Help: Interactions

Structures Back to top

The structures tab contains a table listing all structures containing an interaction between the two selected interacting-partners. This table contains the PBD identifier, the interacting chains, summary of the bonds found in the interaction, and two links to different visualizations of the interaction.

The row bond summary breaks down the type and number of bonds in the interaction.

Van der Waals (V) interactions are grouped by interacting residues, hence the slightly different representation. We count Van der Waals bonds at the residue rather than the atom level because they are general attractive forces that vary in strength based on the distance between two atoms. Thus, the close proximity of two amino residues tends to yield many van der Waals interactions. As a result, it keeps the bond table compact and the iPfam database more scalable. Hydrogen bonds with sidechains (Hs) and backbone (Hb), electrostatic (E) and covalent (C) counts reflect individual bonds between pairs of atoms. All bonds are defined based on both the geometric (distance, angle and planarity) and chemical properties (charge, polarity and size) of the atoms involved.

By selecting either the PDB ID or clicking on the ‘Structure’ button, you will be taken to the 3D rendering of the structure containing the interaction, the details of this page are described here. By clicking the ‘Sequence’ button, you will be taken to the graphical display that represents the interaction on the sequence in two-dimensions, described in the following section.

Sequences Back to top

The sequence display graphically represents the domain organization of each chain, with the positions of interacting residues indicated on a line below each domain organization graphic. Each vertical bar on this line indicates the position of a residue that is involved in forming the interaction interface, and is coloured according to the most energetically significant bond found at that position. To change the interaction currently being views, select the desired interaction from the drop down in the top of the graphic.

Placing your mouse cursor over the vertical bar causes the interacting residues in the other sequence to be highlighted, by increasing the line height. The details of the interaction(s) between the subject residue and residue(s) from the other domain are also displayed in a box to the right of the graphic.

Similarly, with domain-ligand interactions the sequence containing the interacting domain is represented graphically, with bond forming residues shown below. We do not represent the ligand in this view, with the interactions between domain residues and ligand simply listed in the ‘Interaction Details’ box. All of the residue interaction details may be downloaded using the adjacent download tab.

Download Back to top

The Download tab offers the ability to download the data presented on the Structure and Sequence tabs as a tab delimited file. This file can easily be opened with most spreadsheet applications and is well suited to machine processing.