There is a Grunt plugin grunt-protractor-coverage which provides code coverage metrics for Protractor tests.
If you are using Angular CLI, code coverage for Protractor isn't supported out of the box yet. There is a feature request to add code coverage for e2e tests here
Unfortunately, as your product code and test code don't occupy the same code base, generating code coverage automatically will be difficult.
An alternative to code coverage for e2e tests is functional/feature coverage. This can be achieved by determining the number of user functions/features your application has and how many of those functions/features are covered by an e2e test. It is then possible to calculate the percentage of functions/features covered. I'm not aware of an automated tool which will do this however.
I have managed to get the e2e coverage by pre-instrumenting the code with Istanbul/nyc and then downloading the coverage info via protractor. You can find a sample solution here: https://github.com/edvlucas/angular-e2e-coverage
