Structural Variability

To assess the structural variability of immunoglobulin variable domains in general, as well as of different types and subtypes of variable domains, a subset of the structurally least variable Ca position was determined by iterative least squares superposition. A superposition of representative domain structures of the different types is shown on the page explaining the AHo numbering scheme. The residues used for superposition (3-7, 20-24, 41-47, 51-57, 78-82, 89-93, 102-108 and 138-144) are indicated in white.

To calculate the structural variability, the domains were superimposed using the program Insight II (MSI/Biosym) and the reoriented Ca-coordinates exported as PDB files. The coordinates were imported into EXCEL, the sequence, residue labels and X-, Y- and Z- coordinates of the different structures collected into separate worksheets, gapped to represent the structurally correct sequence alignment and used to calculate the average Ca-position for each residue. The deviation of each individual Ca position from the average position as well as the average deviation from the average position were calculated and converted to a color code used to indicate the structural variability within a sample structure or a schematic representation of the domains.

Example:
Structural Variability of Antibody Variable Domains:

Macros:

Problem: Under Windows, the xxx_GetFile utilities do not keep the file extensions of the imported files in the worksheet name and therefore do not recognize the individual worksheets properly. For the moment, these macros will only work correctly if you remove the .pdb filename extensions from the filenames. I will correct the problem as soon as possible.

STR_GetFiles

STR_CollectData

STR_ExtractSeq

STR_GapFromAlig

STR_GapFromLbl

STR_GapFromSeq

STR_CaDist

STR_ColorAlig

STR_ColorVal