
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0347AL381_5-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347AL381_5-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A     140      D     134           -
LGA    G     141      P     135           -
LGA    A     142      F     136           -
LGA    L     143      R     137           -
LGA    R     144      S     138           -
LGA    M     145      L     139           -
LGA    A     146      A     140           -
LGA    G     147      G     141           -
LGA    G     148      A     142           -
LGA    Y     149      L     143           -
LGA    A     150      R     144           -
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    -       -      Y     149           -
LGA    -       -      A     150           -
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    -       -      E     158           -
LGA    -       -      F     159           -
LGA    -       -      G     160           -
LGA    -       -      W     161           -
LGA    -       -      A     162           -
LGA    -       -      D     163           -
LGA    -       -      F     164           -
LGA    -       -      L     165           -
LGA    -       -      R     166           -
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    -       -      I     169           -
LGA    -       -      D     170           -
LGA    K     151      R     171           #
LGA    V     152      D     172          2.779
LGA    I     153      L     173          1.765
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    I     154      D     176          1.070
LGA    P     155      S     177          0.782
LGA    F     156      F     178          0.788
LGA    S     157      D     179          0.974
LGA    E     158      D     180          0.641
LGA    F     164      A     181          0.779
LGA    L     165      L     182          0.541
LGA    R     166      A     183          0.101
LGA    R     167      E     184          0.448
LGA    R     168      A     185          0.826
LGA    I     169      M     186          0.761
LGA    D     170      K     187          0.521
LGA    R     171      L     188          0.910
LGA    D     172      A     189          1.065
LGA    L     173      K     190          0.896
LGA    L     174      S     191          1.166
LGA    S     175      R     192          3.130
LGA    D     176      E     193          5.300
LGA    S     177      A     194          5.003
LGA    F     178      R     195          3.162
LGA    D     179      H     196          3.092
LGA    D     180      L     197          4.931
LGA    A     181      -       -           -
LGA    L     182      P     198          2.994
LGA    A     183      G     199          3.070
LGA    E     184      W     200           -
LGA    A     185      C     201           -
LGA    M     186      G     202           -
LGA    K     187      V     203           -
LGA    L     188      E     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44   71    5.0     26    2.37     7.69     29.928     1.051

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.815657 * X  +   0.532898 * Y  +  -0.225220 * Z  + -20.743536
  Y_new =  -0.043772 * X  +   0.445021 * Y  +   0.894450 * Z  + -22.611225
  Z_new =   0.576878 * X  +  -0.719706 * Y  +   0.386310 * Z  + -35.387348 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.078174    2.063419  [ DEG:   -61.7748    118.2252 ]
  Theta =  -0.614902   -2.526691  [ DEG:   -35.2313   -144.7687 ]
  Phi   =  -0.053613    3.087979  [ DEG:    -3.0718    176.9282 ]
 
