
#######################################################
#                                                     #
#                        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   42 (  168),  selected   42 , name T0347AL243_1-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347AL243_1-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R     137      -       -           -
LGA    S     138      -       -           -
LGA    L     139      -       -           -
LGA    A     140      -       -           -
LGA    G     141      -       -           -
LGA    A     142      -       -           -
LGA    L     143      -       -           -
LGA    R     144      D     134          3.681
LGA    M     145      -       -           -
LGA    A     146      P     135          5.123
LGA    G     147      F     136          3.200
LGA    L     165      R     137          2.707
LGA    R     166      S     138          2.215
LGA    R     167      L     139          0.669
LGA    D     170      A     140          2.274
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    R     171      L     143          1.326
LGA    D     172      R     144          3.251
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    L     173      G     147          1.946
LGA    L     174      G     148          4.399
LGA    S     175      Y     149           #
LGA    D     176      -       -           -
LGA    S     177      A     150          2.435
LGA    F     178      K     151          2.860
LGA    D     179      V     152          1.656
LGA    D     180      I     153          4.560
LGA    A     181      I     154          3.458
LGA    L     182      P     155          4.682
LGA    A     183      F     156          2.969
LGA    E     184      S     157          2.854
LGA    A     185      E     158          1.993
LGA    M     186      F     159          1.897
LGA    K     187      G     160          2.002
LGA    L     188      W     161          1.896
LGA    A     189      A     162          2.117
LGA    K     190      D     163          2.895
LGA    -       -      F     164           -
LGA    -       -      L     165           -
LGA    -       -      R     166           -
LGA    -       -      R     167           -
LGA    -       -      R     168           -
LGA    -       -      I     169           -
LGA    -       -      D     170           -
LGA    -       -      R     171           -
LGA    -       -      D     172           -
LGA    -       -      L     173           -
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    -       -      F     178           -
LGA    -       -      D     179           -
LGA    -       -      D     180           -
LGA    -       -      A     181           -
LGA    -       -      L     182           -
LGA    -       -      A     183           -
LGA    -       -      E     184           -
LGA    S     191      A     185          2.457
LGA    -       -      M     186           -
LGA    R     192      K     187          3.079
LGA    E     193      L     188          2.014
LGA    A     194      A     189          2.126
LGA    R     195      K     190          3.339
LGA    H     196      S     191          3.824
LGA    -       -      R     192           -
LGA    -       -      E     193           -
LGA    L     197      A     194          2.391
LGA    -       -      R     195           -
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    -       -      C     201           -
LGA    -       -      G     202           -
LGA    -       -      V     203           -
LGA    -       -      E     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42   71    5.0     32    2.93     6.25     28.558     1.055

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.346638 * X  +   0.885839 * Y  +  -0.308434 * Z  +  36.132519
  Y_new =  -0.908797 * X  +   0.398579 * Y  +   0.123376 * Z  +  68.958412
  Z_new =   0.232226 * X  +   0.237537 * Y  +   0.943211 * Z  + -24.210379 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.246708   -2.894884  [ DEG:    14.1353   -165.8647 ]
  Theta =  -0.234366   -2.907227  [ DEG:   -13.4282   -166.5718 ]
  Phi   =  -1.206405    1.935188  [ DEG:   -69.1219    110.8781 ]
 
