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Monday, November 14, 2005

save direction info in table also


For example, we consider in the paper the motif
>
> 1 3 7 5
> 2 9 8 4 6
>
> the question: Does the rule of handedness allow to change the order of
> strand like
>
> 3 1 7 5
> 2 9 8 4 6
>
-- The answer depends on the durection of strands, specificalle because
you often divide one extended piece ("strand" in a sense of topology)
into two beta-strands ("strand" in a sense of beta-sheet). To avoid
this below? I will mark strands going FROM US by +, and TO US by *,
and - THE MAIN - I WILL DRAW CONNECTION between strans:
by double-line when it is on "our" side of the sheet,
by sindle-line when it is on the opposite side,
by : when it is in the middle, i.e.,an extended piece leaves onr sheet
and goes to another).
Thus, there are two possibilities for strands 1, 2, 3:
1) All beta-strands are full-lenth strands (from one side of
beta-sheet to another)
--------------------- ---------------------
1 3 7 5 1 3 7 5
* * + +
/ or, the same, /
2 9 8 4 6 2 9 8 4 6
+ *
--------------------- ---------------------
Strands 1, 2, 3 form a right-handed turn (anti-clockwise turn of the
chain when it comes to us - follow the connections; we look
perpendicularly to the strands, along axis of the turn formed by
strands 1, 2, 3). Left and right figures have opposite direstion of
the chain, but the same handedness (follow the connections!).
In this case, the change that you propose (1 <=> 3, without changing
dirsctions of the strands) gives:
--------------------- ---------------------
3 1 7 5 3 1 7 5
* * + +
// or, the same, //
2 9 8 4 6 2 9 8 4 6
+ *
--------------------- ---------------------
Handedness changed! - follow the connections!
"Rule of handedness" forbids this change...

2) Beta-strand in the middle of the sheet is a full-lenth strand (from
one side of beta-sheet to another), and two beta-strands at the edge
are "half-srands" (I wrote you about that)
--------------------- ---------------------
1 3 7 5 1 3 7 5
* + + *
: / or, the same, : /
2 9 8 4 6 2 9 8 4 6
* +
--------------------- ---------------------
In this case "handedness" is not defined, sinse we have not a full
(~360deg) turn from strand 1 to 3, but half-a-turn (~180deg).
Actually, in this case - as I recommended you - you should draw
--------------------- ---------------------
1a 2 6 4 1a 2 6 4
* + + *
: / or, the same, : /
1b 8 7 3 5 2b 8 7 3 5
* +
--------------------- ---------------------

In this case, the change that you propose (1 <=> 3, without changing
dirsctions of the strands) gives:
--------------------- ---------------------
3 1 7 5 3 1 7 5
* + + *
: // or, the same, : //
2 9 8 4 6 2 9 8 4 6
* +
--------------------- ---------------------
and "handedness" is not defined again.
"Rule of handedness" is silent in this case...

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