Some docs more than others make us uncomfortable. It isn't so natural to be at the OB/GYN, espcially if you only have to go once in awhile. It helps me to know that my doc and most OB/GYNs that I have been to over the years really care about women and their patients, and want to help. It is awkward on one hand for them too do the exam too b/c they know it is not the usual thing for you to be going through and they understand that.
Sometimes I take along music and/or a book to the doc appointments, that make me the most nervous, helps and soothes me while I'm there. A little dab of lavender oil on my temples or chest too can help for calming. Talking to them a little bit longer or while going through the exam helps as well, doesn't have to be about the gyn stuff, anything to take your mind off it. I've even been known to find a funny pair of socks to wear to catch them off guard, to make us both laugh. Perhaps some of these things will help. Best wishes.