
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   50 (  200),  selected   50 , name T0289AL242_2-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289AL242_2-D2.T0289_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I     224      I     224          1.895
LGA    M     225      M     225          1.938
LGA    E     226      E     226          1.423
LGA    K     227      K     227          0.238
LGA    V     228      V     228          1.382
LGA    D     229      D     229          1.729
LGA    Y     230      Y     230          3.126
LGA    -       -      P     231           -
LGA    P     231      R     232          4.277
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    R     232      V     238          1.673
LGA    N     233      A     239          3.939
LGA    -       -      A     240           -
LGA    E     234      V     241          1.524
LGA    I     242      I     242          0.960
LGA    H     243      H     243          1.983
LGA    -       -      P     244           -
LGA    P     244      N     245          3.407
LGA    N     245      L     246          4.414
LGA    L     246      Q     247          3.140
LGA    Q     247      D     248          2.108
LGA    D     248      Q     249          1.355
LGA    Q     249      D     250          3.206
LGA    D     250      W     251          2.291
LGA    W     251      -       -           -
LGA    K     252      K     252          1.148
LGA    P     253      P     253          0.516
LGA    L     254      L     254          0.780
LGA    H     255      H     255          1.335
LGA    P     256      P     256          2.645
LGA    G     257      G     257          1.671
LGA    -       -      D     258           -
LGA    -       -      P     259           -
LGA    -       -      V     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      S     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    -       -      K     267           -
LGA    -       -      V     268           -
LGA    -       -      I     269           -
LGA    D     258      P     270          3.704
LGA    P     259      L     271          4.562
LGA    V     260      G     272           #
LGA    F     261      G     273          2.148
LGA    V     262      D     274          2.770
LGA    S     263      C     275          2.131
LGA    L     264      T     276          2.808
LGA    D     265      -       -           -
LGA    G     266      V     277          1.126
LGA    K     267      Y     278          1.212
LGA    V     268      P     279          0.511
LGA    I     269      V     280          1.234
LGA    Y     287      F     281          1.923
LGA    Y     288      V     282          1.241
LGA    E     289      N     283          2.003
LGA    K     290      E     284          5.073
LGA    K     291      A     285          3.666
LGA    E     292      A     286          4.468
LGA    A     293      Y     287           #
LGA    F     294      Y     288          3.370
LGA    A     295      E     289          3.431
LGA    K     296      K     290          1.517
LGA    T     297      K     291          3.393
LGA    -       -      E     292           -
LGA    -       -      A     293           -
LGA    -       -      F     294           -
LGA    -       -      A     295           -
LGA    -       -      K     296           -
LGA    -       -      T     297           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50   74    5.0     46    2.61    34.78     39.024     1.697

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.478623 * X  +   0.680495 * Y  +  -0.554839 * Z  + 103.295265
  Y_new =   0.176777 * X  +   0.693665 * Y  +   0.698268 * Z  + -63.866543
  Z_new =   0.860041 * X  +   0.236124 * Y  +  -0.452300 * Z  +  18.268995 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.660460   -0.481133  [ DEG:   152.4331    -27.5669 ]
  Theta =  -1.035349   -2.106243  [ DEG:   -59.3211   -120.6789 ]
  Phi   =   2.787789   -0.353804  [ DEG:   159.7285    -20.2715 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0289AL242_2-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289AL242_2-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50   74   5.0   46   2.61   34.78  39.024
