./1sca.pdb 1sca { ALL 0.54066 0.15854 -0.82617 -0.34935 0.83199 -0.24602 0.49726 -41.34871 -0.12442 -0.95621 -0.26492 121.16165 } ./1ubnA.pdb 1ubn { ALL -0.82563 0.56184 0.05172 63.09498 0.29865 0.51295 -0.80479 44.14487 -0.47869 -0.64902 -0.59130 70.54329 } ./1ak9.pdb 1ak9 { ALL 0.99959 0.01535 -0.02397 -0.10917 -0.01509 0.99982 0.01115 -0.33840 0.02414 -0.01079 0.99965 0.36505 } ./1scjA.pdb 1scj { ALL -0.49302 -0.58658 0.64254 33.47313 -0.34193 -0.54847 -0.76306 65.09751 0.80001 -0.59591 0.06984 27.37673 } Alignment score Sc = 9.561831 Alignment length Lp = 277 RMS deviation after fitting on 270 atoms = 0.464313 Secondary structures are from DSSP >1sca (cluster A) sequence >1ubn (cluster B) sequence >1ak9 (cluster B) sequence >1scj (cluster B) sequence >space >1sca_dssp (cluster A) secondary structure from DSSP >1ubn_dssp (cluster B) secondary structure from DSSP >1ak9_dssp (cluster B) secondary structure from DSSP >1scj_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 ABBB ABBBequiv Pij Distance Pij' * iteration 1 AAAA ???? 1 0.94311 0.67473 9.75600 QQQQ ???? 1 0.93718 0.39953 9.69600 TSSS ???? 1 0.91711 0.83285 9.49300 VVVV ???? 1 0.93213 0.68556 9.64500 PPPP ???? 1 0.95013 0.32623 9.82700 YYYY ???? 1 0.95112 0.23384 9.83700 GGGG ???? 1 0.93312 0.61363 9.65500 IVVI ???? 1 0.91908 0.86924 9.51300 PSSS ???? 1 0.91908 0.86866 9.51300 LQQQ ???? 1 0.94212 0.40689 9.74600 IIII ???? 1 0.95309 0.48774 9.85700 KKKK ???? 1 0.95210 0.34699 9.84700 AAAA ???? 1 0.94410 0.60546 9.76600 DPPP ???? 1 0.92917 0.82583 9.61500 KAAA ???? 1 0.93411 0.70679 9.66500 VLLL ???? 1 0.91009 0.91969 9.42200 QHHH ???? 1 0.90712 0.94336 9.39200 ASSS ???? 1 0.92512 0.84835 9.57400 QQQQ ???? 1 0.93312 0.77938 9.65500 GGGG ???? 1 0.94014 0.64544 9.72600 FYYY ???? 1 0.94914 0.47431 9.81700 KTCT ???? 1 0.95309 0.42204 9.85700 GGGG ???? 1 0.95309 0.47666 9.85700 ASSS ???? 1 0.95013 0.44420 9.82700 NNNN ???? 1 0.94113 0.64975 9.73600 VVVV ???? 1 0.95112 0.34714 9.83700 KKKK ???? 1 0.95418 0.43213 9.86800 VVVV ???? 1 0.95418 0.42801 9.86800 AAAA ???? 1 0.95309 0.45259 9.85700 VVVV ???? 1 0.95210 0.26371 9.84700 LIII ???? 1 0.95112 0.50809 9.83700 DDDD ???? 1 0.95112 0.48139 9.83700 TSSS ???? 1 0.94716 0.61427 9.79700 GGGG ???? 1 0.94914 0.54790 9.81700 IIII ???? 1 0.94212 0.73246 9.74600 QDDD ???? 1 0.92917 0.78833 9.61500 ASSS ???? 1 0.91908 0.83487 9.51300 SSSS ???? 1 0.94311 0.54700 9.75600 HHHH ???? 1 0.95013 0.54172 9.82700 PPPP ???? 1 0.95210 0.54859 9.84700 DDDD ???? 1 0.95112 0.59804 9.83700 LLLL ???? 1 0.95210 0.52033 9.84700 NKKN ???? 1 0.95112 0.53715 9.83700 VVVV ???? 1 0.94815 0.61701 9.80700 VAAR ???? 1 0.94113 0.72480 9.73600 GGGG ???? 1 0.94914 0.59247 9.81700 GGGG ???? 