Comment by tsimionescu

The quarks that are bound in a way we call a proton are held together by the strong force at a certain distance from each other - that distance is what we consider the volume of the proton, with the quarks being "inside that volume". This system of 3 quarks has some amount of potential energy, and/or some amount of kinetic energy from the relative movement of the 3 quarks. The mass of this system is then given essentially by E=mc^2, with E being this kinetic energy.

There is a very good video of a lecture by Leonard Susskind that explains why energy and mass are interchangeable in this way if you want a more in-depth explanation:

https://www.youtube.com/watch?v=JqNg819PiZY