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Amino acids

IMGT classes of the 20 common amino acids star

Citing this page: Pommié, C. et al., J. Mol. Recognit., 17, 17-32 (2004). PMID: 14872534 pdf

IMGT 'Physicochemical' classes of the 20 common amino acids star

Eleven IMGT 'Physicochemical' classes of the 20 common amino acids have been defined by the physicochemical properties of their side chains (Figure 1) [1].
These standardized classes are used in IMGT® databases and tools, for the description of amino acid class changes in mutations and protein engineering.

IMGT classes

Figure 1: The 11 IMGT 'Physicochemical' classes of the 20 common amino acids [1].


The 11 IMGT 'Physicochemical' classes were defined on the 'Hydrophathy', 'Volume', 'Chemical', 'Charge', 'Hydrogen donor or acceptor atoms' and 'Polarity' properties of the side chains (or R- groups).

'Hydropathy'

I V L F C M A W (1) G T S Y P H N D Q E K R
4.5 4.2 3.8 2.8 2.5 1.9 1.8 -0.9 -0.4 -0.7 -0.8 -1.3 -1.6 -3.2 -3.5 -3.5 -3.5 -3.5 -3.9 -4.5
HYDROPHOBIC NEUTRAL HYDROPHILIC

Amino acids are ordered from the most hydrophobic one, Isoleucine (I, on the left hand side) to the most hydrophilic one, Arginine (R, on the right hand side), according to the Kyte-Doolitle scale [2].

(1) Tryptophan, despite its value of -0.9 in the Kyte-Doolittle scale, has been classified in the IMGT 'hydrophobic' class, as it participates to the hydrophobic core of the structural domains.

'Volume'

G A S C D P N T E V Q H M I L K R F Y W
60.1 88.6 89.0 108.5 111.1 112.7 114.1 116.1 138.4 140.0 143.8 153.2 162.9 166.7 166.7 168.6 173.4 189.9 193.6 227.8
VERY SMALL SMALL MEDIUM LARGE VERY LARGE

Amino acids are ordered from the smallest one (G) to the largest one (W).

'Chemical'

'Charge'

The sulfhydryl group of cystein and phenolic hydroxyl group of tyrosine show some degree of pH-dependent ionization.

'Hydrogen donor or acceptor atoms'

There are 4 IMGT 'Hydrogen donor or acceptor atoms' classes. Amino acids in each class are in the order of Table 2:

'Polarity'

References:
[1] Pommié, C. et al., J. Mol. Recognit., 17, 17-32 (2004) PMID: 14872534, LIGM:284 pdf
[2] Kyte, J. and Doolittle, R.F., J. Mol. Biol., 157, 105-132 (1982).