Chapter 3.  Protein Window

String Protein Window

One of the most important parts of String is the protein window: a popup window that appears whenever you click on a particular protein (i.e. when you click on the bubbles of the network or on the small coloured arrows in the other views) .
The protein window shows important information about the protein and also provide links to other sections of String or to other external websites.

The protein window is divided in two part: left and right.
Notice that the right part is displayed only when we have the protein structure (or a model of the protein structure) stored in our database.

Important Note:
For each String release we store in our database the images of crystallized protein (that we take from PDB) as well as the images of protein models (that we take from SwissModel).
Since both PDB and SwissModel are updated more frequently than String, we suggest to directly look for structures/models on the PDB (http://www.rcsb.org/pdb) and SwissModel (http://swissmodel.expasy.org/repository/) websites.

Left - part

The left part is composed by two sections: Actions and Information.

Actions

- Clicking on 'recenter the network on this node' you can recenter the network on the current protein (i.e. look for all the proteins in String that interact with the protein of the window). This is a shortcut with respect to move back to the input page and relaunch String with the corresponding protein identifier
- Clicking on 'add this node to the input node' adds to the network also the proteins that interact with the protein of the window. This is a shortcut with respect to moving back to the input page and relaunch String with both the identifiers (i.e. the input protein and the selected protein)

Information

A description of the protein is shown together with the External Identifier of the protein and a link to the corresponding entry in ENSEMBLE or UNIPROT
Just below the description you find the following links: - 'show protein sequence' opens popup window containing the amino acid sequence of the protein - 'homologs in STRING' brings to a String page where you can see all the homologs of your protein in the same and also in other organisms. - 'Pathway, Functions, Resources (GeneCards)' redirects to the relative entry in the GeneCards database [this link appears only for human proteins]. - 'Show protein domain (SMART)' redirects to the relative entry in the SMART database.

Right - part

Important Notes:
1) If flash player 10 (or greater) is not installed on your computer this part would appear differently from what described here.
2) If no crystal-structure or structure model can be found in our database for the protein (or for similar proteins), this part is not shown at all !
3) The image of the structure may be that of a protein that is similar in sequence to your protein (we also report the identity of the sequence alignment as it is explained below).

In the upper part you will see some coloured shapes placed on a line. The shapes represent different SMART domains and the line represents the protein sequence.
When no domains are found for the protein you just see a grey line with length proportional to the length of the protein sequence.
When the protein is longer than 800 amino acids you will see some dots at the beginning (or end) of the line, indicating that the protein is too long to be displayed on the window.
Clicking on the SMART image you will be redirected to the corresponding entry in the SMART database (http://smart.embl-heidelberg.de/).

Below the SMART domains you will see an image of the protein structure.
This can be either the image of a crystal structure (taken from PDB) or the model of the structure of the protein (taken from SwissModel). You can easily distinguish these two cases simply looking at the small logo just below the structure.
Clicking on the structure you will be redirected to the corresponding entry in the PDB (or SwissModel) database.

Usually the image of the protein structure represents only a section (e.g. a domain) of the protein. To illustrate this we draw an arrow that connects a section of the SMART image to the structure, indicating the region of the protein that is represented by the structure image.
Sometimes a protein may contain more than one identical domain. In this case you will see several arrows connecting different parts of the protein to the structure.

Just for the PDB structures we show the image of the whole protein structure, when this is available. In this case, pointing the mouse cursor over the image will change the image of the whole protein structure with the image of the chain (i.e.the structure of only that part of the protein indicated by the arrow).

When more than a structure/model is present for a protein, two little arrows appear at the bottom. You can click on those arrows to move between the different structures.

For both PDB and SwissModel we indicate the "identity". The identity refers to the alignment of the String protein with the PDB protein.
This alignment is the result of an all-against-all blast search that we execute for all the String proteins against all the PDB proteins (for the SwissModel's protein a similar alignment against PDB templates is performed by the swissModel group).
For this reason, only when you see an identity of 100% you can be sure that you are displaying an image of the structure of your protein (and not of a similar one) !