Amino acids abbreviations, Table

The standard amino acids are 20 common a-amino acids that are found in nearly all proteins. The standard amino acids differ from each other in the structure of the side chains bonded to their a carbon atoms. All the standard amino acids are L-amino acids. Table 24-2 shows the 20 standard amino acids, grouped according to the chemical properties of their side chains. Each amino acid is given a three-letter abbreviation and a one-letter symbol (green) for use in writing protein structures. 

The secret to the functional diversity of proteins lies partly in the chemical diversity of the amino acids but primarily in the diversity of the three-dimensional structures that these building blocks can form, simply by being linked in different sequences. At the heart of the determination of structure by sequence lie the distinctive characteristics of each of the 20 different amino acids. Table 6.1 shows some general properties of the amino acids along with their three- and one-letter abbreviations. 

Listed below are miscellaneous examples used in this work and found elsewhere. See also Table 1.3 for P-containing compounds, Table 10.7 for amino acids, Table 10.15 for bases, nucleosides and nucleotides and Table 14.4 for symbols in use for analytical techniques. Symbols in commercial use for branded products are mostly excluded from all these tables. Symbols for the elements are also excluded. While some symbols and abbreviations appear to be here to stay, it should be remembered that the use of some of them can be very subject to fashion or personal choice. 

Abbreviations for amino acids and their derivatives follow the revised recommendation of the lUPAC-IUB Committee on Biochemical Nomenclature, entitled Nomenclature and Symbohsm for Amino Acids and Peptides (recommendations of 1983). Nomenclature of branched polypeptides is used in accordance with the recommended nomenclature of graft polymers (lUPAC-lUB recommendations, 1984). For the sake of brevity codes of branched polypeptides were constracted by us using the one-letter symbols of amino acids (Table 1). The abbreviations used in this paper are the following. AK, poly[Lys-(DL-Ala )] AXK, poly[Lys-(DL-Ala -Xi)] XAK, poly[Lys(Xi-DL-Ala )] X = Ser (SAK), Om (OAK), Glu (EAK), or Ac-Glu (Ac-EAK). All amino acids are of L-configuration unless otherwise stated. DPH, l,6-diphenyl-l,3,5-hexatriene ANS, sodium anilino naphthalene sulfonate DPPC, dipalmitoyl phosphatidyl choline PG, phosphatidyl glycerol Z, benzyloxycarbonyl Pep, pentachlorophenol P, polarisation. 

This table lists the and pi (pH at the isoelectric point) values of a-amino acids commonly found in proteins along with their abbreviations. The dissociation constants refer to aqueous solutions at 25°C. 

The Chains and Averages of Polymers Table 1.3 Name, Abbreviation, and R Group for Some Common Amino Acids ... 

Refs. 21, 22, 155. Abbreviations AHV, a-amino-(3-hydroxyvaleric acid Horn, L-homoserine AEG, (3 -(2-aminoethyl)-L-cysteine ppc, phosphoenolpymvate carboxylase the strain improvement largely depends on the transduction technology sensitive resistant —, auxotroph or deficient , leaky auxotroph +, prototrophic revertant. Table 7. Amino Acid Production from Hydrocarbons ... 

The structures, abbreviations (both three- and one-letter), and pKa values of the 20 amino acids commonly found in proteins are shown in Table 26.1. All are... 

Table 26.1 The 20 Common Amino Acids in Proteins (continued) Name Abbreviations MW Stricture...

The long, repetitive sequence of —N—CH-CO- atoms that make up a continuous chain is called the protein s backbone. By convention, peptides are written with the N-terminal amino acid (the one with the free -NH3 1 group) on the left and the C-terminal amino acid (the one with the free -C02 group) on the right. The name of the peptide is indicated by using the abbreviations listed in Table 26.1 for each amino add. Thus, alanylserine is abbreviated Ala-Ser or A-S, and serylalanine is abbreviated Ser-Ala or S-A. Needless to say, the one-letter abbreviations are more convenient than the older three-letter abbreviations. 

Table 8.1 The genetic code as a three-letter code, with the normal abbreviations for the 20 pro-teinogenic amino acids. The first base corresponds to the 5 end, the third to the 3 end of the nucleotide chain... 

Fig. 2a-d. Multiple alignment of primary structures from 36 PHA synthases. A comparison of amino acid sequences derived from PH A synthase genes is shown. Amino acids are specified by the standard one-letter abbreviations. The consensus sequence represents amino acid residues (shaded) which are present in at least 50% of the PHA synthases. Highly conserved amino acids, which are present in at least 70% of the PHA synthases, are additionally underlined in the consensus sequence and the eight amino acid residues, which are present in all PHA synthases, are indicated as bold letters. See Table 1 for references... 

Table 2.2 The 20 commonly occurring amino acids. They may be subdivided into five 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 seguence 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 seguence analysis of over 1000 different proteins...

