CONTENTS

Introduction

Part I NOMENCLATURE

Part 1, Section A: Amino-Acid Nomenclature

3AA-1 Names of Common α-Amino Acids
3AA-2 Formation of Semisystematic Names for Amino Acids and Derivatives
- 2.1 Principles of forming names
- 2.2 Designation of locants
  - 2.2.1 Acyclic amino acids
  - 2.2.2 Proline
  - 2.2.3 Aromatic rings
  - 2.2.4 Histidine
  - 2.2.5 Definition of side chain
- 2.3 Use of the prefix 'homo'
- 2.4 Use of the prefix 'nor'
3AA-3 Configuration at the α-Carbon Atom
- 3.1 Use of D and L
- 3.2 Position of prefix
- 3.3 Omission of prefix
- 3.4 Subscripts to D and L
- 3.5 The RS system
- 3.6 Amino acids derived from amino sugars
- 3.7 Use of meso
- 3.8 Use of DL
3AA-4 Configuration at Centres other than the α-Carbon Atom
- 4.1 The sequence rule
- 4.2 Carbohydrate prefixes
- 4.3 Use of cis and trans
- 4.4 Use of 'allo'
- 4.5 Designation of centres with unknown configurations
- 4.6 Other stereochemical features
3AA-5 Optical Rotation

Part 1, Section B: Nomenclature of Non-Peptide Derivatives of Amino Acids

3AA-6 Ionization of Functional Groups and Naming of Salts
3AA-7 Amino Acids Substituted on Nitrogen
3AA-8 Side Chain Modifications (excluding modifications of carboxyl or nitrogen)
3AA-9 Esters and Amides of the Carboxyl Group
- 9.1 Esters
- 9.2 Amides, anilides and analogous derivatives
- 9.3 Acyl groups
3AA-10 Carboxyl Group Modifications other than Ester and Amide Formation
- 10.1 Removal of the carboxyl group
- 10.2 Ketones
- 10.3 Aldehydes and alcohols

Part 1, Section C: Peptide Nomenclature

3AA-11 Definitions of Peptides
3AA-12 Amino-Acid Residues
- 12.1 Definitions of residues
- 12.2 Ionized forms of residues
3AA-13 The Naming of Peptides
- 13.1 Construction of names
- 13.2 Use of prefixes in peptide names
- 13.3 Names of simple polymers of amino acids
- 13.4 Numbering of peptide atoms
- 13.5 Prefixes formed from peptide names
- 13.6 Conformations of polypeptide chains

Part 2, SYMBOLISM

Part 2, Seetion A: The Three-Letter System

3AA-14 General Considerations on Three-Letter Symbols
3AA-15 Symbols for Amino Acids
- 15.1 Symbols for common amino acids
- 15.2 Symbols for less common peptide constituents
  - 15.2.1 Hydroxyamino acids
  - 15.2.2 Alloisoleucine and allothreonine
  - 15.2.3 'Nor' amino acids
  - 15.2.4 'Homo' amino acids
  - 15.2.5 Higher unbranched amino acids
  - 15.2.6 Carboxylated and oxidized amino acids
  - 15.2.7 Non-amino-acid residues in peptides
3AA-16 Symbolism of Amino-Acid Residues
- 16.4.1 Monocarboxylic acids
- 16.4.2 Dicarboxylic acids
16.5 Cyclic derivatives of amino acids

3AA-17 Substituted Amino Acids

3AA-18 Symbols for Substituents

3AA-19 Peptide Symbolism

19.1 Peptide chains
19.2 Use of configurational prefixes
19.3 Representation of charges on peptides
19.4 Peptides substituted at N-2
19.5 Cyclic peptides
- 19.5.1 Homodetic cyclic peptides
- 19.5.2 Heterodetic cyclic peptides
19.6 Depsipeptides
19.7 Peptide analogues
19.8 Alignment of peptide and nucleic-acid sequences

Part 2, Section B: The One-Letter System

3AA-20 The Need for a Concise Representation of Sequence
- 20.1 General considerations on the one-letter system
- 20.2 Limits of application of the one-letter system
3AA-21 Description of the One-Letter System
- 21.1 Use of the code
- 21.2 The code symbols
- 21.3 Spacing
- 21.4 Known sequences
- 21.5 Punctuation in partly known sequences

Part 3, MODIFICATION OF NAMED PEPTIDES

3AA-22 Names and Symbols for Derivatives of Named Peptides
- 22.1 Replacement of residues
- 22.2 Extension of the peptide chain
- 22.3 Insertion of residues
- 22.4 Removal of residues
- 22.5 Substitution of side chains of residues
  - 22.5.1 Acylation of a side-chain amino group
  - 22.5.2 Other substituents named as prefixes
  - 22.5.3 Acylation by a side-chain carboxyl group
- 22.6 Partial sequences (fragments)
- 22.7 Peptides with reversed sequence and enantiomers
- 22.8 Peptide analogues
- 22.9 Summary of modification nomenclature

Appendix. Amino Acids with Trivial Names

Addenda

1 Amide derivatives of amino acids and peptides
2 Selenium in peptides
3 Use of seco- in partially hydrolysed peptides
4 Structure formed by elimination of water between a β-carboxyl group and an α-NH group

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