./1svn.pdb 1svn { ALL 0.46605 -0.87772 0.11136 16.79288 0.05030 -0.09938 -0.99378 53.98243 0.88333 0.46875 -0.00217 8.60995 } ./1a2q.pdb 1a2q { ALL 0.99861 0.05264 0.00348 -2.51082 -0.05274 0.99759 0.04513 -1.11251 -0.00110 -0.04525 0.99898 2.24606 } ./1sbh.pdb 1sbh { ALL 0.99864 0.05184 0.00465 -2.53065 -0.05200 0.99746 0.04863 -1.20511 -0.00212 -0.04880 0.99881 2.51668 } ./1sca.pdb 1sca { ALL 0.56772 0.12629 -0.81348 -1.32246 0.80664 -0.28268 0.51906 -38.12691 -0.16440 -0.95086 -0.26236 124.25449 } ./3vsb.pdb 3vsb { ALL -0.81035 -0.12758 0.57189 7.07354 0.52159 0.28766 0.80324 9.60690 -0.26699 0.94920 -0.16656 38.75608 } Alignment score Sc = 9.438218 Alignment length Lp = 275 RMS deviation after fitting on 263 atoms = 0.781313 Secondary structures are from DSSP >1svn (cluster A) sequence >1a2q (cluster B) sequence >1sbh (cluster B) sequence >1sca (cluster B) sequence >3vsb (cluster B) sequence >space >1svn_dssp (cluster A) secondary structure from DSSP >1a2q_dssp (cluster B) secondary structure from DSSP >1sbh_dssp (cluster B) secondary structure from DSSP >1sca_dssp (cluster B) secondary structure from DSSP >3vsb_dssp (cluster B) secondary structure from DSSP #T -- '1' = equivalenced residues #P -- averaged Pij #A -- distance between averaged CA atoms in angtroms #G -- Pij' value ABBBB ABBBBequiv Pij Distance Pij' * iteration 1 AAAAA ????? 1 0.94805 0.58843 10.06000 QQQQQ ????? 1 0.94902 0.39270 10.07000 SSSTT ????? 1 0.93910 0.61760 9.96700 VVVVV ????? 1 0.94411 0.60464 10.01900 PPPPP ????? 1 0.94507 0.66298 10.02900 WYYYY ????? 1 0.93303 0.81685 9.90400 GGGGG ????? 1 0.92205 0.88996 9.79000 IVVII ????? 1 0.91203 0.95048 9.68600 SSSPP ????? 1 0.89402 1.03777 9.49900 RQQLL ????? 1 0.92908 0.74365 9.86300 VIIII ????? 1 0.92908 0.86187 9.86300 QKKKK ????? 1 0.91107 1.02101 9.67600 AAAAA ????? 1 0.92407 0.91314 9.81100 PPPDD ????? 1 0.92407 0.78763 9.81100 AAAKK ????? 1 0.93207 0.73739 9.89400 ALLVV ????? 1 0.92908 0.78214 9.86300 HHHQQ ????? 1 0.93110 0.63934 9.88400 NSSAA ????? 1 0.92311 0.81168 9.80100 RQQQQ ????? 1 0.91405 0.94909 9.70700 GGGGG ????? 1 0.91405 0.91496 9.70700 LYYFF ????? 1 0.92407 0.81993 9.81100 TCTKK ????? 1 0.94709 0.55325 10.05000 GGGGG ????? 1 0.94411 0.67308 10.01900 SSSAA ????? 1 0.93804 0.71458 9.95600 GNNNN ????? 1 0.91704 0.92453 9.73800 VVVVV ????? 