You would need to create services that live on the server itself. These services would be methods such as (just as a simple example)
SaveDocument(User, Document)
GetDocument(User, Document)
you would need to configure your web app to call these services and pass in the required parameters. Now as for how to do this, you could write the services in any number of languages (Java using JavaEE, C# using WCF to name a few, but you can also do this in python/ruby/etc) and then generate WSDL interfaces to the services that any number of other languages could call.
There are lots of resources available on the web that cover this, so pick a language you want to learn, or are already proficient in and google around on how to develop web services in that language.
Good luck!