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According to the stuff.co.nz website, Clarke said the discomfort was nothing out of the ordinary and he expects to take the field at Hove on Friday.
The skipper made 51 on day four of Australia's heavy loss, his first half century of the series, and with so much expected of him in this frail batting line-up, Clarke said he needed to get another hit out under his belt.
Australia's batting line-up from 1-6 is expected to remain unchanged for the tour match, with every player in desperate need of runs and confidence.
Ed Cowan is unlikely to get a recall so soon after being dropped and Dave Warner won't rejoin the group from Africa until midway through the Sussex game.
Clarke said he'd line-up if fit, acknowledging the pressure on him to perform.
"I haven't got enough runs and I haven't spent enough time in the middle - it's as simple as that," he said.
"The more time I spend in the middle and the more runs I make hopefully I can carry that confidence and momentum into the next Test match.
"I'm as responsible if not more accountable for the way I got out in the first innings. I felt I was hitting the ball well but my shot selection was extremely poor. I expect better of myself and this team needs me to go on when I make a start like that and make a big score. I've got a lot of work to do over the next few days to get ready for the next Test match."
The last time Australia lost six Tests in a row, Kim Hughes stepped down in tears from the captaincy.
Clarke admits he's taken the losses hard, particularly the 347-run demolition at Lord's.
"I say you probably take it more to heart, or more personally because you care so much about your teammates," he said.
"Half my problem I guess is when I was lucky enough to make my debut at the start of my career, I walked into such a great Australian team that winning was certainly a habit and that's something I've become accustomed to and used to and I don't want that to change.
"At the moment we're not performing as well as I would like."
