Since neither feature build off the other, you should just branch both off of master as you originally would have. This even though they touch a common file (insignificantly).
Then rebase the second pull request (feature2) after the first one (feature1) is merged with the original master (or rebase feature1 if feature2 is merged first).
git fetch upstream
git rebase upstream/master feature2
Here we grab the commits from upstream (original source you've forked from) and then rebase our local feature branch with its commits.
Then fix up any merge conflicts you may encounter and push that commit back up to your fork. The pull request for feature2 will update, now including a commit that fixes up the possible merge conflict and make merging back to the original that much cleaner/easier.
Or the original repository will just grab both of your pull request branches and merge them in themselves, fixing any conflicts that may come up.