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This sketch shows the relationships between the USS positions on a real double helix. Unfortunately it doesn't indicate the relative strengths of the different positions' consensus (as the logo does). And I haven't yet taken the time (or found an easy way) to show which positions are at the back and which are at the front as they wrap around the helix. If you look closely you'll see that the pink and blue strands of the double helix are drawn to coil around each other, but the some of letters get in the way of seeing which strand is in front.When it's drawn properly it will show that the first part of the USS core (the AAGTG) is on the same side of the double helix as the two AT-rich flanking segments. The significance of this will (I hope) be clear once we understand how the USS functions in DNA uptake.
For amino acid alpha helices, you can use software to draw what's called a helical wheel (looking down the helix central axis), which illustrates which side the residues lie on. Is there something similar for DNA helices?
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