By Julien Pretot

LE LIORAN, France (Reuters) - Belgian Greg van Avermaet claimed the overall leader's yellow jersey when he won the fifth stage of the Tour de France at the end of a long breakaway as Alberto Contador appeared to suffer from crash-related injuries on Wednesday.

After hitting the deck twice in the two opening stages, the Spaniard (Tinkoff) looked in pain and cracked in the finale of the middle-mountain stage, losing 23 seconds to the other top riders who finished together more than five minutes behind BMC rider Van Avermaet.

Another big name, Giro d'Italia champion Vincenzo Nibali, (Astana) was dropped in one of the short but hard climbs of the day on the 216km stage from Limoges, ending up 8:38 behind the overall favorites and with slim hopes of winning the race.

Nibali's main task this year, however, was to help fellow Italian Fabio Aru in his first bid to win the Tour.

Van Avermaet was part of a nine-man breakaway that jumped away from the pack after some 20km, shortly after going through Saint Leonard de Noblat, the home town of France's favorite rider, the 80-year-old Raymond Poulidor.

Long labeled an also-ran, just like Poulidor who finished on the Tour podium eight times but never wore the yellow jersey, Van Avermaet added to his Tour stage win of last year.

"It's special for me, it's the best jersey in the world. It's my first time and perhaps the last so I will enjoy every moment," said Van Avermaet, who now has two Tour victories to his name.

"It's the best moment of my career. Winning a stage is already quite something but this takes it to another level."

He and Ukrainian Andriy Grivko plus another Belgian, Thomas de Gendt, went away with 85km left to the finish before Grivko was dropped.

FROOME SAFE

Van Avermaet made his final move on the climb to the Col de Perthus 17km from the line and never looked back.

De Gendt was second and Pole Rafal Majka (Tinkoff), one of the members of the breakaway, took third place at the end of the 216-km ride from Limoges.

Overall, Van Avermaet leads France's Julian Alaphilippe (Etixx-Quick Step) by five minutes 11 seconds and Spaniard Alejandro Valverde (Movistar) by 5:13.

Defending champion Chris Froome (Team Sky) and last year's runner-up Nairo Quintana (Movistar) lie fifth and seventh respectively, 5:17 off the pace.

Contador, who could not follow the best when Frenchman Romain Bardet accelerated in the finale, is 25th, 6:38 behind Van Avermaet.

"I knew it would be hard. The two crashes really hurt, I'm still aching, it's not easy to recover," Contador, who won the Tour in 2007 and 2009, told reporters.

"But I'm hanging in there, the support of the crowd is helping a lot. I'm not feeling down, I'm going to give my best."

Froome lieutenant Geraint Thomas would not rule Contador out.

"It’s just a handful of seconds here. You can’t write Contador off. Obviously, it’s a bonus, but we certainly don’t take anything for granted," he said.

Thursday's sixth stage, a mostly flat 190.5-km ride between Arpajon sur Cere and Montauban, should give Contador some respite before the Tour enters the Pyrenees.

(Reporting by Julien Pretot; Editing by Martyn Herman and Ed Osmond)