1 0.95210 0.44942 9.84700 AAAA ???? 1 0.95210 0.50194 9.84700 SSSS ???? 1 0.95309 0.41468 9.85700 FMFF ???? 1 0.94815 0.54803 9.80700 VVVV ???? 1 0.90712 0.52403 9.39200 APPP ???? 1 0.78809 1.19113 8.18800 GSSS ???? 1 0.68517 1.54117 7.14700 EEE ??? ETTT ???? 0 0.28616 1.86832 3.11100 ANNN ???? 1 0.64909 0.85382 6.78200 YPPP ???? 1 0.94410 0.59620 9.76600 NFFY ???? 1 0.94815 0.61798 9.80700 TQQQ ???? 1 0.94014 0.68875 9.72600 DDDD ???? 1 0.94716 0.52916 9.79700 GNNG ???? 1 0.94716 0.57167 9.79700 NNNS ???? 1 0.93411 0.72925 9.66500 GSSS ???? 1 0.94509 0.47022 9.77600 HHHH ???? 1 0.95112 0.56159 9.83700 GGGG ???? 1 0.95112 0.55631 9.83700 TTTT ???? 1 0.95418 0.42112 9.86800 HHHH ???? 1 0.95517 0.34126 9.87800 VVVV ???? 1 0.95418 0.38192 9.86800 AAAA ???? 1 0.95517 0.33532 9.87800 GGGG ???? 1 0.95309 0.45468 9.85700 TTTT ???? 1 0.95517 0.34403 9.87800 VVVI ???? 1 0.95418 0.22678 9.86800 AAAA ???? 1 0.95112 0.51236 9.83700 AAAA ???? 1 0.95418 0.43195 9.86800 LLLL ???? 1 0.95210 0.45113 9.84700 DNNN ???? 1 0.94914 0.50193 9.81700 NNNN ???? 1 0.94914 0.50762 9.81700 TSSS ???? 1 0.94212 0.61128 9.74600 TIII ???? 1 0.94410 0.46706 9.76600 GGGG ???? 1 0.94410 0.66538 9.76600 VVVV ???? 1 0.94914 0.59597 9.81700 LLLL ???? 1 0.95309 0.42441 9.85700 GGGG ???? 1 0.95309 0.45910 9.85700 VVVV ???? 1 0.95309 0.43545 9.85700 AAAS ???? 1 0.95418 0.29277 9.86800 PPPP ???? 1 0.95309 0.44442 9.85700 SSCS ???? 1 0.95309 0.39442 9.85700 VAAA ???? 1 0.94914 0.59220 9.81700 SSSS ???? 1 0.94509 0.70270 9.77600 LLLL ???? 1 0.94410 0.68124 9.76600 YYYY ???? 1 0.95013 0.43305 9.82700 AAAA ???? 1 0.95112 0.52165 9.83700 VVVV ???? 1 0.95112 0.51355 9.83700 KKKK ???? 1 0.95013 0.46449 9.82700 VVVV ???? 1 0.94617 0.62920 9.78700 LLLL ???? 1 0.94113 0.75508 9.73600 NGGD ???? 1 0.93411 0.83296 9.66500 SAAS ???? 1 0.93817 0.70283 9.70600 SDDT ???? 1 0.94014 0.64281 9.72600 GGGG ???? 1 0.94212 0.58385 9.74600 SSSS ???? 1 0.92314 0.82079 9.55400 GGGG ???? 1 0.93312 0.70717 9.65500 SQQQ ???? 1 0.94410 0.62529 9.76600 YYYY ???? 1 0.93817 0.73234 9.70600 SSSS ???? 1 0.94617 0.47909 9.78700 GWWW ???? 1 0.95210 0.46785 9.84700 IIII ???? 1 0.95112 0.52016 9.83700 VIII ???? 1 0.95210 0.46433 9.84700 SNNN ???? 1 0.95309 0.49271 9.85700 GGGG ???? 1 0.95309 0.46065 9.85700 IIII ???? 1 0.95112 0.50852 9.83700 EEEE ???? 1 0.94509 0.64733 9.77600 WWWW ???? 1 0.95013 0.43567 9.82700 AAAA ???? 1 0.94815 0.41428 9.80700 TIII ???? 1 0.93718 0.70378 9.69600 TAAS ???? 1 0.93213 0.75563 9.64500 NNNN ???? 1 0.94113 0.52078 9.73600 GNNN ???? 1 0.94914 0.47783 9.81700 MMMM ???? 1 0.95112 0.47151 9.83700 DDDD ???? 1 0.95418 0.25404 9.86800 VVVV ???? 1 0.95418 0.41700 9.86800 IIII ???? 1 0.95418 0.31724 9.86800 NNNN ???? 1 0.95517 0.34438 9.87800 MMMM ???? 