# 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: T0347AL243_1-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL243_1-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   71   5.0   32   2.93    6.25  28.558
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL243_1-D2
REMARK Aligment from pdb entry: 1vz0A
ATOM    409  N   ARG   137      -0.142  42.711  -7.256  1.00  0.00              
ATOM    410  CA  ARG   137       0.299  43.099  -5.925  1.00  0.00              
ATOM    411  C   ARG   137      -0.576  44.197  -5.325  1.00  0.00              
ATOM    412  O   ARG   137      -1.362  44.839  -6.019  1.00  0.00              
ATOM    413  N   SER   138      -0.452  44.401  -4.021  1.00  0.00              
ATOM    414  CA  SER   138      -1.239  45.422  -3.355  1.00  0.00              
ATOM    415  C   SER   138      -0.707  46.809  -3.703  1.00  0.00              
ATOM    416  O   SER   138       0.479  46.994  -3.974  1.00  0.00              
ATOM    417  N   LEU   139      -1.595  47.788  -3.700  1.00  0.00              
ATOM    418  CA  LEU   139      -1.187  49.148  -4.002  1.00  0.00              
ATOM    419  C   LEU   139      -0.116  49.610  -3.022  1.00  0.00              
ATOM    420  O   LEU   139       0.804  50.321  -3.394  1.00  0.00              
ATOM    421  N   ALA   140      -0.258  49.213  -1.764  1.00  0.00              
ATOM    422  CA  ALA   140       0.702  49.593  -0.734  1.00  0.00              
ATOM    423  C   ALA   140       2.085  49.029  -1.044  1.00  0.00              
ATOM    424  O   ALA   140       3.097  49.675  -0.778  1.00  0.00              
ATOM    425  N   GLY   141       2.129  47.838  -1.626  1.00  0.00              
ATOM    426  CA  GLY   141       3.404  47.221  -1.978  1.00  0.00              
ATOM    427  C   GLY   141       4.110  48.078  -3.022  1.00  0.00              
ATOM    428  O   GLY   141       5.322  48.314  -2.939  1.00  0.00              
ATOM    429  N   ALA   142       3.349  48.549  -4.002  1.00  0.00              
ATOM    430  CA  ALA   142       3.908  49.391  -5.056  1.00  0.00              
ATOM    431  C   ALA   142       4.382  50.744  -4.501  1.00  0.00              
ATOM    432  O   ALA   142       5.468  51.223  -4.852  1.00  0.00              
ATOM    433  N   LEU   143       3.583  51.353  -3.624  1.00  0.00              
ATOM    434  CA  LEU   143       3.961  52.640  -3.037  1.00  0.00              
ATOM    435  C   LEU   143       5.216  52.496  -2.176  1.00  0.00              
ATOM    436  O   LEU   143       6.103  53.347  -2.219  1.00  0.00              
ATOM    437  N   ARG   144       5.287  51.423  -1.392  1.00  0.00              
ATOM    438  CA  ARG   144       6.456  51.194  -0.545  1.00  0.00              
ATOM    439  C   ARG   144       7.709  50.984  -1.377  1.00  0.00              
ATOM    440  O   ARG   144       8.770  51.509  -1.065  1.00  0.00              
ATOM    441  N   MET   145       7.581  50.211  -2.442  1.00  0.00              
ATOM    442  CA  MET   145       8.715  49.958  -3.307  1.00  0.00              
ATOM    443  C   MET   145       9.223  51.269  -3.914  1.00  0.00              
ATOM    444  O   MET   145      10.434  51.494  -3.978  1.00  0.00              
ATOM    445  N   ALA   146       8.305  52.132  -4.353  1.00  0.00              
ATOM    446  CA  ALA   146       8.707  53.409  -4.955  1.00  0.00              
ATOM    447  C   ALA   146       9.513  54.275  -3.983  1.00  0.00              
ATOM    448  O   ALA   146      10.418  54.996  -4.399  1.00  0.00              
ATOM    449  N   GLY   147       9.197  54.199  -2.694  1.00  0.00              
ATOM    450  CA  GLY   147       9.917  54.987  -1.696  1.00  0.00              
ATOM    451  C   GLY   147      11.421  54.716  -1.701  1.00  0.00              
ATOM    452  O   GLY   147      12.219  55.603  -1.411  1.00  0.00              
ATOM    453  N   LEU   165      11.813  53.496  -2.046  1.00  0.00              
ATOM    454  CA  LEU   165      13.231  53.153  -2.084  1.00  0.00              
ATOM    455  C   LEU   165      14.035  54.034  -3.038  1.00  0.00              
ATOM    456  O   LEU   165      15.242  54.200  -2.861  1.00  0.00              
ATOM    457  N   ARG   166      13.379  54.598  -4.050  1.00  0.00              
ATOM    458  CA  ARG   166      14.091  55.409  -5.028  1.00  0.00              
ATOM    459  C   ARG   166      14.560  56.770  -4.530  1.00  0.00              
