At top left (WPDB window) we see that the hemoglobin structure
with the PDB code 1BAB has been chosen. A sequence alignment between
the A and B chains (Align window) by the method of Needleman and
Wunsch reveals a 44% similarity. These aligned structures are
then superimposed according to the method of Hendrickson based
on their Calpha coodinates (3D view window). The Contact map window
reveals the interactions at a default cut-off of 7 Å between
Calpha atoms. Red indicates intrachain contacts (i.e. contacts
with itself) observed in both 1BAB_A and 1BAB_B; green indicates
intrachain contacts observed in 1BAB_A only and blue - in 1BAB_B
only.
This shows further details of the interaction between the A and
B chains. The Profile window has been zoomed to show the exposure
according to Lee and Richards for a segment of the aligned sequences.
Red represents both the A and the B chain; blue chain A only;
green chain B only. The Contact map window has been zoomed to
show the interaction between individual residues. A further click
would reveal the specific atoms in contact. The 3D view window
shows a solid representation of the molecule in a gray scale where
the darker the color the farther the residue from the viewer.