“They had three notches on the side, representing the three levels of the universe according to their beliefs.”
According to legend, five stones were given to Sankara by the Hindu god Shiva on Mount Kalisa, along with the message that he should go forth and battle evil with them. The stones contained diamonds inside, which would glow when the stones were brought together, as a way to recount the legend of Shiva emerging from the fiery pillar. The diamonds could give warmth and life, but the stones could also be used for fiery destruction for those who betrayed Shiva.
Source: http://indianajones.wikia.com/wiki/Sankara_Stones