
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0289AL044_1-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289AL044_1-D2.T0289_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    I     224      I     224          1.471
LGA    M     225      M     225          1.715
LGA    E     226      E     226          0.928
LGA    K     227      K     227          0.573
LGA    D     229      V     228          1.815
LGA    Y     230      D     229          2.780
LGA    P     231      Y     230          4.360
LGA    -       -      P     231           -
LGA    -       -      R     232           -
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    R     232      G     236           #
LGA    N     233      D     237          1.856
LGA    G     236      V     238          2.864
LGA    -       -      A     239           -
LGA    -       -      A     240           -
LGA    D     237      V     241          1.337
LGA    V     238      I     242          1.121
LGA    A     239      H     243          3.258
LGA    A     240      P     244          2.969
LGA    -       -      N     245           -
LGA    V     241      L     246           #
LGA    I     242      Q     247          4.877
LGA    H     243      D     248          1.935
LGA    P     244      Q     249          2.578
LGA    D     250      D     250          1.992
LGA    W     251      W     251          1.289
LGA    K     252      K     252          1.594
LGA    P     253      P     253          1.607
LGA    L     254      L     254          1.388
LGA    H     255      H     255          2.001
LGA    P     256      P     256          1.908
LGA    G     257      G     257          2.124
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          1.365
LGA    P     259      L     271          1.924
LGA    V     260      G     272           #
LGA    F     261      -       -           -
LGA    L     271      G     273          2.330
LGA    -       -      D     274           -
LGA    -       -      C     275           -
LGA    -       -      T     276           -
LGA    -       -      V     277           -
LGA    -       -      Y     278           -
LGA    -       -      P     279           -
LGA    -       -      V     280           -
LGA    -       -      F     281           -
LGA    G     272      V     282          1.011
LGA    G     273      N     283          2.136
LGA    D     274      E     284          4.778
LGA    C     275      A     285          3.037
LGA    T     276      A     286          3.559
LGA    V     277      Y     287          5.551
LGA    Y     278      Y     288          3.619
LGA    P     279      E     289          2.878
LGA    V     280      K     290          0.571
LGA    F     281      K     291          4.039
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)   41   74    5.0     37    2.65    35.14     32.082     1.346

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.581103 * X  +   0.590284 * Y  +  -0.560254 * Z  + 111.822197
  Y_new =   0.122147 * X  +   0.743879 * Y  +   0.657058 * Z  + -56.616421
  Z_new =   0.804611 * X  +   0.313385 * Y  +  -0.504372 * Z  +  25.722225 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.585632   -0.555961  [ DEG:   148.1458    -31.8542 ]
  Theta =  -0.935020   -2.206573  [ DEG:   -53.5727   -126.4273 ]
  Phi   =   2.934410   -0.207183  [ DEG:   168.1293    -11.8707 ]
 
# 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: T0289AL044_1-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289AL044_1-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   74   5.0   37   2.65   35.14  32.082
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL044_1-D2
REMARK Aligment from pdb entry: 1yw4_A
ATOM    777  N   ILE   224      27.410  28.124  20.347  1.00  0.00              
ATOM    778  CA  ILE   224      26.616  28.976  21.216  1.00  0.00              
ATOM    779  C   ILE   224      26.208  28.173  22.446  1.00  0.00              
ATOM    780  O   ILE   224      25.862  26.997  22.341  1.00  0.00              
ATOM    781  N   MET   225      26.264  28.806  23.610  1.00  0.00              
ATOM    782  CA  MET   225      25.871  28.151  24.850  1.00  0.00              
ATOM    783  C   MET   225      24.463  28.636  25.189  1.00  0.00              
