The immediate connection between Helmholtz and the Savage can be explained by the fact that both of them have a deep appreciation for art. While Helmholtz is conditioned to think about the world in a particular way (which is a monotonous, depressing way), he nevertheless is able to appreciate beauty and emotion. This allows him to connect with John, who also has an unusual sensitivity towards these matters (though a deeper one than Helmholtz).
On the other hand, Bernard is unable to react appropriately to this friendship. His insecurity makes him feel displaced and forgotten, and this pushes him to try to get in the way of the two friends. He mocks their interests and tries to annoy them. This demonstrates that Bernard is not a very good friend.
