Yes, BizTalk Server 2006 R2 supports AS2 out of the box.
There are some Tutorials you can use to understand how BizTalk Server supports AS2. http://msdn.microsoft.com/en-us/library/bb259975(v=bts.20).aspx
Of course, I must recommend you use a more current version, BizTalk Server 2010 at least. BizTalk Server 2006 R2 is at or nearing the end of it's support lifecycle.