Now, are you a male of female?
Suggestion-- Maybe it would help if you both established a relationship on more friendly terms. I've also had this type of feeling with certain individuals, female luckily. It's an awkward feeling, and it seemed like there was a single pulse, very awkward at that...
What helps is lightening up your bond, crack some jokes, be a little more goofy. If things go astray, tell him your situation. Make up a boyfriend/girlfriend.
Please don't do any of the suggestions I listed before you post some more details about your situation, I would hate to lead you in the wrong direction considering this seems to be a very personal issue.
Also, hopefully some other members could implement some suggestions too.