i use kohana framework which have 3 folders applications, system and public. I uploaded public folder to httpdocs but applications and system folders should be away from httpdocs. I should upload upper level of httpdocs but plesk structure doesn't allow that. What should i do ? (i am owner of vps)
The Plesk structure includes a private directory along with your httpdocs/cgi-bin etc.
The private directory has tighter permissions than the httpdocs directory which is readable by the user and the psaserv group.
As it is a VPS you could alter the permissions of the private directory (/var/www/vhosts/domain.com/private or c:\inetpub\vhosts\domain.com\private) to reflect the same permissions as the httpdocs directory. Then you could use the private directory.
I guess there is nothing stopping you creating your own directories with the same permissions as httpdocs.
Note: you may need to do this via SSH or remote desktop as the root/Administrator user. I don't think the plesk file manager will let you do it... but, maybe it will.