From chemistry-request%!at!%www.ccl.net Wed Oct 14 19:27:31 1998 Received: from anugpo.anu.edu.au (anugpo.anu.edu.au [150.203.2.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA00705 Wed, 14 Oct 1998 19:27:28 -0400 (EDT) Received: from hannes.anu.edu.au (hannes.anu.edu.au [150.203.193.229]) by anugpo.anu.edu.au (8.8.8/8.8.8) with SMTP id JAA04400 for ; Thu, 15 Oct 1998 09:27:15 +1000 (EST) Message-Id: <199810142327.JAA04400 ^at^ anugpo.anu.edu.au> From: "Johannes Zuegg" Organization: JCSMR To: CHEMISTRY |-at-| www.ccl.net Date: Thu, 15 Oct 1998 09:26:09 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Q: One letter code for Sugars Reply-to: johannes.zuegg |-at-| anu.edu.au Priority: normal 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 --------------------------------------------------------------------- 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;at;anu.edu.au ---------------------------------------------------------------------