./1ecd.pdb 1ecd { ALL 1.00000 0.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.00000 1.00000 0.00000 } ./4mbn.pdb 4mbn { ALL 0.99999 -0.00198 0.00349 -0.01417 0.00197 1.00000 0.00171 -0.04548 -0.00350 -0.00170 0.99999 0.05043 } ./2hhba.pdb 2hhba { CHAIN A 0.99999 -0.00312 0.00343 -0.02807 0.00311 0.99999 0.00289 -0.09222 -0.00344 -0.00288 0.99999 0.02816 } ./2hhbb.pdb 2hhbb { CHAIN B 0.99999 -0.00182 0.00285 -0.03095 0.00182 1.00000 0.00163 -0.03481 -0.00285 -0.00162 0.99999 0.05694 } Alignment score Sc = 8.347454 Alignment length Lp = 148 RMS deviation after fitting on 123 atoms = 1.851270 Secondary structures are from DSSP >1ecd (cluster A) sequence >4mbn (cluster B) sequence >2hhba (cluster B) sequence >2hhbb (cluster B) sequence >space >1ecd_dssp (cluster A) 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 ABBB ABBBequiv Pij Distance Pij' * iteration 1 V ? VVH ??? LLLL ???? 1 0.75990 1.19219 9.70400 SSST ???? 1 0.57291 1.69534 7.36700 AEPP ???? 1 0.70389 1.49954 9.00400 DGAE ???? 1 0.78687 1.30316 10.04100 QEDE ???? 1 0.85192 1.02142 10.85400 IWKK ???? 1 0.88288 0.97201 11.24100 SQTS ???? 1 0.83888 1.17468 10.69100 TLNA ???? 1 0.88192 0.71411 11.22900 VVVV ???? 1 0.90593 0.72920 11.52900 QLKT ???? 1 0.87792 1.10834 11.17900 AHAA ???? 1 0.88488 1.05754 11.26600 SVAL ???? 1 0.85088 1.13378 10.84100 FWWW ???? 1 0.80991 1.35808 10.32900 DAGG ???? 1 0.76190 1.51401 9.72900 KKK ??? VVVK ???? 1 0.46186 1.87424 5.97900 EGV ??? AA ?? KDHN ???? 0 0.29391 2.03361 3.88000 VAV ??? GAGD ???? 0 0.18686 2.20718 2.54200 GEE ??? DHYV ???? 1 0.38193 1.60780 4.98000 PGGG ???? 1 0.76790 1.47756 9.80400 VQAG ???? 1 0.84392 1.18807 10.75400 GDEE ???? 1 0.85888 1.14734 10.94100 IIAA ???? 1 0.79591 1.44106 10.15400 LLLL ???? 1 0.82591 1.34673 10.52900 YIEG ???? 1 0.82991 1.20748 10.57900 ARRR ???? 1 0.78487 1.42519 10.01600 VLML ???? 1 0.78391 1.50416 10.00400 FFFL ???? 1 0.80591 1.44651 10.27900 KKLV ???? 1 0.73886 1.53294 9.44100 ASSV ???? 1 0.61292 1.72025 7.86700 DHFY ???? 1 0.75286 1.41548 9.61600 PPPP ???? 1 0.82191 1.38286 10.47900 SETW ???? 1 0.78791 1.48843 10.05400 ITTT ???? 1 0.77887 1.41634 9.94100 MLKQ ???? 1 0.70085 1.44156 8.96600 AETR ???? 1 0.66293 1.45513 8.49200 KKYF ???? 1 0.78791 1.06207 10.05400 FFFF ???? 1 0.78791 1.23162 10.05400 TDPE ???? 1 0.52691 1.58715 6.79200 QRHS ???? 1 0.49290 1.52537 6.36700 FFFF ???? 1 0.43585 1.38070 5.65400 AK G ?? ? GHDD ???? 0 0.17485 2.30034 2.39200 L L ? ? KK S ?? ? DT T ?? ? LE P ?? ? EA D ?? ? SELA ???? 1 0.44786 1.66518 5.80400 IMSV ???? 1 0.41889 1.51416 5.44200 KKHM ???? 1 0.58692 1.23518 7.54200 GAGG ???? 1 0.60892 1.26258 7.81700 TSSN ???? 1 0.62892 1.61207 8.06700 AEAP ???? 1 0.75686 1.39595 9.66600 PDQK ???? 1 0.81191 1.30096 10.35400 FLVV ???? 1 0.80687 1.34702 10.29100 EKKK ???? 1 0.82687 1.29643 10.54100 TKGA ???? 1 0.86592 1.16697 11.02900 HHHH ???? 1 0.88288 1.12394 11.24100 AGGG ???? 1 0.89792 1.10714 11.42900 NVKK ???? 1 0.90593 1.05918 11.52900 RTKK ???? 1 0.91489 0.99730 11.64100 IVVV ???? 1 0.86992 1.14435 11.07900 VLAL ???? 1 0.87488 1.10587 11.14100 GTDG ???? 1 0.89192 1.07481 11.35400 FAAA ???? 1 0.91193 0.88055 11.60400 FLLF ???? 1 0.89688 1.01590 11.41600 SGTS ???? 1 0.89392 1.07586 11.37900 KAND ???? 1 0.92489 0.92814 11.76600 IIAG ???? 1 0.91089 0.87972 11.59100 ILVL ???? 1 0.83487 1.15427 10.64100 GKAA ???? 1 0.73790 1.42266 9.42900 EKHH ???? 1 0.75486 1.37683 9.64100 LKVL ???? 1 0.80287 1.01178 10.24100 PGDD ???? 1 0.72086 1.20918 9.21600 NHDN ???? 1 0.77287 1.23070 9.86600 IHML ???? 1 0.85488 0.82469 10.89100 EEPK ???? 1 0.81487 0.74907 10.39100 AANG ???? 1 0.71590 1.10639 9.15400 DEAT ???? 1 0.67085 1.45241 8.59100 VLLF ???? 1 0.74590 1.42143 9.52900 NKSA ???? 1 0.81687 1.06275 10.41600 TPAT ???? 1 0.82287 0.98602 10.49100 FLLL ???? 1 0.86088 1.06830 10.96600 VASS ???? 1 0.83792 1.10950 10.67900 AQDE ???? 1 0.83087 1.12370 10.59100 SSLL ???? 1 0.86792 1.05023 11.05400 HHHH ???? 1 0.89888 0.87015 11.44100 AAC ??? KTHD ???? 1 0.37288 1.89044 4.86700 PKKK ???? 1 0.63893 1.58277 8.19200 RHLL ???? 1 0.76486 1.32838 9.76600 GKRH ???? 1 0.78487 1.27574 10.01600 VIVV ???? 1 0.87192 0.89236 11.10400 TPDD ???? 1 0.85592 0.84507 10.90400 HIPP ???? 1 0.68789 1.48724 8.80400 DKVE ???? 1 0.75790 1.36077 9.67900 QYNN ???? 1 0.85592 1.14074 10.90400 LLFF ???? 1 0.85792 1.26446 10.92900 NEKR ???? 1 0.86592 1.20913 11.02900 NFLL ???? 1 0.89792 1.01920 11.42900 FILL ???? 1 0.87888 1.12919 11.19100 RSSG ???? 1 0.86488 1.22219 11.01600 AEHN ???? 1 0.84888 1.29574 10.81600 GACV ???? 1 0.87888 1.19225 11.19100 FILL ???? 1 0.88792 1.18020 11.30400 VILV ???? 1 0.86488 1.29264 11.01600 SHVC ???? 1 0.83992 1.36108 10.70400 YVTV ???? 1 0.86088 1.24468 10.96600 MLLL ???? 1 0.81487 1.41894 10.39100 KHAA ???? 1 0.77887 1.54622 9.94100 ASAH ???? 1 0.77791 1.54915 9.92900 HRHH ???? 1 0.77791 1.53361 9.92900 HLF ??? TPPG ???? 0 0.31592 1.74899 4.15500 GAK ??? DDEE ???? 0 0.16389 2.05570 2.25500 FFFF ???? 1 0.61188 1.52366 7.85400 GTT ??? AAPP ???? 1 0.57692 1.49372 7.41700 GDAP ???? 1 0.35192 1.91071 4.60500 AAVV ???? 1 0.60492 0.55926 7.76700 EQHQ ???? 1 0.80287 1.25366 10.24100 AGAA ???? 1 0.79687 1.39416 10.16600 AASA ???? 1 0.86792 1.11371 11.05400 WMLY ???? 1 0.81591 1.14194 10.40400 GNDQ ???? 1 0.66693 1.62497 8.54200 AKKK ???? 1 0.70886 1.56750 9.06600 TAFV ???? 1 0.81687 1.23202 10.41600 LLLV ???? 1 0.76286 1.47610 9.74100 DEAA ???? 1 0.70886 1.64651 9.06600 TLSG ???? 1 0.78591 1.47014 10.02900 FFVV ???? 1 0.80287 1.43727 10.24100 FRSA ???? 1 0.79991 1.41604 10.20400 GKTN ???? 1 0.73190 1.53741 9.35400 MDVA ???? 1 0.74390 1.49002 9.50400 IILL ???? 1 0.70790 1.58443 9.05400 FATA ???? 1 0.66493 1.68975 8.51700 SASH ???? 1 0.63788 1.68250 8.17900 KKK ??? Y ? K ? KE ?? MLYY ???? 1 0.58388 1.82633 7.50400 GRH ??? Y ? Q ? G ? *