
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0289AL243_2-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289AL243_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          1.487
LGA    M     225      M     225          1.512
LGA    E     226      E     226          1.077
LGA    K     227      K     227          0.280
LGA    V     228      V     228          0.914
LGA    D     229      D     229          1.936
LGA    R     232      Y     230          2.273
LGA    N     233      P     231          4.563
LGA    E     234      R     232          1.417
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    S     235      V     238          2.468
LGA    D     250      A     239          2.509
LGA    W     251      A     240          1.386
LGA    K     252      V     241          2.735
LGA    L     254      I     242          2.917
LGA    -       -      H     243           -
LGA    -       -      P     244           -
LGA    H     255      N     245          3.206
LGA    P     256      L     246          2.950
LGA    G     257      Q     247          3.389
LGA    D     258      D     248          2.934
LGA    P     259      Q     249          3.400
LGA    V     260      D     250          2.290
LGA    F     261      W     251          1.439
LGA    V     262      K     252          1.363
LGA    S     263      P     253          0.912
LGA    L     264      L     254          1.658
LGA    D     265      H     255          2.457
LGA    G     266      P     256          3.811
LGA    K     267      G     257          2.080
LGA    V     268      D     258          2.698
LGA    I     269      P     259          2.827
LGA    P     270      V     260          2.196
LGA    L     271      F     261          3.608
LGA    -       -      V     262           -
LGA    -       -      S     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    -       -      K     267           -
LGA    -       -      V     268           -
LGA    G     272      I     269          5.398
LGA    G     273      P     270           -
LGA    D     274      L     271           -
LGA    -       -      G     272           -
LGA    -       -      G     273           -
LGA    -       -      D     274           -
LGA    C     275      C     275          3.333
LGA    T     276      T     276          2.418
LGA    V     277      V     277          0.729
LGA    Y     278      Y     278          0.734
LGA    P     279      P     279          0.267
LGA    V     280      V     280          0.252
LGA    F     281      F     281          0.258
LGA    V     282      V     282          0.232
LGA    N     283      N     283          1.114
LGA    -       -      E     284           -
LGA    -       -      A     285           -
LGA    -       -      A     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      E     289           -
LGA    -       -      K     290           -
LGA    -       -      K     291           -
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)   43   74    5.0     41    2.41    41.46     36.804     1.632

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.358878 * X  +   0.120532 * Y  +  -0.925569 * Z  +  14.551767
  Y_new =  -0.826841 * X  +  -0.419029 * Y  +  -0.375165 * Z  +  65.397743
  Z_new =  -0.433060 * X  +   0.899937 * Y  +  -0.050720 * Z  + -42.104618 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.627096   -1.514497  [ DEG:    93.2257    -86.7743 ]
  Theta =   0.447885    2.693708  [ DEG:    25.6619    154.3381 ]
  Phi   =  -1.161298    1.980295  [ DEG:   -66.5375    113.4625 ]
 
# 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: T0289AL243_2-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289AL243_2-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   74   5.0   41   2.41   41.46  36.804
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL243_2-D2
REMARK Aligment from pdb entry: 2g9dA
ATOM    821  N   ILE   224      26.051  27.759  20.183  1.00  0.00              
ATOM    822  CA  ILE   224      25.373  28.748  21.002  1.00  0.00              
ATOM    823  C   ILE   224      25.167  28.067  22.342  1.00  0.00              
ATOM    824  O   ILE   224      24.535  27.016  22.423  1.00  0.00              
ATOM    825  N   MET   225      25.714  28.662  23.393  1.00  0.00              
ATOM    826  CA  MET   225      25.600  28.100  24.728  1.00  0.00              
ATOM    827  C   MET   225      24.293  28.533  25.369  1.00  0.00              
