When I first started playing electric guitar, one question that I constantly asked myself was how do great metal guitarists play solos with an overdriven tone, and yet still manage to sound clean. Their sound to me was like polished steel or chrome; pure, smooth and shiny, whereas mine was like a rusty bar; pitted and corroded.
It took me a long time to work out why my single-note tone was so rough.
I eventually found that distorted tone makes its presence felt when harmony is introduced into the equation. So the conclusion was that my single notes' were nothing of the sort. There was harmonic interference, and this was causing the crunch.
Pythagoras discovered that if you start with a pitch, say an A, and tune 7 pure octaves to arrive at the same pitch 7 octaves higher, the pitch arrived at will be flatter than it would be if you started with the same pitch and tuned 12 pure fifths to get to the same point. This discrepancy is known as the Pythagorean comma. It's this that causes the crunch, and the further you go up the harmonic series, the more this makes its presence felt, and the crunchier things become. Distortion is particularly good at exposing this flaw'.
INTERVALS IN ORDER OF PURITY
A unison, two notes of exactly the same pitch, isn't really an interval, but it is the purest 'two note' sound. Play the E at the 5th fret of the 2nd string, and the open E of the 1st, and provided all other strings are muted, your guitar is in tune and well intonated, there should be no crunch.
Next comes the octave. They should sound pretty clean and pure.
A fifth is the purest of the intervals that are made up of different notes. A bit of crunch comes in but it's not too bad. This is why metal progressions tend to contain 5s.
A fourth is a fifth inverted. It's slightly less pure, and so a touch crunchier.
Major thirds are where the crunch really starts to become a problem'. This is why major chords played with a distorted tone don't always sound that great.
Not sure which comes next, but let's just say things are going to get crunchier not cleaner from here on. A real stinker is a minor second. Try playing the Bb at the 3rd fret of the 3rd string together with the open 2nd B string. Yuck! This sound is what I mean by the rusty bar.
And here's the point: you can get this rusty sound by playing single notes, especially when hammering on and pulling off.
Without muting any of the strings, pick the A at the 5th fret of the 1st string, and hammer on to the Bb at the 6th. You should hear the same rusty sound as before. This is because the open strings are being vibrated partly due to sympathetic vibration, and partly because the hammer on sent vibrations through the neck and this set the strings off even worse. So mute the 5 open strings in whatever way you like, and pick and hammer the A to Bb again. Hey Presto! A clean tone from a distorted sound. So to cut a long boring story short, if you want clean tone while playing with distortion, keep things neat by muting off open strings. There are lots of ways to do it. Go read about them, and see which ones work best for you.