This pages provides an overview of notations, formulae, and accessible thermodynamic properties for the 20 “standard” α-amino acids plus pyrrolysine and selenocysteine. These 22 chemical compounds are proteinogenic amino acids found in proteins and being naturally coded for in the standard genetic code.

All α-amino acids have molecules in which an amino group is adjacent to a Cα-atom next to a carboxylic acid group. A characteristic side chain at the Cα-atom is responsible for physicochemical properties and functionality of the different types of amino acids. In the glycine molecule, this “side chain” simply is a H-atom. Hence, the Cα-atom of a glycine molecule has two equivalent H-atoms and the molecule is achiral. All other amino acids possess a chiral Cα-atom. Naturally occurring amino acids are typically L-amino acids, but D-form enantiomers have been identified in bacteria proteins.

Amino acids are listed in the following table in alphabetical order of their three-letter codes (3LCs). Corresponding one-letter codes (1LCs) are shown in the second column. There are 22 plus 1 rows representing the 22 proteinogenic amino acids and one virtual amino acid as a placeholder for an unspecified amino acid. Selected references on the nomenclature and use of these abbreviations as amino acid identifiers are given in the bibliography herein. The third and fourth column show the common name and brutto formula of the amino acids, followed by a side chain description (based on Figure 1.9 in [1]) in the fifth column. The majority of the considered amino acids have acyclic (linear or branched) side chains. Cyclic side chains are indicated using the abbreviations cycl. (cyclic, non-aromatic) and arom. (aromatic). Side chains containing a functional group, such as a carboxylic acid (-COOH) or a NHn (n = 0,1, or 2) group, are negatively or positively charged under physiological pH conditions. The last column provides links to thermodynamic data in the ThermoML Archive via the ThermoML Bibliography.
3LC 1LC Common name Formula Side chain chemistry
Ala A alanine C3H7NO2 nonpolar, hydrophobic
Arg R arginine C6H14N4O2 positively chargable
Asn N asparagine C4H8N2O3 uncharged, polar
Asp D aspartic acid C4H7NO4 negatively chargable
Cys C cysteine C3H7NO2S uncharged, polar
Gln Q glutamine C5H10N2O3 uncharged, polar
Glu E glutamic acid C5H9NO4 negatively chargable
Gly G glycine C2H5NO2 nonpolar, hydrophobic
His H hystidine C6H9N3O2 positively chargable, arom.
Ile I isoleucine C6H13NO2 nonpolar, hydrophobic
Leu L leucine C6H13NO2 nonpolar, hydrophobic
Lys K lysine C6H14N2O2 positively chargable
Met M methionine C5H11NO2S nonpolar, hydrophobic
Phe F phenylalanine C9H11NO2 nonpolar, hydrophobic, arom.
Pro P proline C5H9NO2 nonpolar, hydrophobic, cycl.
Pyl O pyrrolysine C12H21N3O3 multifunctional
Sec U selenocysteine C3H7NO2Se uncharged, polar
Ser S serine C3H7NO3 uncharged, polar
Thr T threonine C4H9NO3 uncharged, polar
Trp W tryptophan C11H12N2O2 nonpolar, hydrophobic, arom.
Tyr Y tyrosine C9H11NO3 uncharged, polar, arom.
Val V valine C5H11NO2 nonpolar, hydrophobic
Xaa X unspecified

Bibliography and links: Notations for amino acids

[1] K. E. van Holde, W. C. Johnson and P. S. Ho: Principles of Physical Biochemistry. Prentice Hall, Upper Saddle River, New Jersey 07458 , 1998; Figure 1.19 on page 29.
[2] D. Hellwinkel: Systematic Nomenclature of Organic Chemistry. Springer-Verlag, Berlin und Heidelberg, Germany, 2001; Table 26 on pages 209 and 210.
[3] D. R. Lide (Editor): Handbook of Chemistry and Physics. 88-th Edition. CRC Press, Boca Raton, Florida, 2007-2008; Section 7: Biochemistry.
[4] IUPAC-IUB Commision on Biochemical Nomenclature: A One-Letter Notation for Amino Acid Sequences. Tentative Rules. J. Biol. Chem. 1968,243 (13), pp. 3557-3559. PDF:
[5] G. S. Revesz, C. E. Granito and E. Garfield
One-Letter Notation for Calculating Molecular Formulas and Searching Long-Chain Peptides in the Index Chemicus Registry System. J. Chem. Doc. 1970,10 (3), pp. 212-215.
DOI: 10.1021/c160038a012.
[6] G. P. Moss (preparation of World-Wide-Web version):
Nomenclature and Symbolism for Amino Acids and Peptides (Recommendation 1983).
[7] Abreviations: Amino Acids.

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