Fig. 1.

Distance difference matrices (DDMs)

Notations: Short thick bars or segments of thin double lines along the tops and sides of the triangular matrices denote positions of α-helices or β-strands (taken from PDB file). Tick marks on the top and left are at intervals of twenty residues; mostly black triangular areas means that DDs in them are below 0.5Å and these areas represent likely rigid blocks in the conformational transitions between the two compared molecules; the gray areas mean that DDs are between 0.5Å and 1Å; white spaces means that the absolute values of the distance differences (DDs) between the corresponding pair of C^α-s in the two structures (e.g., PDB entries) is more than 1Å;

1. 2tbvAC for the molecules A and C in the unit cell of the 2tbv virus capsid protein; the mostly white rectangle at the DDM’s top right, providing straight white borders of the “rigid body triangles” of this DDM, indicates that most DDs between the two “rigid bodies” are larger than 1Å, meaning that most C^α-C^α distances between the “rigid bodies” differ in two molecules by more than 1Å.
2. 4ape5er2 of the apo-holo structures of endothiapepsin; this DDM has only some white spots and no straight white borders of the black “rigid triangles”; such borders can be provided by drawing white lines encompassing almost all white spots in a rectangle and thus delineating the mostly black “rigid” triangles (see also text on thermolysin below).