Hi Damayanti,
I don't have experience working with protractor, however when working with hybrid apps and Appium in general, you will need to check to make sure that you are in the correct context to interact with element in question, either NATIVE_APP or WEBVIEW. I would guess that you need to switch back to the NATIVE_APP context to interact with the pop up. Also make sure that your test has some sort of explicit wait defined to ensure the element is clickable.