Washington: That noise heard overnight on Friday was the sound of jaws hitting desks in NATO bunkers either side of the Atlantic, as the uncertain fate of Turkish President Recep Tayyip Erdogan posed threats to the US-led war against the so-called Islamic State, and to Europe's jury-rigged effort to staunch the flood of war refugees to the continent.

And it wasn't heard in isolation. In the midst of weeks of crazy, dangerous developments in Europe – think a wave of terror attacks and Britain's Brexit vote – and it's as though the pillars of democracy might topple.

A measure of the confusion among foreign policy experts was this assessment by Professor Omer Taspinar, at the Brookings Institution, who in recent months has warned of a Turkish coup: "This will rattle the Turkish markets. It will tarnish the country's image. My analysis is that this will certainly be embarrassing for Erdogan. The signs are chaotic right now, but I think the rumours of Erdogan's demise would be highly exaggerated given he has been on TV."

Any instability in Turkey puts at risk the war against IS in neighbouring Syria and Iraq. As a member of NATO, Turkey is a reluctant linchpin in the war effort; and as an aspiring member of the European Union, Ankara has succeeded in demanding billions of dollars from the EU for its cooperation in slowing the refugee flood from the war.

Taspinar said the intervention was especially embarrassing for the Turkish president because of the history of Turkish coups. "Each time the military intervened in the past it was at a time when the government was very unpopular," Taspinar told The Guardian.

The signal that caused many to exhale in relief was the absence of the head of the Turkish military from the airwaves, an appearance that would have signalled that the coup had the full backing of the military. Similarly, no reports on military factions turning their guns on each other was another reason to relax, if just a little.

World leaders scrambled as events unfolded, with Washington, Berlin and United Nations and EU headquarters among others issuing statements of support for what was generally described as Turkey's democratically elected government – notwithstanding that they find Erdogan to be irritating, manipulative and wrong-headed.

It's difficult to see how instability and suspicion in the Turkish military will not act as a drag on vital co-operation with NATO and its allied forces in Syria and Iraq. Conversely, IS would be rubbing its hands in glee at the prospect of instability and uncertainty in the sprawling Turkish security apparatus.

Any loss of NATO or US access to a series of Turkish military bases would be a significant setback for the war on IS – particularly the Incirlik Air Base, which now accounts for about one-third of the in-air refuelling of fighter aircraft over Syria and Iraq.

The foreboding in NATO rests on the prickliness of the relationship with Erdogan – and how any diminution of his standing as a result of the attempted coup might be the cause of his feeling a need to score points off the Americans and their allies.

US officials accuse Erdogan of divided loyalties – his country became the "jihad highway" for volunteer fighters flooding in from across the world to fight with IS and the border region has become a major supply and rest zone for IS.

What burns up Erdogan is the American reliance on Kurdish forces fighting IS and the Assad regime in Syria – the Turkish president is driven by a near paranoid belief that Washington will reward the Kurds by supporting their quest for autonomy in any post-conflict division of territory in Syria and that such an outcome would turbo-charge autonomy demands from the significant Kurdish minority in Turkey.

At the US State Department, deputy spokesman Mark Toner recently trod delicately in attempting to explain the problem with Erdogan: "Turkey is playing an important role with regard to Syria, with regard to the conflict there, both from the Assad regime as well as with [IS]. So I don't want to underplay that. But they have, as many countries do within the coalition, sometimes different priorities, different ideas about how to go about that, and that's something we're in constant dialogue with them about and working to coordinate better."

An attempted coup could make that difficult little equation so much more difficult.