__proto__ VS. prototype in JavaScript

__proto__ is the actual object that is used in the lookup chain to resolve methods, etc. prototype is the object that is used to build __proto__ when you create an object with new:

( new Foo ).__proto__ === Foo.prototype
( new Foo ).prototype === undefined

prototype is a property of a Function object. It is the prototype of objects constructed by that function.

__proto__ is an internal property of an object, pointing to its prototype. Current standards provide an equivalent Object.getPrototypeOf(obj) method, though the de facto standard __proto__ is quicker.

You can find instanceof relationships by comparing a function's prototype to an object's __proto__ chain, and you can break these relationships by changing prototype.

function Point(x, y) {
    this.x = x;
    this.y = y;
}

var myPoint = new Point();

// the following are all true
myPoint.__proto__ == Point.prototype
myPoint.__proto__.__proto__ == Object.prototype
myPoint instanceof Point;
myPoint instanceof Object;

Here Point is a constructor function, it builds an object (data structure) procedurally. myPoint is an object constructed by Point() so Point.prototype gets saved to myPoint.__proto__ at that time.