GlyTorsion: Analysis of Carbohydrate Torsion Angles found in the Protein Data Bank (PDB)
Introduction
Such as protein conformation can be described by the backbone torsion angles, a carbohydrate structure is mainly characterised by its linkage torsions. With the aid of pdb2linucs, a dataset of carbohydrate torsion angles was derived from from carbohydrate structures found in the PDB.
This weekly updated dataset contains, besides linkage torsions, also ring torsions, omega torsions, N-acetyle group torsions and sidechain torsions of Asn residues involved in Glycan bonds. It can be queried by GlyTorsion.
The same data is used by carp to generate PDB-derived plot backgrounds.


General Settings

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Structure Viewer: Jmol
Chime
Viewer Size:  x  pixel
Resolution (Å) Only torsions received from pdb-files with an resolution better or equal to the selected value are analysed.
To switch off resolution check, put in "0.0"
Experimental Method:
Chain type
Chain length Defines the minimal number of monosaccharides which the chain a torsion belongs to consists of.
Type in "0" to switch off chain length check.
Angle1 Range
Angle2 Range

Linkage Torsion Analysis

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Linkage Type:
-( )-
-( )-
Wildcards:
* matches anything,
? matches any single character.
Definition of linkage angles:
NMR definition:
Φ phi: H1-C1-O1-C′X
Ψ psi: C1-O1-C′X-H′X
ω omega: O1-C′6-C′5-H′5
Crystallographic definition:
Φ phi: O5-C1-O1-C′X
Ψ psi: C1-O1-C′X-C′X+1
ω omega: O1-C′6-C′5-O′5
further info
Angle 1:
Angle 2:
Output Type:


Ring Torsion Analysis

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Pyranose Rings
  Angle 1:  
  Angle 2:  
  Residue:    
Furanose Rings
  Residue:    
  Angle 1:  
  Angle 2:  
Omega Torsions
  Residue:   Definition of omega torsions:
O5-C5-C6-O6
Output Type:




NAc Torsion Analysis

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Residue:  
Angle 1: Definition of NAc torsions:
ω2a omega2a: Cn-1-Cn-NNAc-CNAc
ω2b omega2b: Cn-NNAc-CNAc-ONAc
Angle 2:
Output Type:




ASN Torsion Analysis

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Angle 1: Definition of ASN Torsion Angles:

Χ1 Chi1: N-Cα-Cβ-Cγ
Χ2 Chi2: Cα-Cβ-Cγ-O
Angle 2:
Output Type:








When citing glytorsion, please refer to:

 Lütteke T , Frank M , von der Lieth CW:
Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB
Nucleic Acids Res 2005, 33: D242-6.

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