Q: One letter code for Sugars



 Dear CCL-List,
 I am modelling oligosaccharide on proteins and had to build up a
 residue library (within AMBER), where I could use only 3 letters
 for the residues.
 Is there any standard way of naming sugar-units in oligosaccharides ?
 I used  a code were:
 - the first letter is a code for the sugar type (M=Man, G=Glc,
 N=GlcNAc, K=Gal, S=sialic acid...)
 - the second is the glycosidic linkage type (A=alpha, B=beta, N=alpha
 with N as different partial charges ...)
 - the third is the type of linkage to other sugars (1=only at 1,
 2= 1 and 2, 6=1 and 6, A=1,2 and 6, Z= 1,2,3,4 and 6)
 eg:
          1- a-D-Man    4 - a-D-GlcNAc 1(N) --- ASN
           |    MA1          |          NN4
          2                      1
 a-D-Gal 1 ----- 6  b-D-Man 2 --- 1 a-D-Man
        KA2                MBA                 MA1
 For the sugar code I just used a letter which does not interfere with the amino
 acids. But, do you know if there is a default one
 letter code for saccharides ?
 Thanks for any comments and suggestions
 Johannes
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 John Curtin School of Medical Research
 Australian National University
 Dept. Biochemistry and Molecular Biology
 PO Box 334
 Canberra, ACT 2612, Australia
 Tel: +61 2 6279 8301
 Fax: +61 2 6249 0415
 EMail: johannes.zuegg -8 at 8- anu.edu.au
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