The recommended pinout for the 6-pin PDI connector is shown in AVR PDI Pinout.
Connection to a 6-pin 100-mil PDI Header
Use the AVR 6-pin adapter board to connect to connect to a standard 100-mil PDI header.
Connection to a 6-pin 50-mil PDI Header
Use the AVR 6-pin mini adapter board to connect to a standard 50-mil PDI header.