Help understanding the wiring in this electrical box
OK, so it sounds like Cable 2 is your actual power supply to this circuit.  Black is hot and white is neutral. 

Cable 5

goes off to a 3-way switch.  There may also be one or more 4-ways in between the 3way and here.  The 3 wires in  cable 5 are:  (all the way through any 4-ways to the far 3-way): 


Always-hot (white, by law, but also requires black tape or sleeving) 
Traveler (black; I recommend yellow tape or sleeving)
Traveler (red; I recommend yellow tape or sleeving)


The 3-way's job is to connect always-hot to one or the other travelers.   If there are any 4-ways in the line, they will swap the travelers (or not), alternating which one has always-hot. 

The always-hot must be white because neutral is not present, so white is being reused for a hot, and if always-hot is present, it must be the white so it is more clear that it's not neutral.  It also requires the sleeving. 

Cable 4

Cable 4 carries the other fork of the 3-way circuit.  Down cable 4, there will be a 3-way switch, as well as any number of 4-way switches; and then at one of those switches, a branch will come off going to the lamp.  The three wires are: 


Neutral (white, by law) 
Traveler (black; I recommend yellow tape or sleeving)
Traveler (red; I recommend yellow tape or sleeving)


So that pretty much "wraps up with a bow" the cable 2-4-5 relationship.   But now, we've got a problem. 

Cables 1 and 3 seem unrelated to the others

If cables 1 and 3 were both downline circuits that got their "hots" from cable 2, I'd be like "Okay, that's normal enough".  But what you seem to be saying is that their hots only connect to each other, not cable 2.   If that's the case, the neutrals mustn't connect, either. 

If cables 1 and 3 are shut off by a different circuit breaker than cable 2, then it's absolutely vital they be separated.  You cannot mix neutrals of different circuits! 

Granted, you're supposed to clump together all grounds.  But because of this, people often think they can do the same with neutrals.  No.  Nothing prevents both circuits' current from returning on the same neutral (e.g. if one wire broke).  This can cause a 200% overload on the active neutral wire, and what will detect that? Nothing. Neutrals don't have breakers.  Also, it will cause trouble if a GFCI or AFCI breaker is fit to either circuit, because they monitor differential current between wires. 

If separation is called for, you might want to just break this out into a totally separate junction box, to reduce further chance of mistake.