Connection between EC2 instance and RDS

We have the database of 3 websites on a single RDS mySQL instance, and sometimes 1 website gets disconnected from the database and goes down without affecting other websites. We came to the conclusion that the disconnection could be due to one the 2 cases below:-

1. Something is going wrong in the connection the Database and EC2 instance on which the website is hosted.
2. There may be a connection pool issue on the application end as we manually set up the connection pool in the code of the website as we use Jave.

To figure out the root cause of the disconnection if any as per point 1), we activated VPC flow logs, but are unable to figure out how to filter the logs such that we can know what goes on when the disconnection happens. The custom log format we have set is below:

${instance-id} ${srcaddr} ${srcport} ${pkt-srcaddr} ${pkt-src-aws-service} ${dstaddr} ${dstport} ${pkt-dstaddr} ${pkt-dst-aws-service} ${flow-direction} ${traffic-path} ${action} ${log-status}

How do we filter the logs based on traffic flowing from the suspected EC2 instance and the RDS so we can figure out what is happening and what is the cause for the disconnection?