Two really important things happen here and they are often mistaken to be linked. First, John finds Irene attractive. Whether he’s gay, bi or whatever, we know he’s had girlfriends so women are not entirely uninteresting to him. Seeing a naked one at an unexpected time is bound to turn him on a little. Irene is a smart woman and she has him wound around pinky finger from the first second. Next, he begins to feel jealous over Sherlock. This is where the confusion sets in. With a naked woman in front of him, he figures Sherlock has to find her attractive, but we should know better than that. After all John truly knows Sherlock by now. He as seen his cold, removed actions and has come to accept them. His jealousy seems to be from a different angle. Knowing Sherlock, he knows just how special he is to be considered a friend. Even with the doubts in his mind that are still an episode or two from being resolved he fully realizes that he is different from anyone Sherlock has ever met before. Now Irene comes in and all of a sudden those doubts are intensified. He doesn’t seem to be scared so much that Sherlock will want to sleep with her. John must have had that fantasy more than once already as well. His anxiousness comes from the disappointment of losing the coveted title. He used to be the only person that Sherlock shows so much affection to and interest in. Then in struts this woman and takes it away on one sweep. Jealousy doesn’t always need to be sexual. Losing that spot of being the centre of attention to one person is bound to make anyone jealous. Now the fact that he counted how many time Sherlock’s phone moaned… that’s another story.