A calorie is a unit of energy.
1 gram of protein has about 4 calories, 1 gram of fat about 9 calories, 1 gram of carbs about 4 calories. This is how much energy is released from these substances if you literally burn them in a test tube.
You body processes these three substances in three different ways, none of which include setting fire to them.
Your goal as a bodybuilder is to increase lean mass and reduce fat. To do this you need to eat enough protein not only to maintain your current lean mass, but to enable you to increase it. About a gram of complete (all essential amino acids in useful ratios, eg. meat,fish,eggs,whey etc.) protein per lb of existing lean body mass will do. Exact numbers will vary slightly from individual to individual.
Maintaining lean mass and increasing it requires energy, which your body gets most efficiently from carbs, and less efficiently from fats, even though fats are more calorie-dense. In extremes it will use existing lean mass for energy, though this is less efficient still.
You therefore need supply your body with carbs and fats. If you don't, your body will start using existing muscle tissue for energy to maintain itself/move about/log on to the internet and jerk off to the cuties thread in the porn section here etc.
You DO NOT need to eat so many carbs/fats that you increase in blubber, while gaining lean mass. Gaining lean mass while maintaining existing amounts of blubber will in itself decrease your bodyfat percentage.
To lose fat you need to deplete your body of carbs and ingest small enough amounts of fat that it is forced to use existing fat stores for energy. Reduce breakdown of existing lean mass by maintaining high enough protein intake and preferably using suitable anabolic compounds. Without the latter you ARE going to lose muscle as well as fat when dieting. Muscle is metabolically expensive to maintain and your body will try to get rid of it in times of stress to reduce your resource requirements. It is greatly hindered in its endeavours in this regard by a hormonal environment aggressively encouraging protein synthesis.
Expend more energy than you take in and you will lose fat. Take in enough energy to maintain and grow muscle and you will do just that.
THESE TWO PROCESSES ARE NOT MUTUALLY EXCLUSIVE.
Thus:
Count grams of protein. It's calorific value should be of no interest to you.
Count carb/fat calories. Experience (and the mirror) will tell you if you are eating enough, too little, or too many.
Hope all that was clear.
Captain Fucking Obvious, over and out.