1 0.95517 0.28590 9.87800 SSSS ???? 1 0.95418 0.37532 9.86800 LLLL ???? 1 0.95309 0.27002 9.85700 GGGG ???? 1 0.94914 0.41375 9.81700 GGGG ???? 1 0.94815 0.53221 9.80700 APPP ???? 1 0.93718 0.68506 9.69600 SSST ???? 1 0.90613 0.92134 9.38200 GGGG ???? 1 0.85809 1.12200 8.89600 SSSS ???? 1 0.90514 0.85880 9.37200 TAAT ???? 1 0.91118 0.95667 9.43300 AAAA ???? 1 0.92017 0.92234 9.52400 MLLL ???? 1 0.93718 0.79954 9.69600 KKKK ???? 1 0.93915 0.75673 9.71600 QAAT ???? 1 0.93817 0.73438 9.70600 AAAV ???? 1 0.94509 0.62731 9.77600 VVVV ???? 1 0.94113 0.73683 9.73600 DDDD ???? 1 0.94410 0.62923 9.76600 NKKK ???? 1 0.93915 0.72624 9.71600 AAAA ???? 1 0.94509 0.64917 9.77600 YVVV ???? 1 0.94716 0.54956 9.79700 AAAS ???? 1 0.93915 0.68784 9.71600 RSSS ???? 1 0.94410 0.64500 9.76600 GGGG ???? 1 0.95112 0.52131 9.83700 VVVI ???? 1 0.95210 0.48631 9.84700 VVVV ???? 1 0.95418 0.19330 9.86800 VVVV ???? 1 0.95210 0.43017 9.84700 VVVA ???? 1 0.94914 0.51586 9.81700 AAAA ???? 1 0.94914 0.50884 9.81700 AAAA ???? 1 0.95309 0.35523 9.85700 AAAA ???? 1 0.95418 0.29825 9.86800 GGGG ???? 1 0.95309 0.34864 9.85700 NNNN ???? 1 0.94815 0.53590 9.80700 SEEE ???? 1 0.94509 0.65711 9.77600 GGGG ???? 1 0.94914 0.51737 9.81700 NTTS ???? 1 0.87914 0.61393 9.10900 SSSS ???? 1 0.76318 1.33563 7.93600 GGGG ???? 1 0.85018 1.05367 8.81600 SSSS ???? 1 0.89516 0.62982 9.27100 TSST ???? 1 0.86016 1.05371 8.91700 NSSS ???? 1 0.91908 0.58116 9.51300 TTTT ???? 1 0.95112 0.32800 9.83700 IVVV ???? 1 0.95112 0.50224 9.83700 GGGG ???? 1 0.95210 0.46566 9.84700 YYYY ???? 1 0.95210 0.48299 9.84700 PPPP ???? 1 0.95112 0.47112 9.83700 AGAA ???? 1 0.94815 0.56169 9.80700 KKKK ???? 1 0.94410 0.70702 9.76600 YYYY ???? 1 0.94212 0.73273 9.74600 DPPP ???? 1 0.93213 0.87355 9.64500 SSSS ???? 1 0.93817 0.73664 9.70600 VVVT ???? 1 0.94716 0.49847 9.79700 IIII ???? 1 0.95112 0.53773 9.83700 AAAA ???? 1 0.95309 0.43350 9.85700 VVVV ???? 1 0.95418 0.37171 9.86800 GGGG ???? 1 0.95517 0.14230 9.87800 AAAA ???? 1 0.95309 0.39790 9.85700 VVVV ???? 1 0.94815 0.59016 9.80700 DDDN ???? 1 0.93817 0.64848 9.70600 SSSS ???? 1 0.91513 0.93860 9.47300 NSSS ???? 1 0.90811 1.00512 9.40200 SNNN ???? 1 0.89012 1.07294 9.22000 NQQQ ???? 1 0.90218 0.98755 9.34200 RRRR ???? 1 0.92917 0.84259 9.61500 AAAA ???? 1 0.93915 0.72695 9.71600 SSSS ???? 1 0.93718 0.73710 9.69600 FFFF ???? 1 0.93915 0.75585 9.71600 SSSS ???? 1 0.94914 0.52326 9.81700 SSSS ???? 1 0.95309 0.44216 9.85700 VVVA ???? 1 0.95112 0.24591 9.83700 GGGG ???? 1 0.94212 0.60925 9.74600 APPS ???? 1 0.93213 0.76221 9.64500 EEEE ???? 1 0.94617 0.47226 9.78700 LLLL ???? 1 0.95210 0.49208 9.84700 EDDD ???? 1 0.95210 0.49312 9.84700 VVVV ???? 1 0.95418 0.22496 9.86800 MMMM ???? 