He's just down the pecking order this year with Lichtsteiner, Asamoah, Giaccherini, De Ceglie, Caceres all preferred instead.
Pepe is more suitable when Conte used to field 4-3-3 with the forward three in the form of two flanks and one striker (so a 4-5-1 if you will, with deep wingers) ; and also Conte's classic 4-2-4 used early in the pre-season/calcio season in 2011.