Fig. 2

Distance matrices consisting of the mean smallest distance between residue pairs for (a) hTopoII (K-loop and α-helix) and (b) ScTopoII (K-loop and HLR) (See Table 1 for the sequence). Plots show short contacts between K-loop and helix region averaged over a time interval of 50 ns from 1 µs to 2 µs (short helix formation stabilized after 1µs) trajectory length. The short helix (SH1) formation from HLR region of ScTopoII encircled with black dashed lines. c) representative snapshot taken after 1 µs of hTopoII and showcasing interaction of K-loop and helix (showing just monomer), and rotated view is shown below e) same snapshot as c) is an interaction of inter chain α-helix (H1 and H2) (showing fragments from dimer). d) is a representative snapshot showcasing K-loop, HLR; taken after 1 µs of ScTopoII (showing just monomer) and rotated view is shown below. f) same snapshot as d) is an interaction of inter chain HLR regions of ScTopoII (showing fragments from dimer). Chain A (B) of the protein in light yellow (orange) and the colour coding of residues are based on residue type (non-polar residues (grey), basic residues (blue), acidic residues (red) and polar residues (green)).