1 0.95517 0.24586 9.87800 AAAA ???? 1 0.95309 0.31924 9.85700 PPPP ???? 1 0.95013 0.56117 9.82700 GGGG ???? 1 0.95210 0.48773 9.84700 AVVV ???? 1 0.94716 0.57004 9.79700 GSSS ???? 1 0.93213 0.77086 9.64500 VIII ???? 1 0.94617 0.44190 9.78700 YQQQ ???? 1 0.95309 0.46471 9.85700 SSSS ???? 1 0.95418 0.25972 9.86800 TTTT ???? 1 0.95210 0.35260 9.84700 YLLL ???? 1 0.92017 0.66489 9.52400 PPPP ???? 1 0.86609 1.10282 8.97700 TGGG ???? 1 0.89111 1.01707 9.23000 NNNG ???? 1 0.91810 0.81800 9.50300 TKKT ???? 1 0.93718 0.62819 9.69600 YYYY ???? 1 0.94716 0.34914 9.79700 AGGG ???? 1 0.94113 0.61090 9.73600 TAAA ???? 1 0.94509 0.58577 9.77600 LYKY ???? 1 0.95210 0.46457 9.84700 NNSN ???? 1 0.95112 0.55102 9.83700 GGGG ???? 1 0.95309 0.46331 9.85700 T TT ? ?? STSC ???? 1 0.72818 1.18987 7.58200 MMMM ???? 1 0.81518 0.30571 8.46200 AAAA ???? 1 0.95418 0.37419 9.86800 SSST ???? 1 0.95517 0.33559 9.87800 PPPP ???? 1 0.95517 0.41023 9.87800 HHHH ???? 1 0.95517 0.35060 9.87800 VVVV ???? 1 0.95517 0.29282 9.87800 AAAA ???? 1 0.95517 0.30195 9.87800 GGGG ???? 1 0.95517 0.37010 9.87800 AAAA ???? 1 0.95517 0.31027 9.87800 AAAA ???? 1 0.95309 0.44826 9.85700 AAAA ???? 1 0.95210 0.53713 9.84700 LLLL ???? 1 0.95112 0.54052 9.83700 IIII ???? 1 0.95418 0.35491 9.86800 LLLL ???? 1 0.95418 0.36012 9.86800 SSSS ???? 1 0.95309 0.42715 9.85700 KKKK ???? 1 0.95112 0.49612 9.83700 HHHH ???? 1 0.94716 0.54841 9.79700 PPPP ???? 1 0.93411 0.72808 9.66500 NNNT ???? 1 0.92017 0.82296 9.52400 LWWW ???? 1 0.93915 0.64724 9.71600 STTT ???? 1 0.94113 0.69407 9.73600 ANNN ???? 1 0.93718 0.55685 9.69600 STTA ???? 1 0.92512 0.74446 9.57400 QQQQ ???? 1 0.93411 0.75946 9.66500 VVVV ???? 1 0.94716 0.55801 9.79700 RRRR ???? 1 0.94815 0.47025 9.80700 NSSD ???? 1 0.94410 0.66714 9.76600 RSSR ???? 1 0.95013 0.54980 9.82700 LLLL ???? 1 0.95112 0.48933 9.83700 SEEE ???? 1 0.94617 0.62657 9.78700 SNNS ???? 1 0.94815 0.60067 9.80700 TTTT ???? 1 0.95013 0.51799 9.82700 ATTA ???? 1 0.94815 0.53208 9.80700 TTTT ???? 1 0.94509 0.56147 9.77600 KY ?? L ? YKG ??? LLLL ???? 1 0.68616 0.55301 7.15700 GGGG ???? 1 0.93312 0.56401 9.65500 SDDN ???? 1 0.94311 0.64997 9.75600 SSSS ???? 1 0.94914 0.52073 9.81700 FFFF ???? 1 0.95210 0.43740 9.84700 YYYY ???? 1 0.95309 0.41582 9.85700 YYYY ???? 1 0.95210 0.32966 9.84700 GGGG ???? 1 0.94509 0.59760 9.77600 KKKK ???? 1 0.95013 0.44505 9.82700 GGGG ???? 1 0.95210 0.31464 9.84700 LLLL ???? 1 0.95112 0.48421 9.83700 IIII ???? 1 0.95210 0.42158 9.84700 NNNN ???? 1 0.95309 0.46307 9.85700 VVVV ???? 1 0.95210 0.49609 9.84700 EQQQ ???? 1 0.95210 0.50368 9.84700 AAAA ???? 1 0.95210 0.48170 9.84700 AAAA ???? 1 0.95309 0.41899 9.85700 AAAA ???? 1 0.94410 0.44606 9.76600 QQQQ ???? 1 0.93213 0.65796 9.64500 *