Your body can use protein as energy but it has to go into a catabolic state in order to use protein as energy. That is bad. Stick to carbs and fat as energy sources.
serbstyle, if you really want to take an amino acid suppliment pre-cardio, I would go with 5-10 grams of BCAA's in order to reduce the catabolic effects of your cardio.
Amino acids certainly have calories and can be used as energy (especially during low carb/low energy diet). Read my recent (2002) paper on protein metabolism etc.: