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Top-ranked similarities (based on backbone shifts), as measured by a combination of score and contiguity.
Some relevant parameters:  
        HELIX min length: 5     STRAND min length: 3
        shift-tolerance = -10    permissible-violations = 4   max-breaks = NIL   retain-m = 100   best-n = 100
        anglethresh = 0.5    septhresh = 5   min_length = 4   rmsd-tol = 9.9999999999999E12

Legend:
( ix1 chain1 )  ( ix2 chain2 )   rho___12 rho___21 L2_ERROR (Xbad Xsig Xtot) BRK   maxrho12 maxrho21  SS1 SS2

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( 5841 1sqh_A)  (  433 1bo4_A)     0.3635   0.7955   5.4030 (   1   22   28)   0     0.4090   0.8960   22  10
( 5841 1sqh_A)  (  435 1bob  )     0.3635   0.3808   5.3784 (   1   21   28)   0     0.3635   0.3808   22  21
( 5841 1sqh_A)  (  610 1cjw_A)     0.4544   0.7670   6.1680 (   1   31   45)   0     0.4999   0.8454   22  13
( 5841 1sqh_A)  ( 1657 1fy7_A)     0.3182   0.3684   7.0390 (   0   16   21)   0     0.3636   0.4210   22  19
( 5841 1sqh_A)  ( 1831 1ghe_A)     0.3936   0.4363   6.0511 (   9   40   55)   0     0.4999   0.8451   22  13
( 5841 1sqh_A)  ( 2356 1i12_A)     0.4545   0.9966   4.3222 (   1   33   45)   0     0.4545   0.9966   22  10
( 5841 1sqh_A)  ( 2668 1iyk_A)     0.4080   0.7876   5.7906 (   2   26   36)   0     0.4080   0.7876   22  11
( 5841 1sqh_A)  ( 2669 1iyk_A)     0.4532   0.6186   5.4264 (   2   28   45)   0     0.4539   0.6220   22  16
( 5841 1sqh_A)  ( 3485 1kzf_A)     0.4089   0.5617   6.3085 (   1   24   36)   0     0.4957   0.6673   22  16
( 5841 1sqh_A)  ( 3712 1lrz_A)     0.4445   0.6955   7.1850 (   4   33   45)   0     0.4445   0.6955   22  12
( 5841 1sqh_A)  ( 3713 1lrz_A)     0.4545   0.6661   4.5334 (   1   32   45)   0     0.4545   0.6661   22  15
( 5841 1sqh_A)  ( 3828 1m44_A)     0.4538   0.7069   6.5478 (   2   33   45)   0     0.4993   0.7787   22  14
( 5841 1sqh_A)  ( 3954 1mk4_A)     0.4537   0.8168   6.0644 (   2   32   45)   0     0.4545   0.8318   22  12
( 5841 1sqh_A)  ( 4148 1n71_A)     0.4536   0.8148   6.1763 (   2   31   45)   0     0.4995   0.9059   22  12
( 5841 1sqh_A)  ( 4210 1ne9_A)     0.2798   0.2904   8.4262 (  11   32   45)   0     0.4086   0.5222   22  10
( 5841 1sqh_A)  ( 4211 1ne9_A)     0.4544   0.8307   5.7840 (   1   32   45)   0     0.4544   0.8307   22  12
( 5841 1sqh_A)  ( 4377 1nsl_A)     0.3855   0.4231   5.6781 (  10   43   55)   0     0.4999   0.8450   22  13
( 5841 1sqh_A)  ( 4852 1p0h_A)     0.8165   0.9439   5.3083 (   3  107  153)   0     0.8165   0.9439   22  19
( 5841 1sqh_A)  ( 5189 1q2y_A)     0.4544   0.9947   5.5944 (   1   35   45)   0     0.4544   0.9947   22  10
( 5841 1sqh_A)  ( 5445 1qso_A)     0.4516   0.8332   4.0781 (   3   34   45)   0     0.4516   0.8332   22  11
( 5841 1sqh_A)  ( 5446 1qst_A)     0.4537   0.8840   6.0559 (   2   32   45)   0     0.4999   0.9953   22  11
( 5841 1sqh_A)  ( 5557 1r57_A)     0.3182   0.8746   3.7161 (   0   10   21)   0     0.3182   0.8746   22   8
( 5841 1sqh_A)  ( 5841 1sqh_A)     1.0000   1.0000   0.0000 (   0  202  231)   0     1.0000   1.0000   22  22
( 5841 1sqh_A)  ( 6003 1ufh_A)     0.4079   0.9146   5.9775 (   2   25   36)   0     0.4079   0.9146   22   9
( 5841 1sqh_A)  ( 6244 1vhs_A)     0.4540   0.7612   3.8597 (   2   34   45)   0     0.4995   0.8392   22  13

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