Calculating Fragment Antigen-Binding (Fab) elbow angle

Overview

Each FAB is made of two chains, Heavy (H) and Light (L), and two domains, Variable (V) and Constant (C or C1, The heavy domain has three parts). The angle between the variable and constant domains is the FAB elbow angle. It is the angle between rotation axes, the pseudo-dyad axes, defined by aligning the light portion of each domain, on-to the heavy one.

Command line options:

  • light: chain ID of light domain, by default set to L
  • heavy: chain ID of heavy domain, by default set to H
  • limit_l: the number of the residue separating between variable and constant domains in the light chain, by default 107
  • limit_H: the number of the residue separating between variable and constant domains in the heavy chain, by default 113
  • h: help

Usage:

>>>phenix.fab_elbow_angle fab_name.pdb [light=L] [heavy=H] [limit_l=107] [limit_h=113]

Examples:

>>>phenix.fab_elbow_angle 7fab.pdb light=L heavy=H limit_l=104 limit_h=117

123.00

>>>phenix.fab_elbow_angle 1bbd.pdb

126.34