Kaworu is touching Shinji’s back first, then lets his hands slide to his neck. Imagine someone wrapping their hands around your neck directly from behind. You would get scared or panic, right? Because it is a visceral fear of being restrained or chocked. Touching someone’s back on the other hand carries a message of sympathy and reassurance. Considering Shinji is already affected by the choker, and won’t listen to anything in his current state anyways, Kaworu is telling him that he wants no harm by touching his back first and giving him a feeling of safety.