Yet another numbering scheme for immunoglobulin variable domains: An automatic modeling and analysis tool

A common residue numbering scheme for all immunoglobulin variable domains ( immunoglobulin light chain lambda (V-lambda) and kappa (V-kappa) variable d omains, heavy chain variable domains (V-H) and T-cell receptor alpha (V-alp ha), beta (V-beta), gamma (V-gamma) and delta (V-delta) variable domains) h as been devised. Based on the spatial alignment of known three-dimensional structures of immunoglobulin domains, it places the alignment gaps in a way that minimizes the average deviation from the averaged structure of the al igned domains. This residue numbering scheme was applied to the immunoglobu lin variable domain structures in the PDB database to automate the extracti on of information on structural variations in homologous positions of the d ifferent molecules. A number of methods are presented that allow the automa ted projection of information derived from individual structures or from th e comparison of multi-structure alignments onto a graphical representation of the sequence alignment. (C) 2001 Academic Press.