Table 6.1 Abbreviations BAN, BANYULS bHLH, basic helix-loop-helix CHS, chalcone synthase CHI, chalcone isomerase DFR, dihydroflavonol reductase F3H, flavonol 3-hydroxylase F3 H, flavonoid 3 -hydroxylase FLS, flavonol synthase icx, increased chalcone synthase expression LDOX, leucoanthocyanidin dioxygenase LCR, leucoanthocyanidin reductase MATE, multidrug and toxic compound extrusion NR, not yet reported tt, transparent testa ttg, transparent testa glabrous the WD40 and WRKY transcription factors are named for conserved amino acid sequences within these proteins. PC = personal communication.

AMINO ACIDS, PEPTIDES AND PROTEINS Table 13.1 Amino acids structures and standard abbreviations... 

The tripeptide formed from L-alanine, L-phenylala-nine and L-serine by two condensation reactions is alanyl-phenylalanyl-serine, considering each additional amino acid residue as a substituent on the previous. This would be more commonly represented as Ala-Phe-Ser, using the standard three-letter abbreviations for amino acids shown in Table 13.1. 

The tripeptide precursor is called ACV, an abbreviation for 8-(L-a-aminoadipyl)-L-cysteinyl-D-valine. ACV is an acronym, and does not refer to the systematic abbreviations for amino acids described in Table 13.1. ACV is the linear tripeptide that leads to isopenicillin N, the first intermediate with the fused-ring system found in the penicillins. 

There are two generally accepted systems of abbreviation for trivial names, using either one or three letters. The choice of form to use is generally determined by circumstances. Normally, three-letter symbols are used, and one-letter symbols are reserved for long sequences of amino acids. A list of such symbols is shown in Table 7.1. 

Table 7.1 Names and their abbreviations and symbols for amino acids. ...

Shown here are deduced consensus sequences (in roman type) and actual sequences from known substrates (italic). The Ser (S), Thr (T), orTyr (Y) residue that undergoes phosphorylation is in red all amino acid residues are shown as their one-letter abbreviations (see Table 3-1). X represents any amino acid B, any hydrophobic amino acid Sp,Tp, and Yp, already phosphorylated Ser, Thr, and Tyr residues,... 

Table 27.1 includes three-letter and one-letter abbreviations for the amino acids. Both enjoy wide use. 

The structures and names of some particularly important a-amino acids are shown in Table 25-1. You will notice that the names in common use for amino acids are not descriptive of their structural formulas but at least they have the advantage of being shorter than the systematic names. The abbreviations Gly, Glu, and so on, that are listed in Table 25-1 are particularly useful in designating the sequences of amino acids in proteins and peptides, as will become evident later in the chapter. 

Amino acid residues have the l configuration unless stated otherwise. bpep, peptide, other abbreviations as in Table 3. 

Abbreviations DNP, dinitrophenyl SNP, sulfonyloxynitrophenyl TFA, tri-fluoroacetyl and others as explained in Table V footnote. In the polyamino acid derivatives the subscript is the total number of residues added to the protein molecule. These residues are distributed among the number of amino groups listed in column 3. In column 3, analytical number of modified residues is given except where an amino acid prefix occurs the number then refers to the position in the amino acid sequence. 

Amino acids are often abbreviated by three-letter symbols when this proves to be too cumbersome (as in certain kinds of charts and figures), one-letter symbols are used. Both designations are given in table 3.1, together with the molecular weight (Mr) of each amino acid. 

Fig. 1. Occurrence of H3 receptors inhibiting release of acetylcholine, of amino acid and monoamine neurotransmitters in the mammalian CNS in vitro. The schematic drawing represents a midsagittal section of the human brain three areas with a more lateral position are shown by broken line (substantia nigra and part of the hippocampus and of the striatum). For each of the six regions of the CNS (subregions given in brackets), in which H3 heteroreceptors have been identified, the neurotransmitter(s) and the species are indicated. The superscripts refer to the numbers of the papers as listed under References. Own unpublished data suggest that an H3 receptor-mediated inhibition of noradrenaline release also occurs in the human cerebral cortex and hippocampus and in the guinea-pig cerebral cortex. Note that a presynaptic location has not been verified for each of the H3 heteroreceptors or has been even excluded (for details, see Table 1). Abbreviations ACh, acetylcholine DA, dopamine GABA, y-aminobutyric acid Glu, glutamate 5-HT, 5-hydroxytryptamine, serotonin NA, noradrenaline...

The names and structures of the twenty natural amino acids are given in Table 1.13. The International Union of Pure and Applied Chemistry (IUPAC) uses the three-letter abbreviations shown in the second column of Table 1.13 to describe amino acids. These are widely used in biological circles as well but are inappropriate when long peptide or protein sequences need to be described. For example, when proinsulin is cleaved, it forms the biologically important peptide insulin and another peptide usually called C-peptide. The human peptide consists of a linear chain of 31 amino acids that have the sequence, from amino to carboxyl, H2N-Glu-Ala-Glu-Asp-Leu-Gln-Val-Glu-Gln-Glu-Leu-Gly-Gly-Gly-Pro-Gly-Ala-Gly-Ser-Leu-Gln-Pro-Leu-Ala-Leu-Glu-Gly-Ser-Leu-Gln-OH. This is readily comprehensible to most chemists because the abbreviations are typically the first three letters of the amino acid. Thus, alanine is Ala and arginine is Arg. Aspartic acid and asparagine cannot both be named Asp so the latter is distinguished as Asn. 

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