If an atom were to pass through your hand at 99% of the speed of light, you would not feel it in the same way you would feel a physical object moving through your hand at a slower speed. At such high velocities, the effects of special relativity come into play.
According to special relativity, as an object approaches the speed of light, its mass increases, and its length contracts in the direction of motion. These effects become more significant as the speed gets closer to the speed of light. In the case of an atom traveling at 99% of the speed of light, its mass would be significantly increased, and its length would be contracted.
As a result of these relativistic effects, the interaction between the atom and your hand would be drastically altered. The increased mass of the atom would make it more difficult for it to transfer momentum to your hand, and the contracted length might affect the nature of the interaction. It is unlikely that you would feel a distinct sensation or pain from the atom passing through your hand at such high speeds.
It's important to note that this scenario is purely hypothetical since it is currently beyond our technological capabilities to accelerate atoms to such speeds. The discussion of relativistic effects at extreme speeds is based on theoretical predictions and experiments conducted with subatomic particles, but their applicability to macroscopic objects like atoms is limited.