(I can be wrong but) as far as I understand E is based on objects and messages as primary mechanisms, that is, we do not know where objects exist, how they are managed and how messages are transferred. Concept-oriented programming (COP) is a references-first approach while objects are defined as being functions of references, that is, object is a derived (secondary) element of the model and the goal is to be able to have full control over this mechanism (custom heap, custom garbage collection, custom access control and security model etc.)

What I see similar in object-capability model and COP is that they both try to treat object access as a highly important part of a system behavior. In COP, I used to write that it is more important what happens during access rather than in the object itself. Hence, being able to make these intermediate actions integral part of the program (and develop good PL for that purpose) is very important.