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL242_2-D2
REMARK Aligment from pdb entry: 1yw4_A
ATOM    865  N   ILE   224      26.139  27.660  20.559  1.00  0.00              
ATOM    866  CA  ILE   224      25.518  28.582  21.495  1.00  0.00              
ATOM    867  C   ILE   224      25.180  27.826  22.773  1.00  0.00              
ATOM    868  O   ILE   224      24.728  26.682  22.726  1.00  0.00              
ATOM    869  N   MET   225      25.414  28.460  23.915  1.00  0.00              
ATOM    870  CA  MET   225      25.104  27.850  25.201  1.00  0.00              
ATOM    871  C   MET   225      23.786  28.455  25.680  1.00  0.00              
ATOM    872  O   MET   225      22.870  27.736  26.074  1.00  0.00              
ATOM    873  N   GLU   226      23.703  29.782  25.632  1.00  0.00              
ATOM    874  CA  GLU   226      22.505  30.514  26.035  1.00  0.00              
ATOM    875  C   GLU   226      22.614  31.975  25.592  1.00  0.00              
ATOM    876  O   GLU   226      23.717  32.490  25.397  1.00  0.00              
ATOM    877  N   LYS   227      21.472  32.640  25.437  1.00  0.00              
ATOM    878  CA  LYS   227      21.467  34.037  25.020  1.00  0.00              
ATOM    879  C   LYS   227      21.357  34.965  26.221  1.00  0.00              
ATOM    880  O   LYS   227      20.763  34.615  27.244  1.00  0.00              
ATOM    881  N   VAL   228      21.938  36.153  26.091  1.00  0.00              
ATOM    882  CA  VAL   228      21.896  37.149  27.155  1.00  0.00              
ATOM    883  C   VAL   228      20.637  37.983  26.983  1.00  0.00              
ATOM    884  O   VAL   228      20.673  39.043  26.362  1.00  0.00              
ATOM    885  N   ASP   229      19.525  37.496  27.526  1.00  0.00              
ATOM    886  CA  ASP   229      18.250  38.197  27.429  1.00  0.00              
ATOM    887  C   ASP   229      18.325  39.535  28.162  1.00  0.00              
ATOM    888  O   ASP   229      18.670  39.587  29.341  1.00  0.00              
ATOM    889  N   TYR   230      18.007  40.617  27.462  1.00  0.00              
ATOM    890  CA  TYR   230      18.046  41.937  28.076  1.00  0.00              
ATOM    891  C   TYR   230      16.669  42.503  28.416  1.00  0.00              
ATOM    892  O   TYR   230      15.722  42.405  27.634  1.00  0.00              
ATOM    893  N   PRO   231      16.579  43.089  29.605  1.00  0.00              
ATOM    894  CA  PRO   231      15.355  43.705  30.096  1.00  0.00              
ATOM    895  C   PRO   231      15.712  44.847  31.047  1.00  0.00              
ATOM    896  O   PRO   231      16.675  44.751  31.812  1.00  0.00              
ATOM    897  N   ARG   232      14.936  45.924  30.979  1.00  0.00              
ATOM    898  CA  ARG   232      15.141  47.114  31.806  1.00  0.00              
ATOM    899  C   ARG   232      16.490  47.758  31.503  1.00  0.00              
ATOM    900  O   ARG   232      16.695  48.323  30.428  1.00  0.00              
ATOM    901  N   ASN   233      20.406  46.853  33.797  1.00  0.00              
ATOM    902  CA  ASN   233      21.079  46.355  32.604  1.00  0.00              
ATOM    903  C   ASN   233      22.444  47.002  32.406  1.00  0.00              
ATOM    904  O   ASN   233      22.555  48.225  32.306  1.00  0.00              
ATOM    905  N   GLU   234      23.476  46.165  32.344  1.00  0.00              
ATOM    906  CA  GLU   234      24.854  46.622  32.160  1.00  0.00              
ATOM    907  C   GLU   234      25.712  45.517  31.555  1.00  0.00              
ATOM    908  O   GLU   234      25.760  44.401  32.074  1.00  0.00              
ATOM    909  N   ILE   242      26.390  45.842  30.458  1.00  0.00              
ATOM    910  CA  ILE   242      27.261  44.895  29.765  1.00  0.00              
ATOM    911  C   ILE   242      28.695  45.097  30.261  1.00  0.00              
ATOM    912  O   ILE   242      29.336  46.096  29.940  1.00  0.00              
ATOM    913  N   HIS   243      29.191  44.138  31.037  1.00  0.00              
ATOM    914  CA  HIS   243      30.529  44.222  31.612  1.00  0.00              
ATOM    915  C   HIS   243      31.698  43.974  30.658  1.00  0.00              
ATOM    916  O   HIS   243      32.700  43.366  31.034  1.00  0.00              
ATOM    917  N   PRO   244      31.564  44.449  29.425  1.00  0.00              
ATOM    918  CA  PRO   244      32.616  44.311  28.425  1.00  0.00              
ATOM    919  C   PRO   244      32.685  45.586  27.601  1.00  0.00              
ATOM    920  O   PRO   244      31.661  46.223  27.342  1.00  0.00              
ATOM    921  N   ASN   245      33.896  45.956  27.196  1.00  0.00              
ATOM    922  CA  ASN   245      34.110  47.153  26.388  1.00  0.00              
ATOM    923  C   ASN   245      33.209  47.113  25.158  1.00  0.00              
ATOM    924  O   ASN   245      32.953  46.046  24.599  1.00  0.00              
ATOM    925  N   LEU   246      32.737  48.281  24.734  1.00  0.00              
ATOM    926  CA  LEU   246      31.852  48.374  23.578  1.00  0.00              
ATOM    927  C   LEU   246      32.483  47.768  22.329  1.00  0.00              
ATOM    928  O   LEU   246      31.780  47.348  21.412  1.00  0.00              
ATOM    929  N   GLN   247      33.810  47.725  22.301  1.00  0.00              
ATOM    930  CA  GLN   247      34.535  47.176  21.162  1.00  0.00              
ATOM    931  C   GLN   247      35.055  45.763  21.415  1.00  0.00              
ATOM    932  O   GLN   247      35.954  45.300  20.713  1.00  0.00              
ATOM    933  N   ASP   248      34.509  45.078  22.416  1.00  0.00              
ATOM    934  CA  ASP   248      34.955  43.717  22.721  1.00  0.00              
ATOM    935  C   ASP   248      34.898  42.832  21.472  1.00  0.00              
ATOM    936  O   ASP   248      33.903  42.831  20.748  1.00  0.00              
ATOM    937  N   GLN   249      35.970  42.086  21.221  1.00  0.00              
ATOM    938  CA  GLN   249      36.037  41.209  20.051  1.00  0.00              
ATOM    939  C   GLN   249      35.168  39.967  20.199  1.00  0.00              
ATOM    940  O   GLN   249      34.910  39.505  21.312  1.00  0.00              
ATOM    941  N   ASP   250      34.719  39.425  19.069  1.00  0.00              
ATOM    942  CA  ASP   250      33.908  38.218  19.096  1.00  0.00              
ATOM    943  C   ASP   250      34.781  37.056  19.555  1.00  0.00              
ATOM    944  O   ASP   250      35.988  37.029  19.290  1.00  0.00              
ATOM    945  N   TRP   251      34.151  36.103  20.231  1.00  0.00              
ATOM    946  CA  TRP   251      34.809  34.909  20.756  1.00  0.00              
ATOM    947  C   TRP   251      35.736  35.222  21.919  1.00  0.00              
ATOM    948  O   TRP   251      36.624  34.436  22.244  1.00  0.00              
ATOM    949  N   LYS   252      35.534  36.378  22.547  1.00  0.00              
ATOM    950  CA  LYS   252      36.355  36.744  23.696  1.00  0.00              
ATOM    951  C   LYS   252      36.053  35.761  24.824  1.00  0.00              
ATOM    952  O   LYS   252      34.894  35.571  25.190  1.00  0.00              
ATOM    953  N   PRO   253      37.102  35.144  25.365  1.00  0.00              
ATOM    954  CA  PRO   253      36.984  34.168  26.446  1.00  0.00              
ATOM    955  C   PRO   253      36.492  34.792  27.754  1.00  0.00              
ATOM    956  O   PRO   253      36.994  35.834  28.183  1.00  0.00              
ATOM    957  N   LEU   254      35.511  34.150  28.383  1.00  0.00              
ATOM    958  CA  LEU   254      34.959  34.632  29.647  1.00  0.00              
ATOM    959  C   LEU   254      35.508  33.791  30.803  1.00  0.00              
ATOM    960  O   LEU   254      35.153  32.631  30.960  1.00  0.00              
ATOM    961  N   HIS   255      36.378  34.375  31.637  1.00  0.00              
ATOM    962  CA  HIS   255      36.956  33.633  32.765  1.00  0.00              
ATOM    963  C   HIS   255      35.943  33.157  33.795  1.00  0.00              
