Show the protein-protein interface when you want to see which residues of an antibody touch its antigen, or how two proteins of a complex interact.
Prerequisites: a structure with at least two chains shown in the 3D viewer. Example: 7KPB, a Fab bound to TNF (chains F and G are the Fab, chains A, B and C are TNF).
- In the 3D viewer selection toolbar, click Create component (+) and select Protein-Protein interactions.
- In Group 1, select the chains on one side of the interface. Example: chains F and G.
- In Group 2, select the chains on the other side. Example: chains A, B and C.
- Optional: change the Component name, the Radius, Å (default 4.5) or As whole residues.
- Click Create.
Result: the camera zooms to the interface, the contacting residues are shown as sticks with dashed interaction lines, and the component is listed in State Tree → Custom Components → PPIs.
- Hide the interface again: click the eye icon of the component in the State Tree.
- Compare with another complex: superpose the second structure first (see How to superpose structures), then create a PPI component for it too.