How many photos do you have in Camera Roll?
You can look in Settings/General/Usage to see what's taking up your storage on the iPhone. The apps themselves are not a part of the backup although any data and settings related to the app are. I find many people now use their devices as photo storage devices which can quickly add up in a hurry. The photos sync from a computer are not a part of the back up but photos and video in the Camera Roll are and can quickly consume the 5GBs of iCloud storage.