Output descriptions

• Residue based analysis
  In this step, the frequency of amino acids around monosaccharides with properties matching those defined in the Analysis Parameters is determined.
  Results are displayed in a table and, if selected, additionally in a graphical form. Possible graphic formats are SVG (Scalable Vector Graphics) ? and GIF.
  Three different representations of results can be requested:
  
  1. Absolute numbers:
     This mode list the number of hits for each kind of amino acid.
  2. Percentage:
     Here, the absolute numbers are devided by the total number of amino acids analysed to derive the relative frequency of each amino acid type.
  3. Deviation from standard percentage values:
     To be able to easily judge amino acid frequencies, this mode shows the deviation of the observed frequencies from those expected for average structures.
  A click on an amino acid name in the results table reveals a list of carbohydrate - amino acid atom pairs forming the closest contacts between the involved residues (see next step). Below the results table, a link showing this list for all amino acids at once is offered.


• Atom-Pair based analyis
  Here, a statistic on the atoms involved in the closest contacts between monosaccharide and amino acid residues is performed. Counts are grouped by atom names. Since these names are not standardised in the HETATM records of pdb-files, carbohydrate atoms are renamed when generating the vicinity datasets from PDB entries. Amino acid atom names are taken over like they are present in pdb-files.
  Clicking on an atom name leads to a list of detailed results for this atom (see next step), clicking on a count value leads to the details on the respective atom pair.


• Detailed results list
  This mode lists details on PDB entries, carbohydrate chains, monosaccharide residues and amino acids matching the properties selected in the previous steps.
  Visualiation mode is reached by clicking on the PDB residue label of a carbohydrate residue or on the atom names within the amino acid section.


• Structure visualisation
  For 3D structure visualisation, the java-applet JMOL or the plugin CHIME can be used. The preferred tool can be selected at the GlyVicinty start page. This selection can be changed in this step, too.