Site

Sites Green LinksSites Green Links

The Sites green links in Proteopedia highlight the residues (as sticks) that make up functional sites. You may have to zoom in to see them clearly. For example, at the Main Page (or if not there, at 1eve), below the molecule, are green links to highlight a catalytic site, and an inhibitor binding site. These two sites were abbreviated in the atomic coordinate file as CAT and IHB, respectively. Clicking on the green links displays the full name of the site immediately below the molecule.

Identifying Residues in SitesIdentifying Residues in Sites

You can identify the residues in the site by touching them (not clicking them) with the mouse. A small box, called a "hover report", will appear in a few seconds, identifying the atom, residue, and chain touched with the mouse. Any atom can be identified in this way, regardless of whether it is in a site. In order to be sure you have touched the intended atom, you must be careful that the mouse is not near other atoms. This is best accomplished by positioning the molecule so that the atom of interest has nothing in front of it, and has only blank background behind it.

Missing SitesMissing Sites

In order for Proteopedia to be able to highlight functional sites, the authors of the atomic coordinate file must have defined these sites when the file was published. Often, authors may not have defined known functional sites in the atomic coordinate file when they published it. Sometimes, the structure may have been determined before functional sites were known, and hence they will be absent in the atomic coordinate file. Thus, the absence of green links for Sites does not mean that there are no functional sites.

Of course, in Proteopedia, when a known functional site was not included in the atomic coordinate file, it is relatively easy to add a green link that shows it.