# 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: T0347AL381_5-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL381_5-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44   71   5.0   26   2.37    7.69  29.928
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL381_5-D2
REMARK Aligment from pdb entry: 1oc2A
ATOM    297  N   ALA   140      -2.856  62.204  -8.443  1.00  0.00              
ATOM    298  CA  ALA   140      -3.265  62.753  -7.159  1.00  0.00              
ATOM    299  C   ALA   140      -4.296  63.860  -7.283  1.00  0.00              
ATOM    300  O   ALA   140      -4.481  64.663  -6.340  1.00  0.00              
ATOM    301  N   GLY   141      -5.009  63.884  -8.376  1.00  0.00              
ATOM    302  CA  GLY   141      -5.941  64.989  -8.657  1.00  0.00              
ATOM    303  C   GLY   141      -7.032  65.124  -7.585  1.00  0.00              
ATOM    304  O   GLY   141      -7.459  66.233  -7.276  1.00  0.00              
ATOM    305  N   ALA   142      -7.524  64.014  -7.060  1.00  0.00              
ATOM    306  CA  ALA   142      -8.622  64.106  -6.083  1.00  0.00              
ATOM    307  C   ALA   142      -8.204  64.853  -4.839  1.00  0.00              
ATOM    308  O   ALA   142      -8.936  65.740  -4.341  1.00  0.00              
ATOM    309  N   LEU   143      -7.094  64.420  -4.261  1.00  0.00              
ATOM    310  CA  LEU   143      -6.560  65.046  -3.051  1.00  0.00              
ATOM    311  C   LEU   143      -6.291  66.532  -3.271  1.00  0.00              
ATOM    312  O   LEU   143      -6.571  67.338  -2.409  1.00  0.00              
ATOM    313  N   ARG   144      -5.693  66.861  -4.403  1.00  0.00              
ATOM    314  CA  ARG   144      -5.406  68.245  -4.763  1.00  0.00              
ATOM    315  C   ARG   144      -6.687  69.068  -4.862  1.00  0.00              
ATOM    316  O   ARG   144      -6.810  70.151  -4.291  1.00  0.00              
ATOM    317  N   MET   145      -7.621  68.581  -5.659  1.00  0.00              
ATOM    318  CA  MET   145      -8.918  69.243  -5.894  1.00  0.00              
ATOM    319  C   MET   145      -9.731  69.424  -4.613  1.00  0.00              
ATOM    320  O   MET   145     -10.180  70.489  -4.291  1.00  0.00              
ATOM    321  N   ALA   146      -9.883  68.336  -3.874  1.00  0.00              
ATOM    322  CA  ALA   146     -10.823  68.313  -2.762  1.00  0.00              
ATOM    323  C   ALA   146     -10.254  68.962  -1.514  1.00  0.00              
ATOM    324  O   ALA   146     -10.980  69.688  -0.833  1.00  0.00              
ATOM    325  N   GLY   147      -8.982  68.693  -1.210  1.00  0.00              
ATOM    326  CA  GLY   147      -8.404  69.119   0.080  1.00  0.00              
ATOM    327  C   GLY   147      -7.380  70.191  -0.040  1.00  0.00              
ATOM    328  O   GLY   147      -6.932  70.708   0.976  1.00  0.00              
ATOM    329  N   GLY   148      -6.983  70.543  -1.273  1.00  0.00              
ATOM    330  CA  GLY   148      -6.085  71.655  -1.474  1.00  0.00              
ATOM    331  C   GLY   148      -4.629  71.360  -1.156  1.00  0.00              
ATOM    332  O   GLY   148      -3.821  72.295  -1.077  1.00  0.00              
ATOM    333  N   TYR   149      -4.307  70.086  -0.995  1.00  0.00              
ATOM    334  CA  TYR   149      -2.926  69.671  -0.726  1.00  0.00              
ATOM    335  C   TYR   149      -2.069  69.874  -1.926  1.00  0.00              
ATOM    336  O   TYR   149      -2.467  69.584  -3.073  1.00  0.00              
ATOM    337  N   ALA   150      -0.864  70.413  -1.692  1.00  0.00              
ATOM    338  CA  ALA   150       0.128  70.518  -2.755  1.00  0.00              