ATOM    964  O   HIS   255      34.854  33.716  33.919  1.00  0.00              
ATOM    965  N   PRO   256      36.303  32.109  34.529  1.00  0.00              
ATOM    966  CA  PRO   256      35.421  31.570  35.555  1.00  0.00              
ATOM    967  C   PRO   256      35.254  32.622  36.646  1.00  0.00              
ATOM    968  O   PRO   256      36.226  33.026  37.284  1.00  0.00              
ATOM    969  N   GLY   257      34.015  33.061  36.845  1.00  0.00              
ATOM    970  CA  GLY   257      33.722  34.078  37.839  1.00  0.00              
ATOM    971  C   GLY   257      32.649  35.036  37.351  1.00  0.00              
ATOM    972  O   GLY   257      31.508  34.999  37.825  1.00  0.00              
ATOM    973  N   ASP   258      29.716  36.394  35.350  1.00  0.00              
ATOM    974  CA  ASP   258      28.623  35.752  34.624  1.00  0.00              
ATOM    975  C   ASP   258      27.417  36.687  34.595  1.00  0.00              
ATOM    976  O   ASP   258      27.530  37.865  34.943  1.00  0.00              
ATOM    977  N   PRO   259      26.266  36.183  34.179  1.00  0.00              
ATOM    978  CA  PRO   259      25.085  37.030  34.122  1.00  0.00              
ATOM    979  C   PRO   259      24.179  36.814  35.332  1.00  0.00              
ATOM    980  O   PRO   259      23.998  35.683  35.791  1.00  0.00              
ATOM    981  N   VAL   260      23.630  37.907  35.857  1.00  0.00              
ATOM    982  CA  VAL   260      22.737  37.853  37.011  1.00  0.00              
ATOM    983  C   VAL   260      21.871  39.112  37.059  1.00  0.00              
ATOM    984  O   VAL   260      20.683  39.045  37.386  1.00  0.00              
ATOM    985  N   PHE   261      27.139  27.083  33.422  1.00  0.00              
ATOM    986  CA  PHE   261      27.207  28.415  34.013  1.00  0.00              
ATOM    987  C   PHE   261      28.524  29.115  33.681  1.00  0.00              
ATOM    988  O   PHE   261      28.556  30.051  32.878  1.00  0.00              
ATOM    989  N   VAL   262      29.608  28.659  34.301  1.00  0.00              
ATOM    990  CA  VAL   262      30.925  29.247  34.073  1.00  0.00              
ATOM    991  C   VAL   262      32.031  28.218  34.294  1.00  0.00              
ATOM    992  O   VAL   262      31.914  27.344  35.150  1.00  0.00              
ATOM    993  N   SER   263      33.100  28.326  33.512  1.00  0.00              
ATOM    994  CA  SER   263      34.205  27.395  33.644  1.00  0.00              
ATOM    995  C   SER   263      35.434  27.827  32.865  1.00  0.00              
ATOM    996  O   SER   263      36.337  27.029  32.615  1.00  0.00              
ATOM    997  N   LEU   264      35.475  29.099  32.483  1.00  0.00              
ATOM    998  CA  LEU   264      36.609  29.599  31.729  1.00  0.00              
ATOM    999  C   LEU   264      36.663  29.041  30.319  1.00  0.00              
ATOM   1000  O   LEU   264      37.682  29.154  29.633  1.00  0.00              
ATOM   1001  N   ASP   265      35.566  28.436  29.883  1.00  0.00              
ATOM   1002  CA  ASP   265      35.490  27.864  28.543  1.00  0.00              
ATOM   1003  C   ASP   265      34.562  28.658  27.623  1.00  0.00              
ATOM   1004  O   ASP   265      34.691  28.601  26.400  1.00  0.00              
ATOM   1005  N   GLY   266      33.630  29.399  28.214  1.00  0.00              
ATOM   1006  CA  GLY   266      32.686  30.174  27.428  1.00  0.00              
ATOM   1007  C   GLY   266      33.305  31.423  26.792  1.00  0.00              
ATOM   1008  O   GLY   266      34.325  31.930  27.249  1.00  0.00              
ATOM   1009  N   LYS   267      32.684  31.897  25.717  1.00  0.00              
ATOM   1010  CA  LYS   267      33.151  33.084  25.014  1.00  0.00              
ATOM   1011  C   LYS   267      31.924  33.882  24.589  1.00  0.00              
ATOM   1012  O   LYS   267      30.847  33.321  24.390  1.00  0.00              
ATOM   1013  N   VAL   268      32.088  35.189  24.456  1.00  0.00              
