The collusion was likely with Flynn and Manafort. It's almost 100% certain at this point that Flynn (who intends to plead the fifth and not comply with the Senate subpoena) committed a crime by not registering as a foreign agent.
That said, Flynn and Manfort's crimes occurred most likely without Trump knowing (until he became president). Just like Nixon didn't order or know about the break in at Watergate initially.
However, instead of letting Flynn and Manafort fall, Trump's ego (similar to Nixon's paranoia) has caused him to want to stop the investigation, although its legally warranted. Thus the cover up. When Trump learned Flynn was being investigated for being a foreign agent, he hired him anyway...giving him access to highly classified info and giving him input in important US military matters. Trump now knows that his hiring of Flynn despite these obvious problems was incredibly stupid on his part. Since Trump's ego would never admit to a mistake, he resorted to obstructing the Flynn investigation to try to make it go away.