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Amino acids

IMGT classes of the 20 common amino acids

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

IMGT 'Physicochemical' classes of the 20 common amino acids

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.

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).

1 class contains 4 amino acids:
- Aliphatic: A, I, L, V.
1 class contains 3 amino acids:
- Basic: R, H, K.
4 classes contain 2 amino acids:
- Sulfur: C, M.
- Hydroxyl: S, T.
- Acidic: D, E.
- Amide: N, Q.
5 classes contain a single amino acid: G, F, P, W, Y. They have been individualized from 'Chemical' (G and P from 'aliphatic', F, W and Y from 'aromatic') classes, based on the structural properties of the amino acids in protein domains.

'Hydropathy'

There are 3 IMGT 'Hydropathy' classes. Amino acids in each class are in the order of Table 2 :

Hydrophobic: A, C, I, L, M, F, W, V.
Neutral: G, H, P, S, T, Y.
Hydrophilic: R, N, D, Q, E, K.

HYDROPHOBIC								NEUTRAL						HYDROPHILIC
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

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'

There are 5 IMGT 'Volume' classes (volume in Å³). Amino acids in each class are in the order of Table 2:

Very small [60-90]: A, G, S.
Small [108-117]: N, D, C, P, T.
Medium [138-154]: Q, E, H, V.
Large [162-174]: R, I, L, K, M.
Very large [189-228]: F, W, Y.

VERY SMALL			SMALL					MEDIUM				LARGE					VERY LARGE
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

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

'Chemical'

There are 7 'Chemical' classes [1]. Amino acids in each class are in the order of Table 2:

Aliphatic: A, G, I, L, P, V.
Aromatic: F, W, Y.
Sulfur: C, M.
Hydroxyl: S, T.
Basic: R, H, K.
Acidic: D, E.
Amide: N, Q.

'Charge'

There are 3 IMGT 'Charge' classes. Amino acids in each class are in the order of Table 2:

Positive charged: R, H, K.
Negative charged: D, E.
Uncharged: A, N, C, Q, G, I, L, M, F, P, S, T, W, Y, V.

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:

Donor: R, K, W.
Acceptor: D, E.
Donor and acceptor: N, Q, H, S, T, Y.
None: A, C, G, I, L, M, F, P, V.

'Polarity'

There are 2 IMGT 'Polarity' classes, based on the presence or absence of hydrogen donor and/or acceptor atoms. Amino acids in each class are in the order of Table 2:

Polar: R, N, D, Q, E, H, K, S, T, Y.
Nonpolar: A, C, G, I, L, M, F, P, W, V.

The 'polar' class comprises amino acids with hydrogen donor and/or acceptor atoms, except tryptophan. Indeed, tryptophan, despite its hydrogen donor atom, has been classified in the IMGT 'nonpolar' class, as it participates to the nonpolar core of the structural domains.Regarding the 'Charge', the 'polar' class includes the 5 charged (R, H, K, D, E) and 5 uncharged (N, Q, S, T, Y) amino acids.

The 'nonpolar' class comprises amino acids without hydrogen donor or acceptor atoms ('none'), and also includes tryptophan. Regarding the 'Charge', the 'nonpolar' class includes the other 10 uncharged (A, C, G, I, L, M, F, P, W, V) amino acids.

Table 2: IMGT classes of the 20 common amino acids side chain properties.

Amino acid	Abbreviations		IMGT classes of the amino acids side chain properties [1]
			Hydropathy (3 classes)	Volume (5 classes)	Chemical (7 classes)	Physicochemical (11 classes)	Charge (3 classes)	Polarity (2 classes)	Hydrogen donor or acceptor atom (4 classes)
Alanine	Ala	A	hydrophobic (1)	very small (1)	aliphatic (1)	aliphatic (1)	uncharged(3)	nonpolar (2)	none (4)
Arginine	Arg	R	hydrophilic (3)	large (4)	basic (5)	basic (5)	positive charged (1)	polar (1)	donor (1)
Asparagine	Asn	N	hydrophilic (3)	small (2)	amide (7)	amide (2)	uncharged (3)	polar (1)	donor and acceptor (3)
Aspartic acid	Asp	D	hydrophilic (3)	small (2)	acidic (6)	acidic (6)	negative charged (2)	polar (1)	acceptor (2)
Cysteine	Cys	C	hydrophobic (1)	small (2)	sulfur (3)	sulfur (3)	uncharged (3)	nonpolar (2)	none (4)
Glutamine	Gln	Q	hydrophilic (3)	medium (3)	amide (7)	amide (2)	uncharged (3)	polar (1)	donor and acceptor (3)
Glutamic acid	Glu	E	hydrophilic (3)	medium (3)	acidic (6)	acidic (6)	negative charged (2)	polar (1)	acceptor (2)
Glycine	Gly	G	neutral (2)	very small (1)	aliphatic (1)	G (11)	uncharged (3)	nonpolar (2)	none (4)
Histidine	His	H	neutral (2)	medium (3)	basic (5)	basic (5)	positive charged (1)	polar (1)	donor and acceptor (3)
Isoleucine	Ile	I	hydrophobic (1)	large (4)	aliphatic (1)	aliphatic (1)	uncharged (3)	nonpolar (2)	none (4)
Leucine	Leu	L	hydrophobic (1)	large (4)	aliphatic (1)	aliphatic (1)	uncharged (3)	nonpolar (2)	none (4)
Lysine	Lys	K	hydrophilic (3)	large (4)	basic (5)	basic (5)	positive charged (1)	polar (1)	donor (1)
Methionine	Met	M	hydrophobic (1)	large (4)	sulfur (3)	sulfur (3)	uncharged (3)	nonpolar (1)	none (4)
Phenylalanine	Phe	F	hydrophobic (1)	very large (5)	aromatic (2)	F (7)	uncharged (3)	nonpolar (1)	none (4)
Proline	Pro	P	neutral (2)	small (2)	aliphatic (1)	P (10)	uncharged (3)	nonpolar (1)	none (4)
Serine	Ser	S	neutral (2)	very small (1)	hydroxyl (4)	hydroxyl (4)	uncharged (3)	polar (2)	donor and acceptor (3)
Threonine	Thr	T	neutral (2)	small (2)	hydroxyl (4)	hydroxyl (4)	uncharged (3)	polar (2)	donor and acceptor (3)
Tryptophan	Trp	W	hydrophobic (1)	very large (5)	aromatic (2)	W (8)	uncharged (3)	nonpolar (1)	donor (1)
Tyrosine	Tyr	Y	neutral (2)	very large (5)	aromatic (2)	Y (9)	uncharged (3)	polar (2)	donor and acceptor (3)
Valine	Val	V	hydrophobic (1)	medium (3)	aliphatic (1)	aliphatic (1)	uncharged (3)	nonpolar (1)	none (4)

Numbers between parentheses indicate the class number, for a given property.

Color menu for the 3 IMGT amino acid 'Hydropathy' classes
Color menu for the 5 IMGT amino acid 'Volume' classes
Color menu for the 7 IMGT amino acid 'Chemical' classes
Color menu for the 11 IMGT amino acid 'Physicochemical' classes
Color menu for the 3 IMGT amino acid 'Charge' classes
Color menu for the 2 IMGT amino acid 'Polarity' classes
Color menu for the 4 IMGT amino acid 'Hydrogen donor or acceptor atom' classes

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

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