ATOM    828  O   MET   225      23.615  27.750  26.037  1.00  0.00              
ATOM    829  N   GLU   226      23.946  29.792  25.152  1.00  0.00              
ATOM    830  CA  GLU   226      22.726  30.360  25.697  1.00  0.00              
ATOM    831  C   GLU   226      22.665  31.819  25.255  1.00  0.00              
ATOM    832  O   GLU   226      23.678  32.400  24.847  1.00  0.00              
ATOM    833  N   LYS   227      21.475  32.401  25.327  1.00  0.00              
ATOM    834  CA  LYS   227      21.305  33.797  24.979  1.00  0.00              
ATOM    835  C   LYS   227      21.304  34.580  26.282  1.00  0.00              
ATOM    836  O   LYS   227      20.942  34.043  27.333  1.00  0.00              
ATOM    837  N   VAL   228      21.720  35.842  26.213  1.00  0.00              
ATOM    838  CA  VAL   228      21.766  36.713  27.383  1.00  0.00              
ATOM    839  C   VAL   228      20.746  37.855  27.201  1.00  0.00              
ATOM    840  O   VAL   228      21.109  39.026  27.099  1.00  0.00              
ATOM    841  N   ASP   229      19.466  37.501  27.150  1.00  0.00              
ATOM    842  CA  ASP   229      18.407  38.493  26.986  1.00  0.00              
ATOM    843  C   ASP   229      18.300  39.374  28.221  1.00  0.00              
ATOM    844  O   ASP   229      18.210  38.874  29.340  1.00  0.00              
ATOM    845  N   ARG   232      18.312  40.687  28.009  1.00  0.00              
ATOM    846  CA  ARG   232      18.221  41.640  29.110  1.00  0.00              
ATOM    847  C   ARG   232      16.788  41.659  29.628  1.00  0.00              
ATOM    848  O   ARG   232      15.839  41.481  28.857  1.00  0.00              
ATOM    849  N   ASN   233      16.638  41.860  30.936  1.00  0.00              
ATOM    850  CA  ASN   233      15.321  41.899  31.556  1.00  0.00              
ATOM    851  C   ASN   233      15.153  43.075  32.508  1.00  0.00              
ATOM    852  O   ASN   233      14.039  43.560  32.715  1.00  0.00              
ATOM    853  N   GLU   234      16.243  43.531  33.112  1.00  0.00              
ATOM    854  CA  GLU   234      16.116  44.665  34.008  1.00  0.00              
ATOM    855  C   GLU   234      16.755  45.905  33.399  1.00  0.00              
ATOM    856  O   GLU   234      17.109  45.913  32.221  1.00  0.00              
ATOM    857  N   SER   235      16.901  46.945  34.210  1.00  0.00              
ATOM    858  CA  SER   235      17.450  48.208  33.750  1.00  0.00              
ATOM    859  C   SER   235      18.848  48.449  34.274  1.00  0.00              
ATOM    860  O   SER   235      19.633  49.160  33.649  1.00  0.00              
ATOM    861  N   ASP   250      19.161  47.871  35.428  1.00  0.00              
ATOM    862  CA  ASP   250      20.488  48.048  36.006  1.00  0.00              
ATOM    863  C   ASP   250      21.421  47.017  35.366  1.00  0.00              
ATOM    864  O   ASP   250      21.995  46.155  36.039  1.00  0.00              
ATOM    865  N   TRP   251      21.551  47.139  34.046  1.00  0.00              
ATOM    866  CA  TRP   251      22.352  46.256  33.206  1.00  0.00              
ATOM    867  C   TRP   251      23.737  46.855  32.925  1.00  0.00              
ATOM    868  O   TRP   251      23.867  48.060  32.704  1.00  0.00              
ATOM    869  N   LYS   252      24.765  46.007  32.935  1.00  0.00              
ATOM    870  CA  LYS   252      26.134  46.462  32.690  1.00  0.00              
ATOM    871  C   LYS   252      27.107  45.309  32.427  1.00  0.00              
ATOM    872  O   LYS   252      26.969  44.230  32.998  1.00  0.00              
ATOM    873  N   LEU   254      28.088  45.552  31.560  1.00  0.00              
ATOM    874  CA  LEU   254      29.097  44.549  31.207  1.00  0.00              
ATOM    875  C   LEU   254      30.471  44.950  31.740  1.00  0.00              
ATOM    876  O   LEU   254      30.624  46.024  32.315  1.00  0.00              
ATOM    877  N   HIS   255      31.471  44.093  31.535  1.00  0.00              
ATOM    878  CA  HIS   255      32.835  44.367  32.005  1.00  0.00              
ATOM    879  C   HIS   255      33.730  44.868  30.874  1.00  0.00              
ATOM    880  O   HIS   255      34.952  44.722  30.915  1.00  0.00              
ATOM    881  N   PRO   256      33.114  45.460  29.862  1.00  0.00              
ATOM    882  CA  PRO   256      33.869  45.986  28.742  1.00  0.00              
