Conserved Hydrogen Bonding Pattern

Lists of the hydrogen bonds in each of the immunoglobulin variable domains were generated using the program InsightII (MSI/Biosym) and exported as ASCII files. These files were collected in an EXCEL worksheet ans analyzed using the HBond macros.

 

They were sorted according to domain subtype (VL divided into Vl, Vk and VH into Types I (H6 E, H10 P), Type II (H6 E, H10 G), Type III (H6 Q, H7#P) and Type IV (H6Q, H7P) as described in Honegger & Plückthun, J.Mol.Biol, 309 (2001)687-699).

VL kappa VH Type I (H6E, H10P) VH Type II (H6E, H10G)

VL lambda VH Type III (H6Q, H7#P) VH Type IV (H6Q, H7P)

For each pair of sequence positions of each domain subtype, main-chain - main-chain, main-chain - side chain, side-chain - main-chain and side-chain - side-chain hydrogen bonds were counted and the bonds indicated in a schematic representation of the domain, color-coded for the percentage of the domains which actually showed that particular hydrogen bond.