ATOM    339  C   ALA   150       1.460  70.032  -2.227  1.00  0.00              
ATOM    340  O   ALA   150       1.824  70.368  -1.085  1.00  0.00              
ATOM    341  N   LYS   151       2.150  69.176  -2.940  1.00  0.00              
ATOM    342  CA  LYS   151       3.472  68.788  -2.494  1.00  0.00              
ATOM    343  C   LYS   151       4.435  69.955  -2.620  1.00  0.00              
ATOM    344  O   LYS   151       4.400  70.730  -3.592  1.00  0.00              
ATOM    345  N   VAL   152       5.352  70.045  -1.679  1.00  0.00              
ATOM    346  CA  VAL   152       6.338  71.099  -1.638  1.00  0.00              
ATOM    347  C   VAL   152       7.700  70.647  -2.148  1.00  0.00              
ATOM    348  O   VAL   152       8.482  71.475  -2.623  1.00  0.00              
ATOM    349  N   ILE   153       7.986  69.348  -2.071  1.00  0.00              
ATOM    350  CA  ILE   153       9.310  68.859  -2.448  1.00  0.00              
ATOM    351  C   ILE   153       9.259  68.191  -3.806  1.00  0.00              
ATOM    352  O   ILE   153       9.456  67.001  -3.949  1.00  0.00              
ATOM    353  N   ILE   154       9.071  68.971  -4.845  1.00  0.00              
ATOM    354  CA  ILE   154       8.928  68.333  -6.148  1.00  0.00              
ATOM    355  C   ILE   154      10.204  68.332  -6.975  1.00  0.00              
ATOM    356  O   ILE   154      10.205  67.826  -8.096  1.00  0.00              
ATOM    357  N   PRO   155      11.291  68.898  -6.473  1.00  0.00              
ATOM    358  CA  PRO   155      12.572  68.869  -7.184  1.00  0.00              
ATOM    359  C   PRO   155      13.297  67.641  -6.578  1.00  0.00              
ATOM    360  O   PRO   155      13.870  67.679  -5.487  1.00  0.00              
ATOM    361  N   PHE   156      13.202  66.544  -7.302  1.00  0.00              
ATOM    362  CA  PHE   156      13.810  65.300  -6.842  1.00  0.00              
ATOM    363  C   PHE   156      15.318  65.392  -6.718  1.00  0.00              
ATOM    364  O   PHE   156      15.902  64.840  -5.774  1.00  0.00              
ATOM    365  N   SER   157      15.987  66.114  -7.643  1.00  0.00              
ATOM    366  CA  SER   157      17.413  66.263  -7.586  1.00  0.00              
ATOM    367  C   SER   157      17.806  66.898  -6.238  1.00  0.00              
ATOM    368  O   SER   157      18.738  66.426  -5.591  1.00  0.00              
ATOM    369  N   GLU   158      17.098  67.943  -5.843  1.00  0.00              
ATOM    370  CA  GLU   158      17.417  68.615  -4.576  1.00  0.00              
ATOM    371  C   GLU   158      17.038  67.742  -3.379  1.00  0.00              
ATOM    372  O   GLU   158      17.795  67.617  -2.408  1.00  0.00              
ATOM    373  N   PHE   164      15.878  67.119  -3.435  1.00  0.00              
ATOM    374  CA  PHE   164      15.468  66.240  -2.352  1.00  0.00              
ATOM    375  C   PHE   164      16.410  65.073  -2.151  1.00  0.00              
ATOM    376  O   PHE   164      16.739  64.707  -1.031  1.00  0.00              
ATOM    377  N   LEU   165      16.882  64.506  -3.265  1.00  0.00              
ATOM    378  CA  LEU   165      17.881  63.447  -3.203  1.00  0.00              
ATOM    379  C   LEU   165      19.198  63.918  -2.648  1.00  0.00              
ATOM    380  O   LEU   165      19.829  63.250  -1.860  1.00  0.00              
ATOM    381  N   ARG   166      19.642  65.085  -3.066  1.00  0.00              
ATOM    382  CA  ARG   166      20.855  65.642  -2.533  1.00  0.00              
