./1lh1.pdb 1lh1 { ALL 0.92875 0.36043 0.08663 1.78050 -0.37068 0.90517 0.20799 3.28968 -0.00345 -0.22529 0.97429 -1.19931 } ./2lhb.pdb 2lhd { ALL 0.92919 0.36001 0.08360 1.86698 -0.36959 0.90528 0.20945 3.26820 -0.00028 -0.22552 0.97424 -1.20732 } ./1ecd.pdb 1ecd { ALL 0.92950 0.36047 0.07803 1.89342 -0.36879 0.90564 0.20931 3.25804 0.00478 -0.22333 0.97473 -1.28738 } ./4mbn.pdb 4mbn { ALL 0.92993 0.35850 0.08190 1.86779 -0.36773 0.90601 0.20957 3.23263 0.00093 -0.22500 0.97436 -1.22813 } ./2hhba.pdb 2hhba { CHAIN A 0.93034 0.35735 0.08226 1.83628 -0.36669 0.90618 0.21066 3.19077 0.00073 -0.22615 0.97409 -1.23948 } ./2hhbb.pdb 2hhbb { CHAIN B 0.92993 0.35865 0.08126 1.85654 -0.36774 0.90597 0.20973 3.24984 0.00160 -0.22492 0.97438 -1.22425 } Alignment score Sc = 7.773767 Alignment length Lp = 160 RMS deviation after fitting on 116 atoms = 2.490356 Secondary structures are from DSSP >1lh1 (cluster A) sequence >2lhd (cluster B) sequence >1ecd (cluster B) sequence >4mbn (cluster B) sequence >2hhba (cluster B) sequence >2hhbb (cluster B) sequence >space >1lh1_dssp (cluster A) secondary structure from DSSP >2lhd_dssp (cluster B) secondary structure from DSSP >1ecd_dssp (cluster B) secondary structure from DSSP >4mbn_dssp (cluster B) secondary structure from DSSP >2hhba_dssp (cluster B) secondary structure from DSSP >2hhbb_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 ABBBBB ABBBBBequiv Pij Distance Pij' * iteration 1 P ? I ? V ? D ? T ? G ? S ? V ? GA V ?? ? AP VVH ?? ??? LLLLLL ?????? 1 0.47133 1.87910 6.86900 TSSSST ?????? 1 0.51233 1.97921 7.44900 EAAEPP ?????? 1 0.57137 1.87679 8.28400 SADGAE ?????? 1 0.62736 1.77749 9.07600 QEQEDE ?????? 1 0.72033 1.61127 10.39100 AKIWKK ?????? 1 0.77032 1.49644 11.09800 ATSQTS ?????? 1 0.77336 1.48010 11.14100 LKTLNA ?????? 1 0.82836 1.32093 11.91900 VIVVVV ?????? 1 0.87135 1.18409 12.52700 KRQLKT ?????? 1 0.84837 1.24924 12.20200 SSAHAA ?????? 1 0.82030 1.29528 11.80500 SASVAL ?????? 1 0.85636 1.16202 12.31500 WWFWWW ?????? 1 0.85233 1.16355 12.25800 EADAGG ?????? 1 0.79535 1.31611 11.45200 EPKKK ????? FVVVVK ?????? 1 0.66632 1.49047 9.62700 NY EGV ?? ??? AS AA ?? ?? NTKDHN ?????? 1 0.50031 1.72619 7.27900 IY VAV ?? ??? PEGAGD ?????? 1 0.33834 2.17145 4.98800 KT GEE ?? ??? HSDHYV ?????? 1 0.67636 1.36386 9.76900 TGPGGG ?????? 1 0.73235 1.53725 10.56100 HVVQAG ?????? 1 0.68131 1.61990 9.83900 RDGDEE ?????? 1 0.76233 1.35692 10.98500 FIIIAA ?????? 1 0.82730 1.04859 11.90400 FLLLLL ?????? 1 0.69432 1.47233 10.02300 IVYIEG ?????? 1 0.63733 1.57960 9.21700 LKARRR ?????? 1 0.72330 1.37684 10.43300 VFVLML ?????? 1 0.78934 1.03505 11.36700 LFFFFL ?????? 1 0.65034 1.50048 9.40100 ETKKLV ?????? 1 0.50731 1.78145 7.37800 ISASSV ?????? 1 0.55334 1.65525 8.02900 ATDHFY ?????? 1 0.75335 1.20290 10.85800 PPPPPP ?????? 1 0.80935 1.04625 11.65000 AASETW ?????? 1 0.73532 1.44891 10.60300 AAITTT ?????? 1 0.81535 1.33226 11.73500 KQMLKQ ?????? 1 0.78036 1.22843 11.24000 DEAETR ?????? 1 0.68732 1.48526 9.92400 LFKKYF ?????? 1 0.83437 1.06660 12.00400 FFFFFF ?????? 1 0.73037 0.88371 10.53300 SPTDPE ?????? 1 0.51735 1.73052 7.52000 FKQRHS ?????? 1 0.54733 1.67434 7.94400 LFFFFF ?????? 1 0.57236 1.23937 8.29800 KKAK G ???? ? GGGHDD ?????? 1 0.39935 1.86477 5.85100 TL L L ?? ? ? STKK S ???? ? ETDT T ???? ? ALE P ??? ? DEA D ??? ? VESELA ?????? 0 0.17135 1.85421 2.62600 PLIMSV ?????? 1 0.35736 1.65072 5.25700 QKKKHM ?????? 