I picked up a cockle shell the other day and it had dark brown,rubbery stuff on the edge of the shells. I'm sure its made of a protein or proteins,but which protein or proteins? 

Thank you.

Impossible to say without a picture (or perhaps even analysis of the material). If it was an empty shell then perhaps some species of marine algae (i.e. seaweed) although this is unlikely on a live animal since cockles burrow in the sand (and algae needs light!)