ATOM    883  C   PRO   256      33.168  47.194  28.153  1.00  0.00              
ATOM    884  O   PRO   256      32.027  47.495  28.511  1.00  0.00              
ATOM    885  N   GLY   257      33.863  47.888  27.255  1.00  0.00              
ATOM    886  CA  GLY   257      33.325  49.084  26.612  1.00  0.00              
ATOM    887  C   GLY   257      32.731  48.785  25.236  1.00  0.00              
ATOM    888  O   GLY   257      31.555  48.440  25.104  1.00  0.00              
ATOM    889  N   ASP   258      33.554  48.929  24.209  1.00  0.00              
ATOM    890  CA  ASP   258      33.114  48.670  22.847  1.00  0.00              
ATOM    891  C   ASP   258      34.271  47.970  22.154  1.00  0.00              
ATOM    892  O   ASP   258      34.105  47.347  21.102  1.00  0.00              
ATOM    893  N   PRO   259      35.732  42.542  21.360  1.00  0.00              
ATOM    894  CA  PRO   259      35.590  41.815  20.114  1.00  0.00              
ATOM    895  C   PRO   259      34.710  40.598  20.311  1.00  0.00              
ATOM    896  O   PRO   259      34.545  40.124  21.431  1.00  0.00              
ATOM    897  N   VAL   260      34.142  40.093  19.220  1.00  0.00              
ATOM    898  CA  VAL   260      33.316  38.896  19.292  1.00  0.00              
ATOM    899  C   VAL   260      34.220  37.737  19.689  1.00  0.00              
ATOM    900  O   VAL   260      35.421  37.761  19.426  1.00  0.00              
ATOM    901  N   PHE   261      33.637  36.719  20.311  1.00  0.00              
ATOM    902  CA  PHE   261      34.382  35.531  20.715  1.00  0.00              
ATOM    903  C   PHE   261      35.408  35.772  21.824  1.00  0.00              
ATOM    904  O   PHE   261      36.411  35.045  21.938  1.00  0.00              
ATOM    905  N   VAL   262      35.147  36.791  22.640  1.00  0.00              
ATOM    906  CA  VAL   262      36.019  37.122  23.763  1.00  0.00              
ATOM    907  C   VAL   262      35.763  36.114  24.886  1.00  0.00              
ATOM    908  O   VAL   262      34.833  36.262  25.683  1.00  0.00              
ATOM    909  N   SER   263      36.600  35.084  24.926  1.00  0.00              
ATOM    910  CA  SER   263      36.487  34.016  25.909  1.00  0.00              
ATOM    911  C   SER   263      36.667  34.457  27.356  1.00  0.00              
ATOM    912  O   SER   263      37.346  35.435  27.653  1.00  0.00              
ATOM    913  N   LEU   264      36.044  33.712  28.257  1.00  0.00              
ATOM    914  CA  LEU   264      36.138  34.004  29.670  1.00  0.00              
ATOM    915  C   LEU   264      36.394  32.697  30.412  1.00  0.00              
ATOM    916  O   LEU   264      35.949  31.630  29.985  1.00  0.00              
ATOM    917  N   ASP   265      37.116  32.783  31.524  1.00  0.00              
ATOM    918  CA  ASP   265      37.437  31.611  32.326  1.00  0.00              
ATOM    919  C   ASP   265      36.401  31.375  33.410  1.00  0.00              
ATOM    920  O   ASP   265      35.473  32.171  33.593  1.00  0.00              
ATOM    921  N   GLY   266      35.635  31.919  36.582  1.00  0.00              
ATOM    922  CA  GLY   266      36.021  32.789  37.679  1.00  0.00              
ATOM    923  C   GLY   266      35.703  34.250  37.417  1.00  0.00              
ATOM    924  O   GLY   266      35.498  35.026  38.353  1.00  0.00              
ATOM    925  N   LYS   267      35.645  34.625  36.143  1.00  0.00              
ATOM    926  CA  LYS   267      35.371  36.007  35.765  1.00  0.00              
ATOM    927  C   LYS   267      33.933  36.280  35.366  1.00  0.00              
ATOM    928  O   LYS   267      33.260  35.432  34.779  1.00  0.00              
ATOM    929  N   VAL   268      33.481  37.486  35.695  1.00  0.00              
ATOM    930  CA  VAL   268      32.137  37.943  35.370  1.00  0.00              
ATOM    931  C   VAL   268      32.274  39.139  34.427  1.00  0.00              
ATOM    932  O   VAL   268      33.075  40.044  34.675  1.00  0.00              
ATOM    933  N   ILE   269      31.495  39.132  33.348  1.00  0.00              
ATOM    934  CA  ILE   269      31.531  40.201  32.352  1.00  0.00              
ATOM    935  C   ILE   269      30.467  41.278  32.575  1.00  0.00              
ATOM    936  O   ILE   269      30.035  41.936  31.628  1.00  0.00              
ATOM    937  N   PRO   270      30.047  41.455  33.824  1.00  0.00              