1 0.94102 0.63857 9.98700 KKKKK ????? 1 0.95210 0.52881 10.10200 VVVVV ????? 1 0.95210 0.39577 10.10200 AAAAA ????? 1 0.95008 0.54618 10.08100 VVVVV ????? 1 0.95403 0.41440 10.12200 LIILL ????? 1 0.95509 0.40051 10.13300 DDDDD ????? 1 0.95403 0.37080 10.12200 TSSTT ????? 1 0.95403 0.39364 10.12200 GGGGG ????? 1 0.95210 0.47108 10.10200 IIIII ????? 1 0.94603 0.64220 10.03900 SDDQQ ????? 1 0.87408 0.59719 9.29200 SSAA ???? TSSSS ????? 0 0.40509 1.54616 4.42300 HHHHH ????? 1 0.82207 0.73219 8.75200 PPPPP ????? 1 0.94208 0.69222 9.99800 DDDDD ????? 1 0.94709 0.62176 10.05000 LLLLL ????? 1 0.94102 0.74885 9.98700 NKKNN ????? 1 0.93004 0.86188 9.87300 IVVVV ????? 1 0.93611 0.70904 9.93600 RAAVV ????? 1 0.93707 0.66755 9.94600 GGGGG ????? 1 0.94603 0.52164 10.03900 GGGGG ????? 1 0.95104 0.44919 10.09100 AAAAA ????? 1 0.95104 0.50596 10.09100 SSSSS ????? 1 0.94902 0.57632 10.07000 FMFFF ????? 1 0.94208 0.70611 9.99800 VVVVV ????? 1 0.90702 0.78370 9.63400 PPPAA ????? 1 0.83102 1.10794 8.84500 GSSGG ????? 1 0.84605 1.00274 9.00100 EEE ??? PTTEE ????? 1 0.59706 1.37440 6.41600 SNNAA ????? 1 0.79307 0.60879 8.45100 PPYY ???? TFFNN ????? 1 0.55111 1.75467 5.93900 QQQTT ????? 1 0.74404 1.18388 7.94200 DDDDD ????? 1 0.91309 0.91650 9.69700 GNNGG ????? 1 0.91810 0.89786 9.74900 NNNNN ????? 1 0.93707 0.69099 9.94600 GSSGG ????? 1 0.94507 0.65768 10.02900 HHHHH ????? 1 0.95104 0.47991 10.09100 GGGGG ????? 1 0.95008 0.57942 10.08100 TTTTT ????? 1 0.95306 0.47582 10.11200 HHHHH ????? 1 0.95306 0.47488 10.11200 VVVVV ????? 1 0.95509 0.36384 10.13300 AAAAA ????? 1 0.95403 0.47554 10.12200 GGGGG ????? 1 0.95210 0.52820 10.10200 TTTTT ????? 1 0.95306 0.48760 10.11200 IVVVV ????? 1 0.95104 0.60773 10.09100 AAAAA ????? 1 0.94805 0.64785 10.06000 AAAAA ????? 1 0.94805 0.63365 10.06000 LLLLL ????? 1 0.94411 0.72389 10.01900 NNDDD ????? 1 0.94305 0.73513 10.00800 NNNNN ????? 1 0.94208 0.71439 9.99800 SSSTT ????? 1 0.94102 0.66846 9.98700 IIITT ????? 1 0.94411 0.64967 10.01900 GGGGG ????? 1 0.94709 0.63100 10.05000 VVVVV ????? 1 0.94805 0.64278 10.06000 LLLLL ????? 1 0.95104 0.56468 10.09100 GGGGG ????? 1 0.95104 0.56774 10.09100 VVVVV ????? 1 0.94902 0.64820 10.07000 AAAAA ????? 1 0.95104 0.57781 10.09100 PPPPP ????? 1 0.95008 0.60356 10.08100 SCSSS ????? 1 0.94709 0.60865 10.05000 AAAVV ????? 1 0.93611 0.80733 9.93600 ESSSS ????? 