ATOM    784  O   MET   225      23.575  27.838  25.477  1.00  0.00              
ATOM    785  N   GLU   226      24.274  29.952  25.143  1.00  0.00              
ATOM    786  CA  GLU   226      22.982  30.576  25.420  1.00  0.00              
ATOM    787  C   GLU   226      23.014  32.048  25.002  1.00  0.00              
ATOM    788  O   GLU   226      24.085  32.656  24.931  1.00  0.00              
ATOM    789  N   LYS   227      21.844  32.618  24.728  1.00  0.00              
ATOM    790  CA  LYS   227      21.765  34.017  24.324  1.00  0.00              
ATOM    791  C   LYS   227      21.449  34.912  25.513  1.00  0.00              
ATOM    792  O   LYS   227      20.781  34.497  26.464  1.00  0.00              
ATOM    793  N   ASP   229      21.939  36.146  25.456  1.00  0.00              
ATOM    794  CA  ASP   229      21.699  37.117  26.516  1.00  0.00              
ATOM    795  C   ASP   229      20.400  37.847  26.215  1.00  0.00              
ATOM    796  O   ASP   229      20.413  38.916  25.610  1.00  0.00              
ATOM    797  N   TYR   230      19.281  37.260  26.631  1.00  0.00              
ATOM    798  CA  TYR   230      17.969  37.854  26.403  1.00  0.00              
ATOM    799  C   TYR   230      17.852  39.181  27.149  1.00  0.00              
ATOM    800  O   TYR   230      18.064  39.243  28.359  1.00  0.00              
ATOM    801  N   PRO   231      17.520  40.245  26.427  1.00  0.00              
ATOM    802  CA  PRO   231      17.382  41.553  27.051  1.00  0.00              
ATOM    803  C   PRO   231      15.934  41.997  27.245  1.00  0.00              
ATOM    804  O   PRO   231      15.088  41.833  26.365  1.00  0.00              
ATOM    805  N   ARG   232      15.668  42.554  28.422  1.00  0.00              
ATOM    806  CA  ARG   232      14.350  43.057  28.782  1.00  0.00              
ATOM    807  C   ARG   232      14.506  44.209  29.775  1.00  0.00              
ATOM    808  O   ARG   232      15.387  44.182  30.639  1.00  0.00              
ATOM    809  N   ASN   233      13.653  45.220  29.632  1.00  0.00              
ATOM    810  CA  ASN   233      13.667  46.408  30.484  1.00  0.00              
ATOM    811  C   ASN   233      14.982  47.167  30.333  1.00  0.00              
ATOM    812  O   ASN   233      15.252  47.765  29.292  1.00  0.00              
ATOM    813  N   GLY   236      18.692  46.553  33.030  1.00  0.00              
ATOM    814  CA  GLY   236      19.529  46.133  31.914  1.00  0.00              
ATOM    815  C   GLY   236      20.848  46.894  31.869  1.00  0.00              
ATOM    816  O   GLY   236      20.865  48.124  31.790  1.00  0.00              
ATOM    817  N   ASP   237      21.948  46.147  31.912  1.00  0.00              
ATOM    818  CA  ASP   237      23.293  46.720  31.882  1.00  0.00              
ATOM    819  C   ASP   237      24.302  45.701  31.365  1.00  0.00              
ATOM    820  O   ASP   237      24.388  44.584  31.877  1.00  0.00              
ATOM    821  N   VAL   238      25.063  46.099  30.350  1.00  0.00              
ATOM    822  CA  VAL   238      26.081  45.239  29.748  1.00  0.00              
ATOM    823  C   VAL   238      27.430  45.551  30.397  1.00  0.00              
ATOM    824  O   VAL   238      28.016  46.605  30.155  1.00  0.00              
ATOM    825  N   ALA   239      30.417  45.158  29.871  1.00  0.00              
ATOM    826  CA  ALA   239      31.578  45.125  28.990  1.00  0.00              
ATOM    827  C   ALA   239      31.627  46.415  28.187  1.00  0.00              
ATOM    828  O   ALA   239      30.586  46.969  27.824  1.00  0.00              
ATOM    829  N   ALA   240      32.839  46.890  27.919  1.00  0.00              
ATOM    830  CA  ALA   240      33.036  48.114  27.147  1.00  0.00              
ATOM    831  C   ALA   240      32.279  48.020  25.827  1.00  0.00              
ATOM    832  O   ALA   240      32.175  46.945  25.235  1.00  0.00              
ATOM    833  N   VAL   241      31.758  49.151  25.363  1.00  0.00              
ATOM    834  CA  VAL   241      30.996  49.189  24.119  1.00  0.00              
ATOM    835  C   VAL   241      31.806  48.659  22.941  1.00  0.00              