ATOM   1014  CA  VAL   268      30.987  36.052  24.056  1.00  0.00              
ATOM   1015  C   VAL   268      31.004  36.161  22.531  1.00  0.00              
ATOM   1016  O   VAL   268      32.070  36.191  21.910  1.00  0.00              
ATOM   1017  N   ILE   269      29.829  36.202  21.923  1.00  0.00              
ATOM   1018  CA  ILE   269      29.754  36.304  20.473  1.00  0.00              
ATOM   1019  C   ILE   269      28.632  37.254  20.072  1.00  0.00              
ATOM   1020  O   ILE   269      27.540  37.204  20.633  1.00  0.00              
ATOM   1021  N   TYR   287      28.923  38.132  19.117  1.00  0.00              
ATOM   1022  CA  TYR   287      27.957  39.107  18.613  1.00  0.00              
ATOM   1023  C   TYR   287      27.274  39.947  19.696  1.00  0.00              
ATOM   1024  O   TYR   287      26.052  40.066  19.723  1.00  0.00              
ATOM   1025  N   TYR   288      28.058  40.553  20.601  1.00  0.00              
ATOM   1026  CA  TYR   288      27.469  41.377  21.663  1.00  0.00              
ATOM   1027  C   TYR   288      26.794  42.638  21.109  1.00  0.00              
ATOM   1028  O   TYR   288      27.342  43.304  20.231  1.00  0.00              
ATOM   1029  N   GLU   289      25.612  42.962  21.622  1.00  0.00              
ATOM   1030  CA  GLU   289      24.886  44.146  21.170  1.00  0.00              
ATOM   1031  C   GLU   289      23.966  44.641  22.282  1.00  0.00              
ATOM   1032  O   GLU   289      22.756  44.404  22.254  1.00  0.00              
ATOM   1033  N   LYS   290      24.531  45.337  23.278  1.00  0.00              
ATOM   1034  CA  LYS   290      23.774  45.872  24.413  1.00  0.00              
ATOM   1035  C   LYS   290      22.883  47.070  24.071  1.00  0.00              
ATOM   1036  O   LYS   290      22.141  47.562  24.920  1.00  0.00              
ATOM   1037  N   LYS   291      22.958  47.529  22.825  1.00  0.00              
ATOM   1038  CA  LYS   291      22.170  48.673  22.378  1.00  0.00              
ATOM   1039  C   LYS   291      20.693  48.341  22.191  1.00  0.00              
ATOM   1040  O   LYS   291      19.829  49.186  22.418  1.00  0.00              
ATOM   1041  N   GLU   292      20.401  47.113  21.778  1.00  0.00              
ATOM   1042  CA  GLU   292      19.019  46.700  21.554  1.00  0.00              
ATOM   1043  C   GLU   292      18.134  46.913  22.779  1.00  0.00              
ATOM   1044  O   GLU   292      17.046  47.480  22.672  1.00  0.00              
ATOM   1045  N   ALA   293      18.602  46.445  23.933  1.00  0.00              
ATOM   1046  CA  ALA   293      17.879  46.565  25.200  1.00  0.00              
ATOM   1047  C   ALA   293      16.348  46.552  25.097  1.00  0.00              
ATOM   1048  O   ALA   293      15.676  47.426  25.655  1.00  0.00              
ATOM   1049  N   PHE   294      15.772  45.566  24.388  1.00  0.00              
ATOM   1050  CA  PHE   294      14.312  45.538  24.284  1.00  0.00              
ATOM   1051  C   PHE   294      13.743  44.436  25.179  1.00  0.00              
ATOM   1052  O   PHE   294      13.520  44.633  26.373  1.00  0.00              
ATOM   1053  N   ALA   295      13.514  43.277  24.575  1.00  0.00              
ATOM   1054  CA  ALA   295      13.005  42.121  25.283  1.00  0.00              
ATOM   1055  C   ALA   295      13.684  40.945  24.615  1.00  0.00              
ATOM   1056  O   ALA   295      13.409  39.782  24.905  1.00  0.00              
ATOM   1057  N   LYS   296      14.588  41.282  23.699  1.00  0.00              
ATOM   1058  CA  LYS   296      15.355  40.306  22.937  1.00  0.00              
ATOM   1059  C   LYS   296      16.708  40.094  23.604  1.00  0.00              
ATOM   1060  O   LYS   296      16.926  40.520  24.739  1.00  0.00              
ATOM   1061  N   THR   297      17.618  39.444  22.885  1.00  0.00              
ATOM   1062  CA  THR   297      18.949  39.171  23.402  1.00  0.00              
ATOM   1063  C   THR   297      19.940  40.238  22.950  1.00  0.00              
ATOM   1064  O   THR   297      19.768  40.853  21.897  1.00  0.00              
END
