral. The free N-terminus adds +1 and the free C-terminus −1 unless they are capped.

Which pKa values do the B2B Kits calculators use?

The isoelectric point calculator defaults to the EMBOSS scale and can switch to the Lehninger or Solomon values shown above. The scales differ by a few tenths, so a computed pI can move by up to about half a unit between them. None of them accounts for neighbouring residues, so treat the result as an estimate.

Reference data for laboratory research use only.