http://msmvps.com/blogs/laflour/archive/2009/01/31/sharepoint-tip-5-do-you-know-that-web-app-permissions-override-site-level-ones.aspxAll permissions set at Web Application level, “Central Administration > Application Management > User Permissions for Web Application” will override the Site level permissions. For example, your user with “Contributor” rights on the site level canenCommunityServer 2008.5 SP2 (Build: 40407.4157)