Interaction class is defined for any SCOP family that is represented by structures of at least three different domains in complex with a double-stranded DNA. An interaction class 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.


A type of contact is included into an interaction class if this contact is detected in at least one structure of each of different domains of the family.


For example, the interaction class “H-Bb H-Mj L-Bb” means that for each domain of the family there is at least one structure where some alpha-helix contacts with the DNA backbone, at least one structure where some alpha-helix contacts with the DNA major groove, and at least one structure where some loop or turn or unstructured segment of the domain contacts with the DNA backbone.