Class 5-1 is the classroom attended by Touma, Fuyuki, and two girls who appear exactly three times in the manga, in minor bit roles. They only appear once in the anime. It has no significance beyond this, and is only seen in one scene, Touma's introduction scene. Its school nurse is Kumada.
In season one, the desks are arranged in pairs. In later seasons, the classroom presumably reverts to a more traditional row-column arrangement, as this is what happens to 5-2.