1 0.93303 0.82531 9.90400 LLLLL ????? 1 0.93804 0.67482 9.95600 YYYYY ????? 1 0.94902 0.46818 10.07000 AAAAA ????? 1 0.95403 0.33453 10.12200 VVVVV ????? 1 0.94902 0.61502 10.07000 KKKKK ????? 1 0.94603 0.63769 10.03900 VVVVV ????? 1 0.93505 0.80993 9.92500 LLLLL ????? 1 0.93910 0.76940 9.96700 GGGNN ????? 1 0.93110 0.77957 9.88400 AAASS ????? 1 0.91010 0.93299 9.66600 SDDSS ????? 1 0.92609 0.72553 9.83200 GGGGG ????? 1 0.93409 0.51817 9.91500 SSSSS ????? 1 0.91608 0.90118 9.72800 GGGGG ????? 1 0.93910 0.68424 9.96700 SQQSS ????? 1 0.93409 0.80745 9.91500 VYYYY ????? 1 0.93409 0.72519 9.91500 SSSSS ????? 1 0.94102 0.58982 9.98700 SWWGG ????? 1 0.93804 0.77871 9.95600 IIIII ????? 1 0.93804 0.75938 9.95600 AIIVV ????? 1 0.94709 0.56021 10.05000 QNNSS ????? 1 0.94902 0.60806 10.07000 GGGGG ????? 1 0.94805 0.64799 10.06000 LIIII ????? 1 0.94805 0.64841 10.06000 EEEEE ????? 1 0.94805 0.66409 10.06000 WWWWW ????? 1 0.94507 0.71292 10.02900 AAAAA ????? 1 0.94411 0.74573 10.01900 GIITT ????? 1 0.94208 0.72809 9.99800 NAATT ????? 1 0.94507 0.62032 10.02900 NNNNN ????? 1 0.93910 0.69602 9.96700 GNNGG ????? 1 0.93611 0.70531 9.93600 MMMMM ????? 1 0.94805 0.47529 10.06000 HDDDD ????? 1 0.94902 0.61804 10.07000 VVVVV ????? 1 0.94805 0.62805 10.06000 AIIII ????? 1 0.95008 0.55689 10.08100 NNNNN ????? 1 0.95210 0.54175 10.10200 LMMMM ????? 1 0.95509 0.28988 10.13300 SSSSS ????? 1 0.95403 0.41187 10.12200 LLLLL ????? 1 0.95008 0.55429 10.08100 GGGGG ????? 1 0.93910 0.59066 9.96700 SGGGG ????? 1 0.92706 0.72746 9.84200 PPPAA ????? 1 0.89806 0.96937 9.54100 SSSSS ????? 1 0.84306 1.12240 8.97000 PGGGG ????? 1 0.73008 1.49585 7.79700 SSSSS ????? 1 0.82303 1.28257 8.76200 AAATT ????? 1 0.86108 1.25533 9.15700 TAAAA ????? 1 0.84605 1.24145 9.00100 LLLMM ????? 1 0.90606 0.89618 9.62400 EKKKK ????? 1 0.92802 0.79835 9.85200 QAAQQ ????? 1 0.90702 1.01860 9.63400 AAAAA ????? 1 0.92311 0.96763 9.80100 VVVVV ????? 1 0.92503 0.87051 9.82100 NDDDD ????? 1 0.89604 1.06247 9.52000 SKKNN ????? 1 0.86204 1.24345 9.16700 AAAAA ????? 1 0.88506 1.16356 9.40600 TVVYY ????? 1 0.87707 1.15817 9.32300 SAAAA ????? 1 0.83603 1.30866 8.89700 RSSRR ????? 1 0.84403 1.30456 8.98000 GGGGG ????? 1 0.88506 1.15820 9.40600 VVVVV ????? 1 0.89305 1.05390 9.48900 LVVVV ????? 1 0.91010 0.93116 9.66600 VVVVV ????? 1 0.92503 0.85203 9.82100 VVVVV ????? 