America has no permanent friends or enemies, only interests.
In 2011 Putin brought up the idea of Eurasian Union with an idea of integrating the Soviet-era States into an economic and political unit, much on the lines of the European Union. Armenia, Azerbaizan, Georgia, Belarus, Khazakistan, Tajikistan and Kyrgystan have shown their interest in such a grouping. Any such grouping is going to be of grave concern for USA. Post Cold war, this would be the first time when the US hegemony as a world power will stand be challenged by a neo-USSR in the name of Eurasian Union, which more than economic and political entity might serve as an strategic entity.
The Syrian crisis and the Russian show of influence in the way the things are going, has already given USA enough reason to rethink its geo-political policies in the Middle East region
Note that Israel and Saudi Arabia (both US allies) badly wanted military intervention in Syria. Syria has been an ally of Shia majority Iran. Syria is a Sunni majority State but is ruled by Alawite ethnic group, who comprise the minority of its population and have sympathies of Iran. The Northern region of Syria is dominated by Kurds, who have been demanding more autonomy. Kurds also, comprise a major population in Southern Turkey and here comes the interest of Turkey in whatever is happening in Syria. The Assad government has been sympathetic to the Kurd demands and Turkey sees this as a possible threat as it can strengthen the Kurdish in Southern Turkey. For Turkey the best thing would be the fal of Assad regime so that a moderate Sunni government can come to power and suppress the Kurdish voices of self assertion. Turkey wont draw itself into the Syrian conflict and has given refuge to the Syrian refugees. But Turkey has huge stakes in whatever emerges after the present Syrian civil war. For Israel and Saudi Arabia, such a shift in power won't mean much. Total isolation of Syria from Iran is what these countries are looking forward for.
Amidst all this, the developments related to controlling the Iranian nuclear programs was also seen by both these States as a possible ticket to militarily confront Iran and weaken its influence in the region. This could have happened with the way Ahmedinijad was handing the developments. With new government coming in the picture seems to be changing now.
No one can have any difficulty in accepting the idea of a possible US-Iranian alliance in future. Already, Rouhani's liberal tone and the Geneva peace agreement coupled with the Syrian crisis slowly shifting to a possible settlement without dismantling of its government or military intervention, has embittered US-Israel and US-Saudi ties. Russia probably proved to be more powerful in deciding the fate of Syrian crisis than the US (by the way, its yet to come to a final conclusion).
US is also having stakes in the East China sea, with China getting assertive by unilaterally declaring an ADIZ. Any US intervention in favor of Japan will affect the US-China ties. Who all would be the allies of the US outside Europe, if all these crises and possible crises escalate? As far as Iran's ideological position and internal resistance against Iran-US ties are concerned, sanctions will weaken all such forces plus what choices does Iran have? Iran has hegemonic aspirations in the middle East. Without US support, with an expansionist Russia and an unstable Afghanistan, who are the Iranian allies on whom Iran can rely upon? Certainly any US-Iranian alliance wont come up just like that, but then I can see no other feasible option for either US or Iran to go ahead in the region without each other and still be able to achieve what they want to.
Russia is again coming face to face with the US like never before post cold-war period and US will not leave any stone un-turned to counter the expansion of Russian influence in the middle east. East China sea, for the time being, may be just an isolated event but there is a possibility of Russia getting assertive in the region too and thereby making the situation more serious for the US.