This one is also hard to explain, since we really don't see these two speak or interact much in the manga or the anime. There is a baseline of the relationship that Isis respects Atem because he is literally her pharaoh, the king of the country, so of course, she shows him respect. We don't know how Atem feels about Isis since the reactions we get are from the memory world, where he is confused and out of depth. He does seem to respect Isis as a high priest, but it might just be him only seeing Ishizu in her, or maybe he does really care for her as a person. It is hard to say because we do not know the true feelings behind the memory.
I do like to think that even if Isis and Atem are not friends, she still cares about him because he was very young when he took the throne, and she might be concerned about him. But because they are not friends but a Pharaoh and a priest, she will always linger just a little behind him and say nothing, even when she can see he is in pain of losing the people he cares about. Maybe she feels it is not her place to comfort him, and it pains her that she can't cross that boundary for different reasons.