1 0.94507 0.46309 10.02900 AAAAA ????? 1 0.95403 0.45925 10.12200 AAAAA ????? 1 0.95104 0.53230 10.09100 SAAAA ????? 1 0.94603 0.61044 10.03900 GGGGG ????? 1 0.94507 0.64897 10.02900 NNNNN ????? 1 0.93611 0.66608 9.93600 SEESS ????? 1 0.89903 1.01256 9.55100 GGGGG ????? 1 0.72709 0.74049 7.76600 TTNN ???? SSSS ???? AGGGG ????? 0 0.03011 2.75438 0.53000 SSSS ???? SSTT ???? GSSNN ????? 0 0.12604 1.95831 1.52600 STTTT ????? 1 0.46211 1.65393 5.01500 IVVII ????? 1 0.79404 0.82772 8.46100 SGGGG ????? 1 0.94102 0.61511 9.98700 YYYYY ????? 1 0.94709 0.69272 10.05000 PPPPP ????? 1 0.94305 0.65579 10.00800 AAAAA ????? 1 0.95104 0.33734 10.09100 RKKKK ????? 1 0.94902 0.26557 10.07000 YYYYY ????? 1 0.93804 0.69507 9.95600 APPDD ????? 1 0.93409 0.77739 9.91500 NSSSS ????? 1 0.93303 0.80147 9.90400 AVVVV ????? 1 0.91608 0.88813 9.72800 MIIII ????? 1 0.92407 0.77340 9.81100 AAAAA ????? 1 0.94507 0.65872 10.02900 VVVVV ????? 1 0.95210 0.52906 10.10200 GGGGG ????? 1 0.95008 0.56577 10.08100 AAAAA ????? 1 0.94603 0.68986 10.03900 TVVVV ????? 1 0.94102 0.65666 9.98700 DDDDD ????? 1 0.90105 0.90184 9.57200 QSSSS ????? 1 0.85202 1.20248 9.06300 NSSNN ????? 1 0.86811 1.15763 9.23000 NNNSS ????? 1 0.90808 0.83032 9.64500 NQQNN ????? 1 0.90808 0.97618 9.64500 RRRRR ????? 1 0.91309 0.95613 9.69700 AAAAA ????? 1 0.93707 0.70893 9.94600 SSSSS ????? 1 0.94902 0.58684 10.07000 FFFFF ????? 1 0.95008 0.56938 10.08100 SSSSS ????? 1 0.95104 0.46197 10.09100 QSSSS ????? 1 0.89806 0.49605 9.54100 YVVVV ????? 1 0.81003 1.21272 8.62700 GGGGG ????? 1 0.87504 1.04124 9.30200 APPAA ????? 1 0.88111 1.06242 9.36500 GEEEE ????? 1 0.90404 1.00359 9.60300 LLLLL ????? 1 0.92706 0.91685 9.84200 DDDEE ????? 1 0.92002 0.87320 9.76900 IVVVV ????? 1 0.93804 0.37327 9.95600 VMMMM ????? 1 0.94603 0.62376 10.03900 AAAAA ????? 1 0.95210 0.42127 10.10200 PPPPP ????? 1 0.95008 0.51935 10.08100 GGGGG ????? 1 0.94902 0.50627 10.07000 VVVAA ????? 1 0.94603 0.59547 10.03900 NSSGG ????? 1 0.94507 0.59096 10.02900 VIIVV ????? 1 0.95210 0.45490 10.10200 QQCYY ????? 1 0.95306 0.48055 10.11200 SSSSS ????? 1 0.95509 0.23977 10.13300 TTTTT ????? 1 0.95403 0.38137 10.12200 YLLYY ????? 1 0.94305 0.48416 10.00800 PPPPP ????? 1 0.91502 0.64984 9.71700 GGGTT ????? 1 0.91704 0.72477 9.73800 SNNNN ????? 1 0.93303 0.62386 9.90400 TKKTT ????? 1 0.94305 0.59213 10.00800 YYYYY ????? 