MySQL?

 I upgraded to the LE2005 DVD MySQL-4.1.
My Java application cannot connect anymore to my database. The most curious is 
that I have PHP application which is not affected by that.
I can still connect thru /usr/bin/mysql.

However the Java Driver sends this message:
Cannot connect to MySQL server on localhost:3306. Is there a MySQL server 
running on the machine/port you are trying to connect to? 
(java.net.ConnectException)SQLState: 08S01VendorError: 0

The answer is yes, there is a MySQL server.
However when I do a nmap scan I don't find mysql (3306)!
Is there something I missed during the upgrade (like mysql switching to a non 
TCP protocol?)