I am converting my project from Arduino uno to a PCB to reduce the size and wanted to know if the i2c channel will still be accessible?
For I2C you need to connect to pins 27 and 28.  In the circuit you have drawn above, they are not connected to anything, though they are labelled A5 and A6.  So as long as you connect them to your I2C bus, and don't connect anything else to them, then it will work.