Not really.
Checking the security of a website could technically be done based on a set of sequential instructions, but you'd either be missing something, or checking way more than is necessary.
security auditing is a lot of instinct and experience and deep understanding of technologies. Not a checklist.
Once you start learning tho, here's some tools that might help you with web app pen testing:
*shameless plug*
http://yaisb.blogspot.com/2006/08/new-bookmarklets.html