"Frank O. Fackelmayer" wrote:
> ChenHA wrote:
>> > On 16 Feb 2000, Mina wrote:
> > > Recently, I found a consensus sequence described as : psi - K - X - E.
> > > Can somebody tell me which amino acids belong to "psi", what
> > > classification is that or just point me to a reference.
> > >
> > one possibility is that psi stands for pseudo - i.e. it means that the
> > amino acids may be a pseudo-amino acid such as pseudo-proline or
> > whatever residue that is unnatural or unusual. For example, the CO
> > or NH group may be replaced by CH2 group so that the peptide bond
> > becomes non-hydrolysable, or the side-chains has other atoms or groups
> > attached or replaced.
>> If it was phi instead of psi, I´d guess it stands for hydroPHobic. I´ve
> seen this nomenclature someplace, but i´ve not been able to find it as a
> standard (IUPAC) assignment. Hydrophobic amino acids are those with
> aliphatic side chains, like e.g. leucine
I had a dig round and found the IUPAC nomenclature at the following:
3AA-19.7. Peptide Analogues
Analogues of peptides in which the -CO-NH- group that joins residues is
replaced by another
grouping may be indicated  by placing a Greek psi, followed by the
replacing group in parenthesis,
between the residue symbols where the change occurs. Examples:
Ala-[psi](NH-CO)-Ala for NH3+ -CHMe-NH-CO-CHMe-COO-
Ala-[psi](CH=CH,trans)-Ala for NH3+ -CHMe-CH=CH-CHMe-COO-
Which is close to what I said. However, the problem is that the original
question was for a consensus sequence, therefore this may not quite fit. I
think that the questioner should read the original paper in which it appears
and there may be better clue as to its meaning.