"The timing was good for that conversation to take place," Obama said, adding that the phone call was the first step in rebuilding trust between Israel and Turkey.
The president opened the last full day of his Mideast trip with a series of stops around Jerusalem and Bethlehem, all steeped in political and religious symbolism.
Accompanied by Netanyahu and Israeli President Shimon Peres, Obama laid wreaths at the graves of Theodor Herzl, the founder of modern Zionism who died in 1904 before realizing his dream of a Jewish homeland, and former Israeli Prime Minister Yitzhak Rabin, who was assassinated in 1995.
Obama and his hosts arrived at the Herzl grave site under cloudless skies. Obama approached Herzl's resting place alone and bowed his head in silence. He turned briefly to ask Netanyahu where to place a small stone in the Jewish custom, then laid the stone atop the grave.
"It is humbling and inspiring to visit and remember the visionary who began the remarkable establishment of the State of Israel," Obama wrote in a guestbook. "May our two countries possess the same vision and will to secure peace and prosperity for future generations."
At Rabin's grave a short walk away, Obama was greeted by members of the late leader's family. He initially placed a stone on Rabin's wife's side of the grave, then returned to place one atop Rabin's side. In a gesture linking the U.S. and Israel, the stone placed on Rabin's grave was from the grounds of the Martin Luther King memorial in Washington, the White House said.
Friday's stop at Herzl's grave, together with Obama's earlier viewing of the Dead Sea Scrolls, the ancient Hebrew texts, were an attempt by the president to emphasize his view that the rationale for Israel's existence rests with its historical ties to the region and with a vision that predated the Holocaust. Obama was criticized in Israel for his 2009 Cairo speech in which he gave only the example of the Holocaust as reason justifying Israel's existence.
Obama was to make a stop Saturday at Petra, Jordan's fabled ancient city, before flying back to Washington.
Associated Press writers Matthew Lee and Jamal Halaby contributed to this report.
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