Reactive Protein Residues Panel

In this panel you can identify reactive sequences in the Workspace structure, by matching them to extended PROSITE patterns that define the reactive sites.

To open this panel, click the Tasks button and browse to Biologics → Reactive Residues.

  • Using
  • Features
  • Additional Resources

Using the Reactive Protein Residues Panel

Reactive residues are identified by matching residue patterns in the sequence. Six patterns are provided by default, for the common reactions: Deamidation, Oxidation, Glycosylation, Isomerization, Free Cysteine, and Proteolysis. You can use these patterns or you can set up and use your own (as a User-defined pattern).

The main workflow in this panel is:

  1. Display the protein you want to analyze in the Workspace
  2. Select options for the reactive residues to identify
  3. (Optional) Define your own reactive residues
  4. Click Analyze Workspace to run the analysis
  5. Examine the results in the table or the Workspace, or both.

To run a reactive residue analysis from the command line, you can use the following command. Run the command with -h for more information.

$SCHRODINGER/run reactive_protein_residues.py

For information on command options, see reactive_protein_residues.py Command Help.

Reactive Protein Residues Panel Features

Analyze Workspace for sequences options

Select an option for the sequences to identify as reactive in the Workspace structure. Though all options are selected by default, you can select one or multiple options from the menu:

  • Deamidation Site
  • Oxidation Site
  • Glycosylation Site
  • Proteolysis Site
  • Asp Isomerization Site
  • Free Cysteine Site
    • Edit patterns button

    Add, edit, or delete patterns that define reactive sites. Opens the pattern, pattern-matching, pattern matching, PROSITE, pattern table, in which you can change the definition of the patterns that define a reactive protein site. The patterns are specified in extended PROSITE syntax, a description of which is given in the panel. A pattern is defined by a name, a definition, and an optional hotspot. See PROSITE, syntax, patterns, reactive residues, motif, motifs for more information. The hotspot is the residue in the pattern that is to be selected instead of the entire pattern, and is defined by the index of the residue in the pattern (starting from 1 for the first residue).

Analyze Workspace button

Click this button to analyze the Workspace structure for its reactive groups. The results are presented in the table below, and the reactive sites are marked with spheres in the Workspace that are colored according to the type of reactive site.

Matched reactive sites table

This table lists the results of the analysis, with the number of matches displayed below the table. You can sort the table by clicking in the heading of the column you want to sort by. Scroll within the table to display additional results.

Type Type of reactive site
Residues Reactive residue identity (chain, residue number and insertion code, 3-letter residue name)
SASA Solvent-accessible surface area of the residue.
Exposure Solvent exposure of the residue (percentage of the surface that is solvent-exposed)
B Factor PDB temperature factor for the residue, if available. The value given is the average over all atoms in the residue.

Note on SASA values: There is no consensus on the ideal SASA cut-off value. A suitable cut-off depends on the goal of the analysis. A small cutoff (10%-20%) may be appropriate if the goal is to identify any residues that are likely to participate in interfacial interactions whereas a >50% cut-off has been recommended in some studies [19] intended to identify residues that pose significant aggregation risk.

Workspace legend

The reactive groups are listed here, colored with the colors used in the Workspace to highlight the reactive residues. Clicking on the color squares in the Workspace Legend will open the Select Color dialog box, where basic and custom colors can be chosen for each type of residue site. Changing the legend color for a residue type will also update the color of the corresponding residues in the Workspace.

Fit to Workspace option

When you select a reactive residue in the table, zoom in on that residue in the Workspace. This option is selected by default.

Filter

Opens a panel with options to filter sites shown in the Matched reaction sites table. Click Apply after making selections to apply any filtering criteria to the table.

Site type

Select from the list of site types and new patterns defined by the user. Only the first four are shown in the list, scroll to view additional site types.

Show only residues with solvent exposure >= N text box

Show in the table and the Workspace only the sites that have a solvent exposure that is greater than the specified percentage. The default value is 15.

Show only residues with B-factor >= X text box

Show in the table and the Workspace only the sites that have a PDB temperature factor (B-factor) that is greater than the specified value. The default value is 0.

Reset button

Clears the Filter panel of all settings and data. This button is disabled if the filter is at its default settings.

Reset Panel button

Clear the panel of all settings and data.

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