If using Linux with Nautilus you can connect directly to the server.
1.) create a config file in .ssh directory.
sudo gedit ~/.ssh/config
Paste the following and save. You may need to edit the path to your pem files.
Host myserver HostName 220.127.116.11 User ubuntu IdentityFile ~/keys/myserver.pem
Now you can connect using terminal with this example:
on command line will connect to your remote amazon ec2 server without anyother info.
Open Nautilus. press Ctrl+L
there you can type ssh://myserver
Note you can also just trasnfer files directly with this example:
scp -i ~/keys/myserver.pem file.txt email@example.com:/var/www/mysqldump/.