Search by VH/VL Orientation

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. Use the search forms below to use it to select antibodies based on their VH/VL orientation.

> Search the database by angle

Click on parts of each graph to select the range of angles to search for.

> Get the orientation of a specific PDB entry

Input a PDB code. To select a specific Fv, use its chain identifiers - for example, 12e8_HL.

> Get the orientations for a subset of the database

Antibody type:

Experimental method:

Species:

Resolution cutoff:

R-factor cutoff:

Antigen type:

Light chain type:

Has constant region:

Has affinity value:

Residue at Chothia position:

> Find antibodies with a similar orientation to another PDB entry

PDB code and chains:

Compare to which species?

Max. deviation in angle (°):

Max. deviation in distance (Å):

> Download ABangle

To run ABangle locally and use more features, download the executable here.

If you use this software please cite the paper.

SAbDab papers

Schneider, C., Raybould, M.I.J., Deane, C.M. (2022) SAbDab in the Age of Biotherapeutics: Updates including SAbDab-Nano, the Nanobody Structure Tracker. Nucleic Acids Res. 50(D1):D1368-D1372 [link]

Dunbar, J., Krawczyk, K. et al. (2014) SAbDab: the Structural Antibody Database. Nucleic Acids Res. 42(D1):D1140-D1146 [link]

Thera-SAbDab paper

Raybould, M.I.J., Marks, C. et al (2020) Thera-SAbDab: the Therapeutic Structural Antibody Database. Nucleic Acids Res. 48(D1):D383-D388. [link]

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