1 0.94603 0.37132 10.03900 AGGAA ????? 1 0.92311 0.77139 9.80100 SAATT ????? 1 0.94102 0.48791 9.98700 LYYLL ????? 1 0.95210 0.42428 10.10200 NSSNN ????? 1 0.95210 0.50022 10.10200 GGGGG ????? 1 0.95104 0.52490 10.09100 T TT ? ?? STSST ????? 1 0.62210 1.45213 6.67600 MMMMM ????? 1 0.75204 0.41341 8.02500 AAAAA ????? 1 0.95509 0.38349 10.13300 TSSSS ????? 1 0.95509 0.36518 10.13300 PPPPP ????? 1 0.95306 0.43849 10.11200 HHHHH ????? 1 0.95104 0.53648 10.09100 VVVVV ????? 1 0.95306 0.51471 10.11200 AAAAA ????? 1 0.95306 0.52585 10.11200 GGGGG ????? 1 0.95210 0.51872 10.10200 AAAAA ????? 1 0.95403 0.46213 10.12200 AAAAA ????? 1 0.95306 0.42755 10.11200 AAAAA ????? 1 0.95104 0.43804 10.09100 LLLLL ????? 1 0.94603 0.66645 10.03900 VIIII ????? 1 0.94603 0.69768 10.03900 KLLLL ????? 1 0.93804 0.77650 9.95600 QSSSS ????? 1 0.93505 0.82404 9.92500 KKKKK ????? 1 0.92802 0.91845 9.85200 NHHHH ????? 1 0.92311 0.90114 9.80100 PPPPP ????? 1 0.92205 0.74111 9.79000 SNNNN ????? 1 0.91502 0.82234 9.71700 WWWLL ????? 1 0.91810 0.88897 9.74900 STTSS ????? 1 0.91010 1.00851 9.66600 NNNAA ????? 1 0.92311 0.97806 9.80100 VTTSS ????? 1 0.90904 1.04020 9.65500 QQQQQ ????? 1 0.91203 0.96711 9.68600 IVVVV ????? 1 0.93611 0.67609 9.93600 RRRRR ????? 1 0.93110 0.81662 9.88400 NSSNN ????? 1 0.91906 0.87325 9.75900 HSSRR ????? 1 0.92908 0.72505 9.86300 LLLLL ????? 1 0.93611 0.78572 9.93600 KEESS ????? 1 0.93611 0.81074 9.93600 NNNSS ????? 1 0.91810 0.91119 9.74900 TTTTT ????? 1 0.89305 1.10641 9.48900 ATTAA ????? 1 0.90211 1.09741 9.58300 TTTTT ????? 1 0.91010 1.01608 9.66600 SKYYY ????? 1 0.90105 1.05917 9.57200 LLLLL ????? 1 0.87408 0.94438 9.29200 GGGGG ????? 1 0.78103 1.36052 8.32600 SDDSS ????? 1 0.87504 1.15993 9.30200 TSSSS ????? 1 0.88602 1.17834 9.41600 NFFFF ????? 1 0.88410 1.17289 9.39600 LYYYY ????? 1 0.89710 1.04501 9.53100 YYYYY ????? 1 0.92108 0.85038 9.78000 GGGGG ????? 1 0.92802 0.88092 9.85200 SKKKK ????? 1 0.91107 1.01244 9.67600 GGGGG ????? 1 0.93110 0.85295 9.88400 LLLLL ????? 1 0.93505 0.73547 9.92500 VIIII ????? 1 0.91608 0.96253 9.72800 NNNNN ????? 1 0.91906 0.91098 9.75900 AVVVV ????? 1 0.87302 1.16115 9.28100 EQQEE ????? 1 0.87302 1.18245 9.28100 AAAAA ????? 1 0.88805 1.06792 9.43700 AAAAA ????? 1 0.85404 1.17768 9.08400 TAAAA ????? 1 0.78710 1.40471 8.38900 RQQQQ ????? 1 0.72305 1.61786 7.72400 *