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Protein Feature Accent Explanation


The Protein Feature Accent tool utilizes JSmol, a javascript framework that displays 3D molecular structures. Our implementation is based on HTML5, and thus does not require your browser to have Java installed.

The Protein Feature Accent tool allows you to:

Input page

On the Protein Feature Accent input page, you can provide two inputs:

  1. PDB structure
    • Choose from the short list of protein structures provided.
    • Choose from the long list of protein structures provided.
    • Or upload a PDB structure for ones not in the list.
  2. Alignment (optional)
    • You may provide your own alignment of protein sequences. These sequences must be for the same protein of the structure you are viewing.
    • If you leave this input blank, you will be shown a reference sequence, aligned to the PDB sequence of the protein being viewed.
Viewing the structure

After you hit "Submit", the tool will display a window that provides many options:

How to type lists of residues

A set of residues can be typed in the 'Highlight residue numbers' box using the following rules:
You can indicate an interval of residue numbers, i.e., residue numbers 112 through 123, using a dash: '112-123'.
Separate residues can be indicated with a comma-separated list: '240, 256, 258'. Spaces after commas are fine.
These two formats can be combined: '112-123, 240, 256, 258'.


The Protein Feature Accent tool identifies potential N-linked glycosylation sites (also called sequons or PNGs) that match the Nx[TS] motif, where 'x' can be any amino acid except proline. The asparagine (N) α-carbon is marked in the graphic. For a more complete analysis of glycosylation sites in your protein sequence set, try the N-GlycoSite tool.

See also Gavel & von Heijne, 1990, Zhang et al., 2004

Carbohydrate glycosylation structures

For certain structure files, such as the SIV gp-120 protein structure 2BF1, full glycosylation structure information is present. In these cases, an option to display these carbohydrates is offered. Note that for two of the display styles, 'cartoon' (the default view) and 'rocket', these carbohydrate structures do not appear. They reappear when the view is switched to one of the other display styles.


When you submit an alignment to the tool, the Shannon entropy is calculated for each alignment column. This information can be visualized on the Jmol graphic by selecting the 'entropy' option under the menu labeled 'pick color scheme'. Zero- and low-entropy residues are colored a 'cool' color (e.g., blue-green), and higher entropy residues are shown in shades of yellow, orange, and red. Residues for which an entropy cannot be calculated (for instance, residues which correspond to an all-gap column in the alignment sequences you provide) are colored a distinctive 'cold' color (e.g., dark blue).

PDB model file upload

You can upload a Protein Data Bank model file and the tool will display your model instead of one of our stored protein models. The tool will extract and display the protein sequence from the PDB file you provide, and you can highlight residues in the graphic by selecting them as usual. If you provide a sequence or an aligned set of sequences, the tool will align the PDB file sequence to your sequence(s) and display the alignment.

last modified: Mon Nov 9 14:45 2015

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