Hi Santosh,
If I understand correctly that you want to connect ABAP system (say ECC) as back-end with JAVA portal (say EP), then the configuration can be established through JCO RFC connectors. JCO RFC can be created through netweaver administrator link of EP (http://:/nwa) .
After creating JCO RFC connection, mention the program ID in ECC system during creation of TCP/IP RFC .
This would create a connection between EP & ECC . Now in order to fetch data from ABAP system in EP, you also need to create JCO connections, which I have elaborated in my blog http://scn.sap.com/community/netweaver-administrator/blog/2013/07/30/jco-connections-required-for-ess-mss-configuration .
Please let me know if any issue.
Regards,
Nilutpal.