ATOM    836  O   VAL   241      31.244  48.197  21.950  1.00  0.00              
ATOM    837  N   ILE   242      33.128  48.727  23.056  1.00  0.00              
ATOM    838  CA  ILE   242      34.014  48.259  21.998  1.00  0.00              
ATOM    839  C   ILE   242      34.622  46.890  22.295  1.00  0.00              
ATOM    840  O   ILE   242      35.626  46.515  21.691  1.00  0.00              
ATOM    841  N   HIS   243      34.031  46.145  23.226  1.00  0.00              
ATOM    842  CA  HIS   243      34.556  44.821  23.567  1.00  0.00              
ATOM    843  C   HIS   243      34.708  43.956  22.313  1.00  0.00              
ATOM    844  O   HIS   243      33.800  43.884  21.485  1.00  0.00              
ATOM    845  N   PRO   244      35.859  43.306  22.173  1.00  0.00              
ATOM    846  CA  PRO   244      36.125  42.457  21.011  1.00  0.00              
ATOM    847  C   PRO   244      35.353  41.144  21.056  1.00  0.00              
ATOM    848  O   PRO   244      35.017  40.645  22.131  1.00  0.00              
ATOM    849  N   ASP   250      35.075  40.586  19.880  1.00  0.00              
ATOM    850  CA  ASP   250      34.371  39.315  19.810  1.00  0.00              
ATOM    851  C   ASP   250      35.285  38.223  20.351  1.00  0.00              
ATOM    852  O   ASP   250      36.511  38.300  20.219  1.00  0.00              
ATOM    853  N   TRP   251      34.668  37.209  20.949  1.00  0.00              
ATOM    854  CA  TRP   251      35.365  36.066  21.532  1.00  0.00              
ATOM    855  C   TRP   251      36.133  36.436  22.791  1.00  0.00              
ATOM    856  O   TRP   251      37.044  35.720  23.205  1.00  0.00              
ATOM    857  N   LYS   252      35.768  37.560  23.402  1.00  0.00              
ATOM    858  CA  LYS   252      36.427  37.974  24.636  1.00  0.00              
ATOM    859  C   LYS   252      36.091  36.951  25.718  1.00  0.00              
ATOM    860  O   LYS   252      34.919  36.659  25.955  1.00  0.00              
ATOM    861  N   PRO   253      37.124  36.415  26.364  1.00  0.00              
ATOM    862  CA  PRO   253      36.974  35.415  27.419  1.00  0.00              
ATOM    863  C   PRO   253      36.294  35.974  28.671  1.00  0.00              
ATOM    864  O   PRO   253      36.657  37.046  29.159  1.00  0.00              
ATOM    865  N   LEU   254      35.308  35.242  29.185  1.00  0.00              
ATOM    866  CA  LEU   254      34.586  35.655  30.385  1.00  0.00              
ATOM    867  C   LEU   254      35.077  34.844  31.588  1.00  0.00              
ATOM    868  O   LEU   254      34.806  33.656  31.697  1.00  0.00              
ATOM    869  N   HIS   255      35.801  35.485  32.515  1.00  0.00              
ATOM    870  CA  HIS   255      36.315  34.774  33.693  1.00  0.00              
ATOM    871  C   HIS   255      35.241  34.199  34.604  1.00  0.00              
ATOM    872  O   HIS   255      34.102  34.663  34.615  1.00  0.00              
ATOM    873  N   PRO   256      35.608  33.172  35.366  1.00  0.00              
ATOM    874  CA  PRO   256      34.670  32.546  36.286  1.00  0.00              
ATOM    875  C   PRO   256      34.299  33.562  37.360  1.00  0.00              
ATOM    876  O   PRO   256      35.159  34.034  38.102  1.00  0.00              
ATOM    877  N   GLY   257      33.013  33.893  37.428  1.00  0.00              
ATOM    878  CA  GLY   257      32.531  34.866  38.392  1.00  0.00              
ATOM    879  C   GLY   257      31.439  35.738  37.798  1.00  0.00              
ATOM    880  O   GLY   257      30.261  35.599  38.145  1.00  0.00              
ATOM    881  N   ASP   258      31.820  36.641  36.896  1.00  0.00              
ATOM    882  CA  ASP   258      30.851  37.527  36.251  1.00  0.00              
ATOM    883  C   ASP   258      29.939  36.719  35.338  1.00  0.00              
ATOM    884  O   ASP   258      30.408  35.948  34.501  1.00  0.00              
ATOM    885  N   PRO   259      28.633  36.881  35.502  1.00  0.00              
ATOM    886  CA  PRO   259      27.682  36.162  34.657  1.00  0.00              
ATOM    887  C   PRO   259      26.412  36.994  34.506  1.00  0.00              
ATOM    888  O   PRO   259      26.387  38.172  34.872  1.00  0.00              
