Energy: Everything having to do with the movement of the player. Crouching would take away the least energy, then walking, swimming, sprinting, elytra!!! (This would slightly nerf the elytra)
Protein: Anything to do with the left and right click buttons. Building, mining, attacking, using a bow, etc.
Vitamins: Everything to do with health. Regen and max health.
I'm interested why you think Protein and Vitamins should be switched around... Part of my changes to mobs was to make farming and feeding mobs be profitable for people interested in getting the maximum possible amount of protein. Plus if you kill all the nearby animals by hunting, you can always grow Vegetables without too much trouble.
Plus it's slightly realistic making protein deal with health and bodily repair... Protein is needed in order to make new cells. The reason many of my vegetables fill a little bit of protein is because vegetables actually do have protein in them, but one single vegetable does not have all the kinds of protein that you need on a daily basis.
(By eating a variety of vegetables you can get all the protein you need, although just one type of meat will contain all the proteins you need, in addition to a few other things like cholesterol.)