Heya,
If we take the normal modes, the Phrygian mode is the one that sounds "Spanishy". E Phrygian has the notes E, F, G, A, B, C, D. A natural minor contains the same notes A, B, C, D, E, F, G. No sharps or flats.
Here's the important bit.
The note "G" in E Phrygian means that it is a minor scale. There are also some other features of the scale that makes it sound "spanish". E-F, is a semitone at the start of the scale, this is unusual to our ears. B-C is a minor 6th, which makes it sound minor, and D-E, outlines a minor 7th, which again is minor.
When we take A harmonic minor A, B, C, D, E, F, G#, and use it in the context of E -- E, F, G#, A, B, C, D. This has all the traits of E Phrygian, it sounds minor,
but the G# makes it a major scale. So when we are listening to the notes, we hear a load of minor tonalities, and then suddenly, once you land on a G#, it flips in your head to a major, which makes it stand out so much.
And yes, if you use D harmonic minor over A, you will get exactly the same.
I hope I'm not making this worse by making it more confusing!!
/Tank
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