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The tables below list the current capabilities of the GLYCAM-Web parameter sets.
Note: these capabilities might differ slightly from those of the point-and-click builder. They should mostly work using the text and URI (URL) builders.
Tables in this document:
- Glycan residues available
- Reducing-end aglycon residues available
- Derivative residues available.
- Common synonymous abbreviations
Table 1: Glycan Availability Table
Table Legend:
- TLC = the “three-letter” code commonly used as an abbreviation for the residue. Note that these are not always three letters in length. But, most are.
- GC = the GLYCAM one- or two-letter code, “none” if there is none.
- Ready = Yes or no: Is this residue currently available?
- Residues due to be released soon are included in this manner.
- Pyr = Abbreviation for the pyranose form if available, “NA” if not
- Fur = Abbreviation for the furanose form if available, “NA” if not
- #C (main) = Number of carbons in the main saccharide chain. That is, although GlcNAc technically contains 7 carbons, it is still a hexose, so the number listed in this column is 6.
- Ano = Anomeric position (1 for aldoses and typically 2 for ketoses)
- Name = Unabbreviated common name.
- Forms and Linkages = linkages available for each available form.
- The available linkages must pair with the forms available.
- Forms consist of three letters:
- First letter: a or b for alpha or beta
- Second letter: D or L for the D or L form
- Third letter: p or f for pyranoside or furanoside
- If a field is omitted, then the specified linkage list applies to both forms. For example:
- “ap” means that the list applies to both the D and L forms, but only for the alpha pyranoside.
- “p” means that the list applies to all variants of alpha, beta, D & L for the pyranoside form.
- “aLp” means the list applies only to the L enantiomer of the alpha pyranoside.
- If a form combination is not listed, then that combination is not available at all.
- Linkage lists refer to all linkage positions and combinations of positions that are available for the indicated form.
- See the notes after the table for a legend.
- If the anomeric position is listed in the attachments list, then this residue can be specified as the reducing-end-terminal residue for anomeric-anomeric linking.
| TLC | GC | Ready | Pyr | Fur | #C (main) | Ano | Name | Forms and Linkages | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| All | N | Y | Allp | NA | 6 | 1 | allose |
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| Alt | E | Y | Altp | NA | 6 | 1 | altrose |
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| Ara | A | Y | Arap | Araf | 5 | 1 | arabinose |
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| Fru | C | Y | Frup | Fruf | 6 | 2 | fructose |
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| Fuc | F | Y | Fucp | NA | 6 | 1 | fucose |
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| Gal | L | Y | Galp | NA | 6 | 1 | galactose |
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| GalA | O | Y | GalpA | NA | 6 | 1 | galacturonate |
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| GalNAc | V | Y | GalpNAc | NA | 6 | 1 | N-acetylgalactosamine |
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| Glc | G | Y | Glcp | NA | 6 | 1 | glucose |
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| GlcA | Z | Y | GlcpA | NA | 6 | 1 | glucuronate |
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| GlcNAc | Y | Y | GlcpNAc | NA | 6 | 1 | N-acetylglucosamine |
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| Gul | K | Y | Gulp | NA | 6 | 1 | gulose |
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| Ido | none | N | NA | NA | 6 | 1 | idose | |||||
| IdoA | U | Y | IdopA | NA | 6 | 1 | iduronate |
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| KDN | none | N | NA | NA | 9 | 2 | 2-keto-3-deoxy-nonulosonate | |||||
| KDO | none | N | NA | NA | 8 | 2 | 2-keto-3-deoxy-octulosonate | |||||
| Lyx | D | Y | Lyxp | Lyxf | 5 | 1 | lyxose |
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| Man | M | Y | Manp | NA | 6 | 1 | mannose |
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| ManNAc | W | Y | ManpNAc | NA | 6 | 1 | N-acetylmannosamine |
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| Neu5Ac | SA | Y | Neup5Ac | NA | 9 | 2 | 5-N-acetylneuraminate |
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| Neu5Gc | GL | Y | Neup5Gc | NA | 9 | 2 | 5-N-glycolylneuraminate |
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| Psi | P | Y | Psip | Psif | 6 | 2 | psicose |
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| Qui | Q | Y | Quip | NA | 6 | 1 | quinovose |
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| Rha | H | Y | Rhap | NA | 6 | 1 | rhamnose |
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| Rib | R | Y | Ribp | Ribf | 5 | 1 | ribose |
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| Sor | B | Y | Sorp | Sorf | 6 | 2 | sorbose |
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| Tag | J | Y | Tagp | Tagf | 6 | 2 | tagatose |
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| Tal | T | Y | Talp | NA | 6 | 1 | talose |
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| Xyl | X | Y | Xylp | Xylf | 5 | 1 | xylose |
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Key to attachment locations:
All codes below, except as noted, indicate an open valence at the anomeric carbon. That is, all except those noted possess the linkage capability in the “0” (zero) residue.
Numbers:
- 0 (zero): The residue has open valence only at the anomeric carbon. It can be used only to terminate the non-reducing end of a chain.
- 1 (one) might mean:
- If 1 is NOT the anomeric position: The residue has open valence at the anomeric carbon and at O1 (oxygen 1).
- If 1 IS the anomeric position: The residue has open valence ONLY at O1 (oxygen 1).
- 2 (two) might mean:
- If 2 is NOT the anomeric position: The residue has open valence at the anomeric carbon and at O2 (oxygen 2).
- If 2 IS the anomeric position: The residue has open valence ONLY at O2 (oxygen 2).
- 3 – 9 (three through nine):
- The residue has an open valence at its anomeric carbon and at the oxygen corresponding to the number.
Letters:
Letters correspond to residues with multiple linkage points. The oxygens that have open valences are listed. All letters also imply an open valence at the anomeric carbon.
- A: 9,8,7,4
- B: 9,8,7
- C: 9,8,4
- D: 9,7,4
- E: 8,7,4
- F: 9,8
- G: 9,7
- H: 8,7
- I: 9,4
- J: 8,4
- K: 7,4
- P: 2,3,4,6
- Q: 3,4,6
- R: 2,4,6
- S: 2,3,6
- T: 2,3,4
- U: 4,6
- V: 3,6
- W: 3,4
- X: 2,6
- Y: 2,4
- Z: 2,3
Table 2: aglycons
See the glycans table notes for a description of the table columns except for
“Formula”, the meaning of which is pretty obvious.
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TLC GC Ready Formula Name
================================================================================
@BEGIN_AGLYCONS
OH ROH Y -OH hydroxyl
OME OME Y -OCH3 O-methyl
OTBU TBT Y -OCH(CH3)2 O-tert-butyl
@END_AGLYCONS
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Table 3: GLYCAM synonyms table
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The table below provides common synonyms for some of the “TLC” codes in the
tables above.
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Recommended
“TLC” List of synonyms
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@BEGIN_SYNONYMS
Neu5Ac NeuNAc
@END_SYNONYMS
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