The relative orientation between the variable domains (VH and VL) influences the topology of the antigen binding site. It is important to consider when building high-resolution models of antibodies.
The VH/VL orientation can be represented by six measures:
|HL||the torsion angle between H1 and L1|
|HC1||the bend angle between H1 and C|
|HC2||the bend angle between H2 and C|
|LC1||the bend angle between L1 and C|
|LC2||the bend angle between L2 and C|
|dc||the length of C|
ABangle is a tool that calculates these angles from a PDB structure. Click on the link below to download it. Documentation is included in the download. For a full description of the software, or if you use it, please refer to: Dunbar, J. et al. ABangle: Characterising the VH-VL orientation in antibodies. PEDS. (2013).
The equivalent angles can also be calculated between the analagous domains in T-cell receptors, Vα and Vβ. For more information on this, please see the following paper: Dunbar, J. et al. Examining variable domain orientations in antigen receptors gives insight into TCR-like antibody design. PLOS Comp. Bio. (2014)Download ABangle