Crystallography Department, Birkbeck College - Peptaibol Database: Nomenclature

Amino acid codes

Peptaibols contain non-standard amino acid residues. Currently, there are four types contained within this database. The names, three and one letter codes for these unusual peptides are :

RESIDUE NAME	3 LETTER CODE	1 LETTER CODE
Aminoisobutyric Acid	Aib	U
Ethylnorvaline	EtN or EtNor	Z
Isovaline	Iva	J
Hydroxyproline	Hyp	O

Undetermined residues

Occasionally, entries contain residues which weren't completely resolved. Two such types of entry occur in the database :
Where leucine could not be distinguished from isoleucine, records are marked Lx or Lxx.
Where valine could not be distinguished from isovaline, records are marked Vx or Vxx.

Unfortunately the one letter code system has to suffer here as we have run out of letters. This does not affect the efficiency of the database though.

N-terminal groups

The N-terminus of a peptaibol is an an alkyl group, this is predominantly the acetyl group although other groups are known. The following descriptions appear within the database :

GROUP SYMBOL	GROUP NAME
Ac	Acetyl
AHMO	(2S, 4S)-2-amino-6-hydroxy-4-methyl-8-oxodecanoic acid
Oc	Octyl
Dec	Decanyl
MDA	(2R)-methyldecanoic acid
Z	Benzyloxycarbonyl
(Z)-4-decenoyl-	Branched decanyl

C-Terminal groups

Peptaibols have unusual C-terminal groups. Mainly, the c-terminal residue is reduced to an amino alochol. I.E. the COOH group becomes CH₂OH.

The nomenclature we use for this is to treat the hydroxyl group as a seperate entity, thus labelling valinol (hydroxylated valine) as Val-OH. This system holds for all residues, even the unusual ones and the undetermined ones.
i.e. Aib-OH and Lxx-OH.
The one letter code sequences adopt the same system, hence the analogous examples would be V-OH , U-OH , Lx-OH.

Some peptaibols have other C-terminal groups, when these occur, they are included in a chemical nomenclature. Occasionally, a sequence contains the Tdol C-terminus, Tdol is an abbreviation for Trichodiaminol.

This nomenclature is adopted for the smooth running of the searching tools. Other nomenclatures for C-terminal groups will become apparent within the literature.