I know little about the unusual happenings of the reptilian genitalia, except for the fact that male snakes have two, barbed penises.
Anyway, right around where you're describing is the cloaca. Not only are his/her genitals located there, it's also where he passes feces and urates. He could've just been getting ready to pass his bowels, but uh, you started touching his/her junk. Give him some time if you don't get an exact answer and see if he defecates when you're not around.
Edit: Nevermind the laughable novice answer, the pros have flown to your rescue!
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