ATOM    383  C   ARG   166      20.750  65.774  -1.002  1.00  0.00              
ATOM    384  O   ARG   166      21.705  65.440  -0.273  1.00  0.00              
ATOM    385  N   ARG   167      19.647  66.306  -0.525  1.00  0.00              
ATOM    386  CA  ARG   167      19.479  66.474   0.924  1.00  0.00              
ATOM    387  C   ARG   167      19.418  65.136   1.642  1.00  0.00              
ATOM    388  O   ARG   167      19.917  64.981   2.741  1.00  0.00              
ATOM    389  N   ARG   168      18.829  64.157   0.981  1.00  0.00              
ATOM    390  CA  ARG   168      18.787  62.812   1.550  1.00  0.00              
ATOM    391  C   ARG   168      20.177  62.183   1.609  1.00  0.00              
ATOM    392  O   ARG   168      20.548  61.579   2.662  1.00  0.00              
ATOM    393  N   ILE   169      20.939  62.301   0.548  1.00  0.00              
ATOM    394  CA  ILE   169      22.307  61.842   0.530  1.00  0.00              
ATOM    395  C   ILE   169      23.070  62.474   1.684  1.00  0.00              
ATOM    396  O   ILE   169      23.807  61.804   2.433  1.00  0.00              
ATOM    397  N   ASP   170      22.944  63.798   1.805  1.00  0.00              
ATOM    398  CA  ASP   170      23.641  64.483   2.896  1.00  0.00              
ATOM    399  C   ASP   170      23.192  63.980   4.290  1.00  0.00              
ATOM    400  O   ASP   170      24.016  63.828   5.184  1.00  0.00              
ATOM    401  N   ARG   171      21.920  63.654   4.455  1.00  0.00              
ATOM    402  CA  ARG   171      21.426  63.170   5.751  1.00  0.00              
ATOM    403  C   ARG   171      22.106  61.837   6.102  1.00  0.00              
ATOM    404  O   ARG   171      22.639  61.672   7.185  1.00  0.00              
ATOM    405  N   ASP   172      22.164  60.909   5.157  1.00  0.00              
ATOM    406  CA  ASP   172      22.813  59.606   5.419  1.00  0.00              
ATOM    407  C   ASP   172      24.288  59.778   5.668  1.00  0.00              
ATOM    408  O   ASP   172      24.879  58.983   6.388  1.00  0.00              
ATOM    409  N   LEU   173      24.893  60.781   5.011  1.00  0.00              
ATOM    410  CA  LEU   173      26.300  61.062   5.172  1.00  0.00              
ATOM    411  C   LEU   173      26.613  61.656   6.554  1.00  0.00              
ATOM    412  O   LEU   173      27.650  61.367   7.148  1.00  0.00              
ATOM    413  N   LEU   174      25.701  62.505   7.019  1.00  0.00              
ATOM    414  CA  LEU   174      25.855  63.192   8.298  1.00  0.00              
ATOM    415  C   LEU   174      25.443  62.348   9.473  1.00  0.00              
ATOM    416  O   LEU   174      25.732  62.762  10.626  1.00  0.00              
ATOM    417  N   SER   175      24.737  61.232   9.243  1.00  0.00              
ATOM    418  CA  SER   175      24.143  60.381  10.304  1.00  0.00              
ATOM    419  C   SER   175      24.538  58.938  10.113  1.00  0.00              
ATOM    420  O   SER   175      23.716  58.010  10.128  1.00  0.00              
ATOM    421  N   ASP   176      25.847  58.761   9.855  1.00  0.00              
ATOM    422  CA  ASP   176      26.336  57.401   9.639  1.00  0.00              
ATOM    423  C   ASP   176      26.128  56.513  10.852  1.00  0.00              
ATOM    424  O   ASP   176      25.872  55.304  10.683  1.00  0.00              
ATOM    425  N   SER   177      26.238  57.073  12.066  1.00  0.00              
ATOM    426  CA  SER   177      25.978  56.262  13.264  1.00  0.00              
ATOM    427  C   SER   177      24.550  55.731  13.317  1.00  0.00              
