Interaction mode is defined for each individual Pfam or SCOP domain contacting with double-stranded DNA in one particular structure of DNA-protein complex. An interaction mode is a set of types of contacts.
Each type of contact is of the form “X-Yy”, where X is H, L or S, and Yy is Bb, Mn or Mj. Here:
H is for alpha-helices,
L is for loops, turns or unstructured regions of protein,
S is for beta-strands,
Bb is for the DNA backbone,
Mn is for the DNA minor groove,
Mj is for the DNA major groove.
For example, the interaction mode “H-Bb H-Mj L-Bb” means that some alpha-helix of the domain contacts with the DNA backbone and the DNA major groove, and some loop, turn or unstructured segment of the domain contact with the DNA backbone.