ATOM    460  O   ARG   166      15.310  57.454  -5.217  1.00  0.00              
ATOM    461  N   ARG   167      14.128  57.183  -3.348  1.00  0.00              
ATOM    462  CA  ARG   167      14.588  58.466  -2.854  1.00  0.00              
ATOM    463  C   ARG   167      15.852  58.288  -2.022  1.00  0.00              
ATOM    464  O   ARG   167      16.418  59.257  -1.533  1.00  0.00              
ATOM    465  N   ASP   170      16.296  57.038  -1.879  1.00  0.00              
ATOM    466  CA  ASP   170      17.526  56.748  -1.146  1.00  0.00              
ATOM    467  C   ASP   170      18.690  57.092  -2.054  1.00  0.00              
ATOM    468  O   ASP   170      18.572  57.029  -3.273  1.00  0.00              
ATOM    469  N   ARG   171      19.832  57.472  -1.475  1.00  0.00              
ATOM    470  CA  ARG   171      20.993  57.807  -2.303  1.00  0.00              
ATOM    471  C   ARG   171      21.507  56.556  -3.022  1.00  0.00              
ATOM    472  O   ARG   171      21.340  55.436  -2.540  1.00  0.00              
ATOM    473  N   ASP   172      22.146  56.735  -4.184  1.00  0.00              
ATOM    474  CA  ASP   172      22.690  55.636  -4.992  1.00  0.00              
ATOM    475  C   ASP   172      23.515  54.579  -4.254  1.00  0.00              
ATOM    476  O   ASP   172      23.348  53.383  -4.494  1.00  0.00              
ATOM    477  N   LEU   173      24.403  55.003  -3.359  1.00  0.00              
ATOM    478  CA  LEU   173      25.223  54.035  -2.639  1.00  0.00              
ATOM    479  C   LEU   173      24.426  53.137  -1.690  1.00  0.00              
ATOM    480  O   LEU   173      24.819  51.998  -1.423  1.00  0.00              
ATOM    481  N   LEU   174      23.300  53.635  -1.189  1.00  0.00              
ATOM    482  CA  LEU   174      22.462  52.825  -0.307  1.00  0.00              
ATOM    483  C   LEU   174      21.748  51.775  -1.159  1.00  0.00              
ATOM    484  O   LEU   174      21.591  50.626  -0.743  1.00  0.00              
ATOM    485  N   SER   175      21.324  52.164  -2.358  1.00  0.00              
ATOM    486  CA  SER   175      20.643  51.222  -3.230  1.00  0.00              
ATOM    487  C   SER   175      21.611  50.120  -3.676  1.00  0.00              
ATOM    488  O   SER   175      21.222  48.963  -3.795  1.00  0.00              
ATOM    489  N   ASP   176      22.874  50.471  -3.904  1.00  0.00              
ATOM    490  CA  ASP   176      23.870  49.482  -4.325  1.00  0.00              
ATOM    491  C   ASP   176      24.138  48.476  -3.222  1.00  0.00              
ATOM    492  O   ASP   176      24.306  47.278  -3.474  1.00  0.00              
ATOM    493  N   SER   177      24.191  48.971  -1.993  1.00  0.00              
ATOM    494  CA  SER   177      24.422  48.102  -0.852  1.00  0.00              
ATOM    495  C   SER   177      23.249  47.138  -0.731  1.00  0.00              
ATOM    496  O   SER   177      23.424  45.997  -0.311  1.00  0.00              
ATOM    497  N   PHE   178      22.053  47.602  -1.096  1.00  0.00              
ATOM    498  CA  PHE   178      20.860  46.762  -1.035  1.00  0.00              
ATOM    499  C   PHE   178      20.959  45.690  -2.111  1.00  0.00              
ATOM    500  O   PHE   178      20.776  44.501  -1.835  1.00  0.00              
ATOM    501  N   ASP   179      24.231  43.630   0.925  1.00  0.00              
ATOM    502  CA  ASP   179      24.978  44.060   2.098  1.00  0.00              
ATOM    503  C   ASP   179      24.037  44.563   3.189  1.00  0.00              
ATOM    504  O   ASP   179      24.403  44.582   4.365  1.00  0.00              
ATOM    505  N   ASP   180      22.829  44.972   2.791  1.00  0.00              
ATOM    506  CA  ASP   180      21.803  45.424   3.734  1.00  0.00              
ATOM    507  C   ASP   180      20.451  44.899   3.245  1.00  0.00              
ATOM    508  O   ASP   180      20.319  44.521   2.086  1.00  0.00              
ATOM    509  N   ALA   181      19.456  44.870   4.125  1.00  0.00              
ATOM    510  CA  ALA   181      18.131  44.375   3.766  1.00  0.00              
ATOM    511  C   ALA   181      17.167  45.509   3.474  1.00  0.00              
ATOM    512  O   ALA   181      17.488  46.679   3.683  1.00  0.00              
