Internet of things (IoT) has now become a fascinating system that improves information technology for its use in homes, cities and medical sectors. IoT works as an extension of internet to realize interconnections among every day object based on platform independent communication protocols. Object forming IoT must possess sensing, communication, and computation capabilities leading to a convenient as well as economical assistance for society. Interaction among heterogeneous objects enhances the security vulnerabilities in IoT. The current four layered communication stack of IoT supports protocols at each layer for enabling connectivity of heterogeneous objects. With security as a prime concern, communication in IoT need to maintained using a secure mechanism to protect the system from attacks. This paper analyzes various existing protocols at each layer with their inherent security mechanisms and exposing their vulnerabilities to different attacks. This paper will unlock new research areas for improving the inbuilt security mechanisms.