Elbow Angle Calculation

Calculation of Antibody Fab Fragment Elbow Angle

by B. Rupp, A. Zemla and R. Stanfield

The purpose of this program is to allow consistent and convenient calculation of antibody Fab fragment elbow angles. The elbow angle is used as a measure for relative displacement of the variable (V) and constant domains (C) upon antigen binding. Please read the following to understand the workings and limitations of the program:

Calculation of elbow angles
Limitations and accuracy

Please cite the published reference when you use this program:

INPUT:
Mandatory: a Fab fragment structure in valid PDB format. Only ATOM records of the light and heavy chain will be read. Kabat numbering of residues optimal but not necessary.
Options:
Chain IDs. Any alphanumeric character, will be converted to uppercase. The preset default ChainID of the chains is L and H. Take care not to swap L <> H chains - the program cannot recognize this error.  
Residue Number of Domain boundaries. Integer. The beginning and end residue number of the VL, VH, CL and CH domains. Preset defaults that work well with Kabat numbering are set. If there are less residues than you specify, only the residues actually found in the PDB file will be used.

OUTPUT:
HTML form: a form containing diagnostics, statistics, and a file list.
Diagnostics. The input file is processed and split into the light and heavy chains defined by ChainID and the four domains VL, VH, CL, and CH. Actually found residue numbers, domain boundaries, and atom numbers.
Superposition. The domains are automatically aligned and superimposed (mobile VL onto static VH, mobile CL onto static CH, both V domains on 1BBD, and the rotation of both C domains of the V-aligned Fab onto 1BBD C) using the LGA program. The superposition statistics (domain alignment, rmsd, transformation matrix) are checked for plausibility.
Calculation. The key steps of the calculation and its validation are reported. Euler angles, Euler vectors, and the pseudo-dyade angle between the two Euler axes are listed. Complement ambiguity is resolved by checking the rotation angle of the C-domains relative to 1BBD (used as standard 127 deg) following the method by Stanfield and Wilson. Unexpected deviations from pseudo-2fold rotation or swapped L/H chain assignments are checked and warnings issued. Please see CAVEATS. And of course, no guarantees and responsibility for anything whatsoever. 
File list. A list superimposed coordinate files of the domains of available for download is provided.

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