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how can I know who enter web server and how can I protect my IP from others?

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up vote 0 down vote accepted

Your access logs should show who accesses what files.

I would install shorewall and allow incoming access only to limited services. It is very flexible in allowing you to log connections into and out of the server.

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filter outgoing traffic. deny all of it and allow only for connections established to your serve and only to few destinations you need [ eg automatic updates checking for some web apps or operating system you have ]. in this way it'll be more difficult to download potentially harmful payload attacker might need. preferably limit on external firewall, in worst case on system itself [ iptables for OUTPUT on linux ]

keep your system/webapps up to date.

use fail2ban or similar to prevent password guessing. allow ftp / ssh / rdp access only from trusted list of hosts.

if you are paranoid - run consistency scans to check for file content replaced without your knowledge.

as part of security via obscurity - leave your default vhost with error page [eg 403 not permitted] and serve your actual content from other vhosts so random bot scanning based on ip address cannot harm you.

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