Subject: One letter code for Sugars

From: "Johannes Zuegg" <[email-masked]>
Date: Wed, 14 Oct 1998 08:57:01 +0000

Dear Net,

I'm modelling oligosaccharide and built a residue library (for AMBER) 
where I am restricted to a three letter code for the sugar residue, 
ending up with the following code: 

- The first letter is a code for the type of sugar (M=Man, G=Glc 
S=silaic acid, H=GlcNAc ... I used just letters which do not interfer 
with the amino acids), 
- thes econd for the glycosidic conformation (A=alpha, B=beta, 
N=N-alpha as the partial charges are different,....) and 
- the third is for the linkage (1= only at 1,  
2=at 1 and 2,... A=at 1,2 and 6, ... Z= at 1,2,3,4 and 6 ).

a-Glc 1----4 b-Man 1 ---- 3 a- Man 1 ----
 GA1             MB4              MA3

My questions is, are there any one letter code for the saccharide 
type, as I used just one which doesn't interfer with the amino acids, 
and/or is there already a standard three letter code 
for oligsaccharides?

Thanks
Johannes

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