The Indians lost 3-6 6-3 5-10 to their unseeded rivals in the second round in one hour and 12 minutes.
The Indians were playing their first match after getting a bye in the first round.
The Americans cashed in on both the break chances before the super tie-breaker.
Paes and Bhupathi converted both the chances in the second set to take the match to decisive super tie-breaker, in which though the Americans prevailed.
Querrey and Isner are in good form and had also defeated Rohan Bopanna and Aisam-ul-haq Qureshi in the Madrid Open recently.
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