My website has implemented by using JAVA. So we have taken VPS and installed Tomcat then deployed My website is appearing like this
whenever I click www.mysite.com
If you don't want a port number in your URL, you have to use the default port number for HTTP, which is 80. If it's anything other than 80, you will be required to put the port number in the URL. That's all there is to it.
Now, if your question is "how do I host my Tomcat website on port 80", well there are plenty of answers to that question both on SA and teh intertubes. Just search.