Amino Acids - special amino acids

Proline

The carbon atoms in proline are numbered as in pyrrolidine, the nitrogen atom being numbered 1, and proceeding towards the carboxyl group.

Aromatic Rings

The carbon atoms in the aromatic rings of phenylalanine, tyrosine and tryptophan are numbered as in systematic nomenclature, with 1 (or 3 for tryptophan) designating the carbon atom bearing the aliphatic chain. The carbon atoms of this chain are designated alpha (for the carbon atom attached to the amino and carboxyl groups) and beta (for the atom attached to the ring system).
Note. This numbering should also be used for decarboxylated products (e.g. tryptamine).

Histidine
The nitrogen atoms of the imidazole ring of histidine are denoted by pros ('near', abbreviated (pi) ) and tele ('far', abbreviated (tau) ) to show their position relative to the side chain. This recommendation [6,10] arose from the fact that two different systems of numbering the atoms in the imidazole ring of histidine had both been used for a considerable time (biochemists generally numbering as 1 the nitrogen atom adjacent to the side chain, and organic chemists designating it as 3). The carbon atom between the two ring nitrogen atoms is numbered 2 (as in imidazole), and the carbon atom next to the (tau) nitrogen is numbered 5. The carbon atoms of the aliphatic chain are designated alpha and beta as in 2.2.1 and 2.2.3 above. This numbering should also be used for the decarboxylation product histamine and for substituted histidine.

Definition of Side Chain

When amino acids are combined in proteins and peptides, C-l, C-2 and N-2 of each residue (the numbering being that of aliphatic amino acids) form the repeating unit of the main chain ('backbone') and the remainder forms a 'side chain'. Hence the words 'side chain' refer to C-3 and higher numbered carbon atoms and their substituents.
 

Use of the Prefix 'homo'

An alpha-amino acid that is otherwise similar to one of the common ones (Table 1), but that contains one more methylene group in the carbon chain, may be named by prefixing 'homo' to the name of that common amino acid. 'Homo' in the sense of a higher homologue (F-4.5 of [15]) is commonly used for homoserine (2-amino-4-hydroxybutanoic acid) and homocysteine (2-amino-4-mercaptobutanoic acid).
 

Use of the Prefix 'nor'

The prefix 'nor' denotes removal of a methylene group (Sections F-4.2 and F-4.4 of [15]), but this is not the sense in which it has been used in the names 'norvaline' and 'norleucine'. Such names, although widely used, may therefore be misinterpreted, so we cannot recommend them, especially since the systematic names for the compounds intended, 2-aminopentanoic acid and 2-aminohexanoic acid, are short.


Source: http://www.chem.qmul.ac.uk/iupac/AminoAcid/AA1n2.html#AA1