ATOM    428  O   SER   177      24.281  54.758  13.986  1.00  0.00              
ATOM    429  N   PHE   178      23.640  56.328  12.575  1.00  0.00              
ATOM    430  CA  PHE   178      22.259  55.854  12.596  1.00  0.00              
ATOM    431  C   PHE   178      22.042  54.537  11.830  1.00  0.00              
ATOM    432  O   PHE   178      21.147  53.736  12.152  1.00  0.00              
ATOM    433  N   ASP   179      22.904  54.290  10.819  1.00  0.00              
ATOM    434  CA  ASP   179      22.779  53.112   9.978  1.00  0.00              
ATOM    435  C   ASP   179      23.947  52.100  10.038  1.00  0.00              
ATOM    436  O   ASP   179      23.782  50.966   9.614  1.00  0.00              
ATOM    437  N   ASP   180      25.134  52.525  10.521  1.00  0.00              
ATOM    438  CA  ASP   180      26.306  51.703  10.359  1.00  0.00              
ATOM    439  C   ASP   180      26.158  50.349  10.996  1.00  0.00              
ATOM    440  O   ASP   180      26.692  49.387  10.464  1.00  0.00              
ATOM    441  N   ALA   181      25.437  50.276  12.108  1.00  0.00              
ATOM    442  CA  ALA   181      25.301  49.007  12.815  1.00  0.00              
ATOM    443  C   ALA   181      24.450  47.987  12.114  1.00  0.00              
ATOM    444  O   ALA   181      24.486  46.833  12.482  1.00  0.00              
ATOM    445  N   LEU   182      23.681  48.412  11.113  1.00  0.00              
ATOM    446  CA  LEU   182      22.801  47.543  10.358  1.00  0.00              
ATOM    447  C   LEU   182      23.386  47.132   9.019  1.00  0.00              
ATOM    448  O   LEU   182      22.903  46.168   8.388  1.00  0.00              
ATOM    449  N   ALA   183      24.443  47.814   8.562  1.00  0.00              
ATOM    450  CA  ALA   183      24.896  47.571   7.199  1.00  0.00              
ATOM    451  C   ALA   183      25.275  46.117   6.868  1.00  0.00              
ATOM    452  O   ALA   183      24.811  45.522   5.887  1.00  0.00              
ATOM    453  N   GLU   184      26.164  45.567   7.652  1.00  0.00              
ATOM    454  CA  GLU   184      26.650  44.206   7.386  1.00  0.00              
ATOM    455  C   GLU   184      25.485  43.217   7.451  1.00  0.00              
ATOM    456  O   GLU   184      25.384  42.353   6.575  1.00  0.00              
ATOM    457  N   ALA   185      24.591  43.375   8.425  1.00  0.00              
ATOM    458  CA  ALA   185      23.475  42.447   8.569  1.00  0.00              
ATOM    459  C   ALA   185      22.477  42.528   7.405  1.00  0.00              
ATOM    460  O   ALA   185      22.006  41.492   6.922  1.00  0.00              
ATOM    461  N   MET   186      22.183  43.734   6.933  1.00  0.00              
ATOM    462  CA  MET   186      21.254  43.859   5.825  1.00  0.00              
ATOM    463  C   MET   186      21.876  43.294   4.540  1.00  0.00              
ATOM    464  O   MET   186      21.219  42.589   3.784  1.00  0.00              
ATOM    465  N   LYS   187      23.127  43.614   4.284  1.00  0.00              
ATOM    466  CA  LYS   187      23.785  43.095   3.088  1.00  0.00              
ATOM    467  C   LYS   187      23.931  41.575   3.130  1.00  0.00              
ATOM    468  O   LYS   187      23.738  40.914   2.111  1.00  0.00              
ATOM    469  N   LEU   188      24.232  41.043   4.314  1.00  0.00              
ATOM    470  CA  LEU   188      24.316  39.585   4.470  1.00  0.00              
ATOM    471  C   LEU   188      22.967  38.948   4.218  1.00  0.00              
ATOM    472  O   LEU   188      22.903  37.860   3.635  1.00  0.00              
END
