From flight day 2, the payload bay, vertical stabilizer, orbital manoeuvring system (OMS) pods and docking mechanism.
The docking is now in progress on NASA TV, times are GMT:
16:00 ...01...20...32...00...End pitch manoeuvre
16:02 ...01...20...34...36...Initiate pitch up manoeuvre (575 ft)
16:04 ...01...20...36...30...RPM start window close
16:14 ...01...20...46...06...+V bar arrival; range: 310 feet
16:15 ...01...20...46...56...Range: 300 feet
16:15 ...01...20...47...38...Sunset
16:19 ...01...20...51...06...Range: 250 feet
16:23 ...01...20...55...16...Range: 200 feet
16:25 ...01...20...57...46...Range: 170 feet
16:27 ...01...20...59...26...Range: 150 feet
16:31 ...01...21...03...36...Range: 100 feet
16:34 ...01...21...06...36...Range: 75 feet
16:38 ...01...21...10...46...Range: 50 feet
16:42 ...01...21...14...06...Range: 30 feet; start station keeping
16:47 ...01...21...19...06...End station keeping; push to dock
16:51 ...01...21...23...26...Range: 10 feet
16:51 ...01...21...23...39...Sunrise
16:53 ...01...21...25...07...DOCKING
EDIT: Atlantis is now docked.