ATOM    889  N   VAL   260      25.358  36.402  33.964  1.00  0.00              
ATOM    890  CA  VAL   260      24.122  37.150  33.786  1.00  0.00              
ATOM    891  C   VAL   260      23.114  36.839  34.890  1.00  0.00              
ATOM    892  O   VAL   260      22.981  35.689  35.317  1.00  0.00              
ATOM    893  N   PHE   261      22.422  37.874  35.360  1.00  0.00              
ATOM    894  CA  PHE   261      21.418  37.726  36.411  1.00  0.00              
ATOM    895  C   PHE   261      20.449  38.908  36.374  1.00  0.00              
ATOM    896  O   PHE   261      19.243  38.737  36.571  1.00  0.00              
ATOM    897  N   LEU   271      27.072  27.420  33.237  1.00  0.00              
ATOM    898  CA  LEU   271      26.964  28.744  33.842  1.00  0.00              
ATOM    899  C   LEU   271      28.246  29.557  33.660  1.00  0.00              
ATOM    900  O   LEU   271      28.284  30.505  32.872  1.00  0.00              
ATOM    901  N   GLY   272      28.217  41.130  20.691  1.00  0.00              
ATOM    902  CA  GLY   272      27.451  41.885  21.690  1.00  0.00              
ATOM    903  C   GLY   272      26.734  43.094  21.075  1.00  0.00              
ATOM    904  O   GLY   272      27.315  43.818  20.267  1.00  0.00              
ATOM    905  N   GLY   273      25.481  43.310  21.461  1.00  0.00              
ATOM    906  CA  GLY   273      24.710  44.437  20.941  1.00  0.00              
ATOM    907  C   GLY   273      23.638  44.835  21.951  1.00  0.00              
ATOM    908  O   GLY   273      22.462  44.499  21.791  1.00  0.00              
ATOM    909  N   ASP   274      24.033  45.559  23.008  1.00  0.00              
ATOM    910  CA  ASP   274      23.116  46.011  24.058  1.00  0.00              
ATOM    911  C   ASP   274      22.169  47.136  23.631  1.00  0.00              
ATOM    912  O   ASP   274      21.301  47.550  24.399  1.00  0.00              
ATOM    913  N   CYS   275      22.337  47.621  22.403  1.00  0.00              
ATOM    914  CA  CYS   275      21.508  48.702  21.883  1.00  0.00              
ATOM    915  C   CYS   275      20.093  48.251  21.534  1.00  0.00              
ATOM    916  O   CYS   275      19.141  49.018  21.673  1.00  0.00              
ATOM    917  N   THR   276      19.952  47.010  21.083  1.00  0.00              
ATOM    918  CA  THR   276      18.641  46.487  20.709  1.00  0.00              
ATOM    919  C   THR   276      17.615  46.606  21.832  1.00  0.00              
ATOM    920  O   THR   276      16.501  47.082  21.612  1.00  0.00              
ATOM    921  N   VAL   277      17.995  46.159  23.027  1.00  0.00              
ATOM    922  CA  VAL   277      17.133  46.198  24.209  1.00  0.00              
ATOM    923  C   VAL   277      15.628  46.059  23.941  1.00  0.00              
ATOM    924  O   VAL   277      14.829  46.865  24.430  1.00  0.00              
ATOM    925  N   TYR   278      15.217  45.041  23.167  1.00  0.00              
ATOM    926  CA  TYR   278      13.785  44.893  22.906  1.00  0.00              
ATOM    927  C   TYR   278      13.218  43.733  23.725  1.00  0.00              
ATOM    928  O   TYR   278      12.853  43.891  24.889  1.00  0.00              
ATOM    929  N   PRO   279      13.153  42.569  23.092  1.00  0.00              
ATOM    930  CA  PRO   279      12.671  41.363  23.732  1.00  0.00              
ATOM    931  C   PRO   279      13.515  40.259  23.132  1.00  0.00              
ATOM    932  O   PRO   279      13.310  39.072  23.382  1.00  0.00              
ATOM    933  N   VAL   280      14.480  40.685  22.322  1.00  0.00              
ATOM    934  CA  VAL   280      15.403  39.789  21.640  1.00  0.00              
ATOM    935  C   VAL   280      16.690  39.679  22.448  1.00  0.00              
ATOM    936  O   VAL   280      16.749  40.103  23.602  1.00  0.00              
ATOM    937  N   PHE   281      17.724  39.119  21.826  1.00  0.00              
ATOM    938  CA  PHE   281      19.010  38.949  22.481  1.00  0.00              
ATOM    939  C   PHE   281      19.950  40.103  22.147  1.00  0.00              
ATOM    940  O   PHE   281      19.841  40.718  21.087  1.00  0.00              
END
