Protein structure - Pharmaceutical Biotechnology: Concepts and Aapplications - page 17

Table 2.2 The 20 commonly occurring amino acids. They may be subdivided into fi ve groups on the basis of
side-chain structure. Their three- and one-letter abbreviations are also listed (one-letter abbreviations are
generally used only when compiling extended sequence data, mainly to minimize writing space and effort).
In addition to their individual molecular masses, the percentage occurrence of each amino acid in an
'average' protein is also presented. These data were generated from sequence analysis of over 1000 different
proteins

Abbreviation

R group
classifi cation

Occurrence in
'average' protein (%) Amino acid 3 letters 1 letter Molecular mass

Nonpolar,
aliphatic

Glycine Gly G 75 7.2

Alanine Ala A 89 8.3

Va l i ne Va l V 117 6.6

Leucine Leu L 131 9

Isoleucine Ile I 131 5.2

Proline Pro P 115 5.1

A r o m a t ic Ty r o si n e Ty r Y 181 3. 2

Phenylalanine Phe F 165 3.9

Tryptophan Trp W 204 1.3

Polar but
uncharged

Cysteine Cys C 121 1.7

Serine Ser S 105 6

Methionine Met M 149 2.4

Threonine Thr T 119 5.8

Asparagine Asn N 132 4.4

Glutamine Gln Q 146 4

Positively
charged

Arginine Arg R 174 5.7

Lysine Lys K 146 5.7

Histidine His H 155 2.2

Negatively
charged

Aspartic acid Asp D 133 5.3

Glutamic acid Glu E 147 6.2

2.2.1 Primary structure

Polypeptides are linear, unbranched polymers, potentially containing up to 20 different monomer
types (i.e. the 20 commonly occurring amino acids) linked together in a precise predefi ned sequence.
The primary structure of a polypeptide refers to its exact amino acid sequence, along with the exact
positioning of any disulfi de bonds present (described later). The 20 commonly occurring amino ac-
ids are listed in Table 2.2, along with their abbreviated and one-letter designations. The structures
of these amino acids are presented in Figure 2.1. Nineteen of these amino acids contain a central
(α) carbon atom, to which is attached a hydrogen atom (H), an amino group (NH 2 ) a carboxyl
group (COOH), and an additional side chain (R) group - which differs from amino acid to amino
acid. The amino acid proline is unusual in that its R group forms a direct covalent bond with the
nitrogen atom of what is the free amino group in other amino acids ( Figure 2.1).