GlyTorsion is a program for statistical analysis of glyco-relevant torsion angles derived from the Protein Data Bank (PDB).

General Settings

The General Settings section defines parameters valid for all torsion analyses. These comprise settings specifying the structures to be analysed, like min. resolution or the type of carbohydrate chains (glycan/ligand) as well as settings influencing output appearance, like the angle range used for plots. This option is useful if most hits are located at an edge of the plot. Then you can shift the output range, e.g from -180 - 180 to -120 - 60 to move the most frequently observed angles towards the center of the plot.
Furthermore, you can use this option to adjust output to the angle range you are most familar with.
In this section, you can also select your preferred structure visualisation program, the Java applet Jmol or the plugin Chime, and adjust the size of the structure viewer to your screen resolution.

Linkage Torsion Analysis

In addition to the general settings described above, the analysis of linkage torsion angles needs some further parameters:

• Linkage Type
  The linkage is defined by the two residues involved in the linkage and the kind of linkage (1-2, 1-3, 1-4, ...). These data can be selected from the pull-down menus or entered directly. Selection from the menus needs java-script to copy the selected value into the field for direct input. There, it can be modified after selection, e.g. to choose sulfated residues. The wildcards * (matches anything) and ? (matches any single character) are allowed within the queries. ?-D-Glcp, for example, matches both a-D-Glcp and b-D-Glcp, while b-D-Glcp* matches any residue starting with "b-D-Glcp", including b-D-Glcp itself as well as modifications like b-D-GlcpNAc, b-D-GlcpA or b-D-Glcp4SO3.
  Examples:
  
  • b-D-GlcpNAc-(1-4)-b-D-GlcpNAc: Gif - SVG
  • a-D-Neup5Ac-(2-3)-b-D-Galp: Gif - SVG
  • a-D-Man-(1-3)-a-D-Manp: Gif - SVG


• Definition of linkage angles
  Linkage torsion angles can be defined in several ways. In GlyTorsion, you can choose between the NMR-like definition and the crystallographic definition (more info).


• Angles
  Here you can select the angles that shall be analysed. Phi and psi angles can be investigated for all linkages, omega torsions only for 1-6 or 2-6 linked residues, of course.


• Output type
  GlyTorsion offers a series of different kinds of output appearance. Scattered plots of angle pairs or diagrams of single angles are offered in GIF and SVG format, plots illustrating the frequency of torsion angles can be obtained in GIF, SVG and in addition in html format.
  Beyond the graphic representations results can be displayed as plain text list or tables.

Ring Torsion / NAc Torsion Analysis

In the Ring Torsions section you can investigate the torsions within pyranose rings or furanose rings, or the omega torsion angles, NAc torsion analysis investigates the torsion angles of NAc groups. Alike to the Linkage Torsions, residues can be selected from a pull-down menu or entered directly. Again, the wildcards * and ? are allowed.
For output options, please see the description within the Linkage Torsions section above.

ASN Torsion Analysis

ASN torsion analysis explores the sidechain torsion angles of Asn residues, to which glycan chains are bound.
Output options are the same as described within the Linkage Torsions section.

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Torsion Selection

On the results page you can select angles by specifying a min. and max. angle value. For example, you may be interested in a further investigation of linkages where phi is between -120 and -80 and psi is between 30 and 40.
You can enter these limitations manually or, if you have selected the html plot output, by clicking the upper left corner of the range you want to select, keeping the mouse-button pressed while moving your mouse to the lower right corner and releasing the button there. Afterwards, the respective values should appear in the input form below the plot.
Beneath that you can select which properties of the selected torsions, e.g. angles, PDB id, resolution, etc., shall be displayed in the results list, and by what the list is sorted.
After submitting this form, you will receive a list of the selected torsions. Here, you can click on an angle value to view the associated PDB structure (the selected angle highlighted) using the structure viewer selected in the first step. Below the structure, there is a button to switch between the structure viewers Jmol and Chime with one click.