how to connect to a database created on an rds instance through code in s3?

I have a problem which I am unable to solve. I have uploaded my phonegap project into S3 bucket. I have a MySQL database running on an RDS instance. I also have a EC2 instance on which I am able to deploy the project from my local machine. I am unable to figure out how to connect the 3 together so that I can deploy my app on the EC2 instance from the S3 bucket directly and also allow the code to access the RDS instance.

Please help.

I am sorry if this is a duplicate but I was unable to find anything which gave me a satisfactory solution to my problem.