protractor coverage support with gulp and istanbul (not tested, this is just extracted from larger files to demonstrate how to get protractor coverage working)

gulpfile.js

var istanbul = require('istanbul'),
	gulp = require('gulp'),
	istanbul = require('gulp-istanbul');

gulp.task('js', function() {
	return gulp.src('js')
		.pipe(istanbul({
			includeUntested: true,
			coverageVariable: '__coverage__'
		}))
		.pipe(gulp.dest('dist/'));
});

protractor.conf.js

var waitPlugin = require('./waitPlugin');
var istanbul = require('istanbul');
var collector = new istanbul.Collector();

// An example configuration file.
exports.config = {
  baseUrl: 'http://localhost:3000/',

  capabilities: {
    'browserName': 'chrome'
  },

  specs: ['e2e/**/*.js'],

  framework: 'jasmine2',

  //see https://github.com/angular/protractor/issues/1938#issuecomment-119690252
  plugins: [{path: './waitPlugin.js'}],

  onPrepare: function() {
    var jasmineEnv = jasmine.getEnv();

    jasmineEnv.addReporter(new function() {
      this.specDone = function(spec) {
        if (spec.status !== 'failed') {
          browser.driver.executeScript('return __coverage__;').then(function(coverageResults) {
            collector.add(coverageResults);
          });
        }
      };
    });
  },
  onComplete: function() {
    istanbul.Report.create('cobertura', {dir: 'results/e2e/cobertura'})
      .writeReport(collector, true);
    istanbul.Report.create('lcov', {dir: 'results/e2e/lcov'})
      .writeReport(collector, true);
    waitPlugin.resolve();
  }
};

waitPlugin.js

//see https://github.com/angular/protractor/issues/1938#issuecomment-119690252
var q = require('q');

var deferred = q.defer();

exports.resolve = function() {
  deferred.resolve.apply(deferred, arguments);
};

exports.teardown = function() {
  return deferred.promise;
};

How does it work?. You run first protractor or gulp?