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ports are just a definition of the signals through a specific module. When you want a chip to talk with the outside world (IOs, other chips, Analog devices) you will usually need to go through a pad, because you need to transform from the internal chip levels of current and voltage, to the outer level, while keeping the signals running fast enough. Board levels of currents and voltages are usually much higher. The pad is a pretty complex analog circuit to do this transformation.