In general, work can be copyrighted if it is an original work and it is "fixed in a tangible medium of expression" (something that is printed or recorded or on an active website, for example). A website is a structure containing content that can be copyrighted.
Content on a website qualifies as intellectual property that can be copyrighted if the work is original, is owned by the applicant, and is clearly described. Your website is protected the minute it goes "live" on a server; you don't have to register the copyright for it to be effective.3
Copyright protection on a website is for the content on that site. The U.S. Copyright Office also says that content is "material that is perceptible to the users of a particular website." It includes just about everything from news articles, literature, blogs, music, audio such as a podcast, webinars, games, and video.
You can only copyright what's already on your website. The U.S. Copyright Office indicates that the registration extends only to the content presented with the registration. Any content you add to the website later, or any updates to the website would require its own registration.