1 0.53531 1.76083 7.77400 NKGAGG ?????? 1 0.37433 2.06975 5.49700 NSTSSN ?????? 1 0.48533 1.93476 7.06700 PAAEAP ?????? 1 0.48837 1.99505 7.11000 EDPDQK ?????? 1 0.58834 1.82319 8.52400 LVFLVV ?????? 1 0.71333 1.55666 10.29200 QREKKK ?????? 1 0.71234 1.57324 10.27800 AWTKGA ?????? 1 0.62637 1.76011 9.06200 HHHHHH ?????? 1 0.75031 1.46688 10.81500 AAAGGG ?????? 1 0.75335 1.41965 10.85800 GENVKK ?????? 1 0.69637 1.59120 10.05200 KRRTKK ?????? 1 0.64334 1.74462 9.30200 VIIVVV ?????? 1 0.72033 1.54066 10.39100 FIVLAL ?????? 1 0.63337 1.75348 9.16100 KNGTDG ?????? 1 0.57236 1.90286 8.29800 LAFAAA ?????? 1 0.62135 1.82335 8.99100 VVFLLF ?????? 1 0.58233 1.85984 8.43900 YDSGTS ?????? 1 0.45132 2.08326 6.58600 EDKAND ?????? 1 0.50335 1.99979 7.32200 AAIIAG ?????? 1 0.58134 1.83534 8.42500 AVILVL ?????? 1 0.44234 2.07127 6.45900 IAGKAA ?????? 1 0.36132 2.17872 5.31300 QSEKHH ?????? 1 0.56932 1.79499 8.25500 L ? EMLKVL ?????? 0 0.04833 2.46624 0.88600 VDPGDD ?????? 0 0.14031 2.45573 2.18700 T ? GD ?? T ? VE ?? VKNHDN ?????? 1 0.33431 1.84461 4.93100 VMIHML ?????? 1 0.33537 1.73095 4.94600 TSEEPK ?????? 1 0.57837 1.48919 8.38300 D ? AMAANG ?????? 0 0.14236 2.55865 2.21600 TKDEAT ?????? 0 0.24735 2.34348 3.70100 LLVLLF ?????? 1 0.47635 1.73588 6.94000 KRNKSA ?????? 1 0.54535 1.86095 7.91600 NNTPAT ?????? 1 0.49734 1.92082 7.23700 LLFLLL ?????? 1 0.70732 1.49450 10.20700 GSVASS ?????? 1 0.64836 1.57710 9.37300 SGAQDE ?????? 1 0.44234 1.99241 6.45900 VKSSLL ?????? 1 0.56833 1.84206 8.24100 HHHHH ????? HA AAC ?? ??? VKKTHD ?????? 1 0.36733 1.91149 5.39800 SSPKKK ?????? 1 0.52131 1.75392 7.57600 KFRHLL ?????? 1 0.65437 1.73135 9.45800 GQGKRH ?????? 1 0.45535 1.90367 6.64300 VVVIVV ?????? 1 0.66936 1.06086 9.67000 ADTPDD ?????? 1 0.82730 0.77487 11.90400 DPHIPP ?????? 1 0.80136 1.03535 11.53700 AEDKVE ?????? 1 0.84632 1.12859 12.17300 HYQYNN ?????? 1 0.85431 1.11632 12.28600 FFLLFF ?????? 1 0.81437 1.27882 11.72100 PKNEKR ?????? 1 0.81535 1.21871 11.73500 VVNFLL ?????? 1 0.86937 0.85162 12.49900 VLFILL ?????? 1 0.88436 0.91093 12.71100 KARSSG ?????? 1 0.85332 1.10038 12.27200 EAAEHN ?????? 1 0.89532 0.76210 12.86600 AVGACV ?????? 1 0.90635 0.85822 13.02200 IIFILL ?????? 1 0.89433 1.03736 12.85200 LAVILV ?????? 1 0.89334 0.89689 12.83800 KDSHVC ?????? 1 0.87835 0.83696 12.62600 TTYVTV ?????? 1 0.85134 1.15336 12.24400 IVMLLL ?????? 1 0.83734 1.05659 12.04600 K KHAA ? ???? E ASAH ? ???? V HRHH ? ???? V HLF ? ??? G TPPG ? ???? A GAK ? ??? KADDEE ?????? 1 0.48137 1.72057 7.01100 W FFFF ? ???? SA GTT ?? ??? E AAPP ? ???? E GDAP ? ???? LGAAVV ?????? 1 0.63337 1.42936 9.16100 NDEQHQ ?????? 1 0.72231 0.98492 10.41900 SAAGAA ?????? 1 0.84434 1.16882 12.14500 AGAASA ?????? 1 0.86732 1.12895 12.47000 WFWMLY ?????? 1 0.86937 1.08394 12.49900 TEGNDQ ?????? 1 0.85933 1.04582 12.35700 IKAKKK ?????? 1 0.86831 1.08262 12.48400 ALTAFV ?????? 1 0.88634 1.08125 12.73900 YMLLLV ?????? 1 0.87637 1.08135 12.59800 DSDEAA ?????? 1 0.87835 0.99707 12.62600 EMTLSG ?????? 1 0.88634 0.96430 12.73900 LIFFVV ?????? 1 0.84837 1.20154 12.20200 ACFRSA ?????? 1 0.85431 1.18412 12.28600 IIGKTN ?????? 1 0.85332 1.09811 12.27200 VLMDVA ?????? 1 0.83635 1.16751 12.03200 ILIILL ?????? 1 0.80737 1.24395 11.62200 KRFATA ?????? 1 0.79931 1.25029 11.50800 KSSASH ?????? 1 0.70930 1.32641 10.23500 KKK ??? Y ? K ? EAKE ???? MYMLYY ?????? 1 0.45231 1.94352 6.60000 D ? D ? A GRH ? ??? A Y ? ? Q ? G ? *