Many quartz crystals have visible areas of previous contact with other crystals. Because the other individual crystals in the family grew so close, and the crystals were not on a parallel growth path, the quartz formed in such a way as to compensate for the other's presence in the ordering of molecules.
It may help to picture the way that a tree growing right next to a chain-link fence will, in time, envelope parts of the fence as it grows. In resting one’s finger or thumb on the contact impression of a quartz crystal one may note that the digit enters below the “surface barrier” of the crystal rather than merely resting on the flat face of the stone.
This point of contact is an ideal way to enter and exchange with the vibrational frequency of the quartz crystal in a way with which it was formerly accustomed. The crystal actually compensated in molecular structuring and formed specifically in order to have an exterior member present in that area.