The application layer protocol plays a significant part in IoT framework as it enables the communication between things, devices or objects with the application interfaces. These protocols are expected to guarantee security, speed, low latency, less power consumption, reliability and efficient transfer of information between the devices. There are several application layer protocols available like Constrained Application Protocol (CoAP), Message Queue Telemetry Transport (MQTT), Websocket, Extensible Messaging and Presence Protocol (XMPP), Advanced Message Queuing Protocol (AMQP), Representational State Transfer (RESTFUL Services) and Data Distribution Services (DDS) that are employed in practice. The suitable protocol is selected based on the nature and requirements of the IoT system. However there are no standard guidelines in deciding a particular protocol for the IoT application. There is always uncertainty in deciding the application protocol suitable for the IoT requirements. Thereby, it is inevitable to know the strengths and weakness of the widely accepted protocols to determine the best-fit scenarios. Amongst these CoAP and MQTT are the most diffused protocols in the IoT landscape. This paper surveys five established protocols – CoAP, MQTT, Websocket, XMPP and AMQP. It discusses the origin of these protocols, the general characteristics, advantages and limitations. Furthermore, the paper does an in-depth comparative analysis of the protocols against the suitability of application areas. Additionally, the paper also explains the standard implementation architecture of the protocols. Thus the detailed evaluation will result in helping to choose the best suited protocol for any given IoT system.