Shell, 54, was in charge of an injury plagued unit that gave up 61 sacks second-most in the league and averaged a mere 3.5 yards per running play as the Falcons went 4-12.
Despite the poor performance of the line, head coach Dan Reeves said it wasn't a forced resignation. Shell is scheduled to interview with the expansion Houston Texans for their head coaching job.
"He had some opportunities that he wants to explore," Reeves said. "This gives him a chance to do it."
Shell, who played on two Super Bowl winning teams with Oakland, was an eight-time All-Pro offensive guard during his 15-year career as a player. He was inducted into the Pro Football Hall of Fame in 1989.
Shell was the first black head coach in the NFL's modern era, leading the Raiders from 1989-1994. He had a 54-38 record, including the AFC West title in 1990.
"I always had great respect for him," Reeves said. "During the four years we spent together, I understand why it was always so hard to beat his teams when he was with the Raiders."
Before joining the Falcons, Shell was offensive line coach for the Kansas City Chiefs in 1995 and 1996 and with the Raiders from 1983-88. He took his job with the Falcons in 1997 when Reeves joined the organization.
"I enjoyed my four seasons with the Falcons," Shell said in a statement. "I have chosen this time to seek other football opportunities. I am grateful for the time that I spent with Dan Reeves and the Atlanta Falcons organization. Dan and I will remain friends."
The Falcons have a combined record of 9-23 over the last two seasons after winning the NFC championship in 1998. Nevertheless, Reeves said he plans no major changes in his staff.
The only other possible change involves Bill Kollar, the defensive line coach for 11 seasons. He is scheduled to interview with the St. Louis Rams for a position on their staff.
"Other than that, hopefully the staff will stay intact," Reeves said.
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