ATOM    938  CA  PRO   270      29.039  42.454  34.117  1.00  0.00              
ATOM    939  C   PRO   270      27.785  41.883  34.760  1.00  0.00              
ATOM    940  O   PRO   270      27.156  40.967  34.221  1.00  0.00              
ATOM    941  N   LEU   271      27.426  42.443  35.915  1.00  0.00              
ATOM    942  CA  LEU   271      26.252  42.029  36.678  1.00  0.00              
ATOM    943  C   LEU   271      24.934  42.448  36.027  1.00  0.00              
ATOM    944  O   LEU   271      24.893  42.801  34.847  1.00  0.00              
ATOM    945  N   GLY   272      23.849  42.399  36.792  1.00  0.00              
ATOM    946  CA  GLY   272      22.546  42.778  36.256  1.00  0.00              
ATOM    947  C   GLY   272      21.636  43.313  37.362  1.00  0.00              
ATOM    948  O   GLY   272      20.419  43.138  37.314  1.00  0.00              
ATOM    949  N   GLY   273      22.236  43.966  38.355  1.00  0.00              
ATOM    950  CA  GLY   273      21.471  44.516  39.460  1.00  0.00              
ATOM    951  C   GLY   273      20.832  43.435  40.311  1.00  0.00              
ATOM    952  O   GLY   273      20.795  43.534  41.537  1.00  0.00              
ATOM    953  N   ASP   274      20.323  42.399  39.654  1.00  0.00              
ATOM    954  CA  ASP   274      19.678  41.276  40.326  1.00  0.00              
ATOM    955  C   ASP   274      20.653  40.095  40.399  1.00  0.00              
ATOM    956  O   ASP   274      21.288  39.859  41.427  1.00  0.00              
ATOM    957  N   CYS   275      34.814  27.161  30.841  1.00  0.00              
ATOM    958  CA  CYS   275      36.168  27.699  30.744  1.00  0.00              
ATOM    959  C   CYS   275      36.473  28.021  29.298  1.00  0.00              
ATOM    960  O   CYS   275      37.060  27.215  28.573  1.00  0.00              
ATOM    961  N   THR   276      36.066  29.217  28.890  1.00  0.00              
ATOM    962  CA  THR   276      36.285  29.647  27.527  1.00  0.00              
ATOM    963  C   THR   276      34.994  30.146  26.900  1.00  0.00              
ATOM    964  O   THR   276      34.987  30.637  25.770  1.00  0.00              
ATOM    965  N   VAL   277      33.894  30.020  27.633  1.00  0.00              
ATOM    966  CA  VAL   277      32.609  30.473  27.130  1.00  0.00              
ATOM    967  C   VAL   277      32.782  31.882  26.575  1.00  0.00              
ATOM    968  O   VAL   277      32.798  32.864  27.321  1.00  0.00              
ATOM    969  N   TYR   278      32.929  31.962  25.256  1.00  0.00              
ATOM    970  CA  TYR   278      33.127  33.226  24.555  1.00  0.00              
ATOM    971  C   TYR   278      31.795  33.920  24.291  1.00  0.00              
ATOM    972  O   TYR   278      30.758  33.270  24.181  1.00  0.00              
ATOM    973  N   PRO   279      31.835  35.242  24.173  1.00  0.00              
ATOM    974  CA  PRO   279      30.630  36.035  23.957  1.00  0.00              
ATOM    975  C   PRO   279      30.550  36.572  22.535  1.00  0.00              
ATOM    976  O   PRO   279      31.574  36.786  21.885  1.00  0.00              
ATOM    977  N   VAL   280      29.332  36.794  22.056  1.00  0.00              
ATOM    978  CA  VAL   280      29.137  37.284  20.702  1.00  0.00              
ATOM    979  C   VAL   280      27.959  38.249  20.663  1.00  0.00              
ATOM    980  O   VAL   280      27.073  38.183  21.512  1.00  0.00              
ATOM    981  N   PHE   281      27.971  39.147  19.677  1.00  0.00              
ATOM    982  CA  PHE   281      26.932  40.170  19.483  1.00  0.00              
ATOM    983  C   PHE   281      26.704  41.071  20.689  1.00  0.00              
ATOM    984  O   PHE   281      25.567  41.450  20.972  1.00  0.00              
ATOM    985  N   VAL   282      27.783  41.453  21.399  1.00  0.00              
ATOM    986  CA  VAL   282      27.659  42.314  22.579  1.00  0.00              
ATOM    987  C   VAL   282      26.912  43.612  22.268  1.00  0.00              
ATOM    988  O   VAL   282      27.532  44.660  22.066  1.00  0.00              
ATOM    989  N   ASN   283      25.587  43.550  22.222  1.00  0.00              
ATOM    990  CA  ASN   283      24.812  44.751  21.939  1.00  0.00              
ATOM    991  C   ASN   283      24.694  45.618  23.187  1.00  0.00              
ATOM    992  O   ASN   283      24.710  45.122  24.313  1.00  0.00              
END
