The commander's seat is located on the left side of the shuttle. The Pilot, who sits on the right side of the shuttle, is the Commander's understudy, and is fully trained to do all the same tasks as needed.
Commanders fly at least once as Pilots before they move into the left seat.
The commander also participates in experiments and on-orbit operations, but with some limitations. They are not allowed to do spacewalks, as the crew can't afford to have them stuck outside during an emergency deorbit. They also don't normally operate the Canadarm, as it is a specialized task separate from flying the vehicle. As the shuttle reenters from orbit, the on-board computers fly the orbiter. The commander, who is trained and ready to take over from the computers, must stay extremely alert during this phase of flight, so that if there is a failure with the on-board computers, the commander can take over manually to adjust to the appropriate angle of attack.