Stored procedure execution time: Query Analyzer vs. Web application

I have a Webserver and a SQL server in same network.
A certain stored procedure named ABC that is present on the SQL Server takes just 5 seconds to execute from the SQL Query Analyzer of Web Server.
But the same sp times out when called from a .Net 1.1 web application of the Webserver. Time out parameter is 30 seconds.
The data to be returned is less than 1000 rows.
What could be the reason?
Secondly, if I make a copy of the same sp with a new name, it works perfectly fine from the web application as well.

Run the sql profiler to see the execution time. When web server sends the request to SQL server, it will complete the execution even web server is timed out. If you don't see any execution of the procedure then your connection string might be an issue.