An example of a useful `loose' similarity between 3D structure detected using
the MAP method and a secondary structure prediction. a) The alignment found by the
method between the predicted pattern for HNF-3 and the helical DNA binding motif
within phage 434 repressor. Boxed, bold-faced, upper-case regions indicate aligned
predicted and experimental secondary structures. Sec denotes the PHD prediction for
HNF-3, and a 3-state DSSP secondary structure assignment for 434 repressor. Bur
shows predicted and experimental states of burial for HNF-3 and 434 repressor:
b = buried, e = exposed; u = intermediate/unknown. b) The equivalent alignment
found using the STAMP (Russell &Barton, 1992) structure comparison algorithm.
Boxed, bold-faced, upper-case regions indicate structural equivalences.
Sec denotes DSSP 3-state secondary structures for both proteins.
c) and d) show the crystallographic structures of the matched regions of HNF-3 and
434 repressor, with structurally equivalent residues shown in ribbon/coil format, and
unequivalent regions shown as trace. The N- and C- termini of the structures are
labelled.