ATOM    513  N   LEU   182      15.979  45.151   2.995  1.00  0.00              
ATOM    514  CA  LEU   182      14.955  46.143   2.698  1.00  0.00              
ATOM    515  C   LEU   182      14.624  46.869   4.002  1.00  0.00              
ATOM    516  O   LEU   182      14.317  48.060   4.003  1.00  0.00              
ATOM    517  N   ALA   183      14.704  46.134   5.111  1.00  0.00              
ATOM    518  CA  ALA   183      14.431  46.711   6.417  1.00  0.00              
ATOM    519  C   ALA   183      15.396  47.845   6.726  1.00  0.00              
ATOM    520  O   ALA   183      14.997  48.900   7.217  1.00  0.00              
ATOM    521  N   GLU   184      16.675  47.624   6.440  1.00  0.00              
ATOM    522  CA  GLU   184      17.696  48.644   6.659  1.00  0.00              
ATOM    523  C   GLU   184      17.376  49.856   5.796  1.00  0.00              
ATOM    524  O   GLU   184      17.475  50.999   6.244  1.00  0.00              
ATOM    525  N   ALA   185      17.011  49.590   4.546  1.00  0.00              
ATOM    526  CA  ALA   185      16.670  50.642   3.600  1.00  0.00              
ATOM    527  C   ALA   185      15.516  51.494   4.128  1.00  0.00              
ATOM    528  O   ALA   185      15.557  52.721   4.037  1.00  0.00              
ATOM    529  N   MET   186      14.490  50.847   4.681  1.00  0.00              
ATOM    530  CA  MET   186      13.344  51.579   5.217  1.00  0.00              
ATOM    531  C   MET   186      13.775  52.402   6.422  1.00  0.00              
ATOM    532  O   MET   186      13.305  53.514   6.628  1.00  0.00              
ATOM    533  N   LYS   187      14.671  51.844   7.223  1.00  0.00              
ATOM    534  CA  LYS   187      15.170  52.552   8.392  1.00  0.00              
ATOM    535  C   LYS   187      15.874  53.828   7.931  1.00  0.00              
ATOM    536  O   LYS   187      15.664  54.897   8.496  1.00  0.00              
ATOM    537  N   LEU   188      16.701  53.716   6.895  1.00  0.00              
ATOM    538  CA  LEU   188      17.417  54.873   6.379  1.00  0.00              
ATOM    539  C   LEU   188      16.463  55.945   5.854  1.00  0.00              
ATOM    540  O   LEU   188      16.779  57.133   5.892  1.00  0.00              
ATOM    541  N   ALA   189      15.301  55.526   5.360  1.00  0.00              
ATOM    542  CA  ALA   189      14.323  56.477   4.843  1.00  0.00              
ATOM    543  C   ALA   189      13.777  57.361   5.957  1.00  0.00              
ATOM    544  O   ALA   189      13.302  58.469   5.704  1.00  0.00              
ATOM    545  N   LYS   190      13.853  56.867   7.191  1.00  0.00              
ATOM    546  CA  LYS   190      13.365  57.614   8.345  1.00  0.00              
ATOM    547  C   LYS   190      14.353  58.685   8.792  1.00  0.00              
ATOM    548  O   LYS   190      14.012  59.557   9.585  1.00  0.00              
ATOM    549  N   SER   191      17.526  63.257   4.770  1.00  0.00              
ATOM    550  CA  SER   191      18.372  63.045   3.594  1.00  0.00              
ATOM    551  C   SER   191      19.879  63.240   3.820  1.00  0.00              
ATOM    552  O   SER   191      20.678  62.413   3.381  1.00  0.00              
ATOM    553  N   ARG   192      20.262  64.317   4.509  1.00  0.00              
ATOM    554  CA  ARG   192      21.678  64.614   4.769  1.00  0.00              
ATOM    555  C   ARG   192      22.364  63.601   5.672  1.00  0.00              
ATOM    556  O   ARG   192      23.587  63.599   5.786  1.00  0.00              
ATOM    557  N   GLU   193      21.584  62.764   6.336  1.00  0.00              
ATOM    558  CA  GLU   193      22.155  61.805   7.270  1.00  0.00              
ATOM    559  C   GLU   193      22.143  60.362   6.791  1.00  0.00              
ATOM    560  O   GLU   193      22.684  59.477   7.453  1.00  0.00              
ATOM    561  N   ALA   194      21.539  60.127   5.636  1.00  0.00              
ATOM    562  CA  ALA   194      21.440  58.780   5.105  1.00  0.00              
ATOM    563  C   ALA   194      22.773  58.112   4.799  1.00  0.00              
ATOM    564  O   ALA   194      22.972  56.948   5.142  1.00  0.00              
ATOM    565  N   ARG   195      23.691  58.830   4.167  1.00  0.00              
ATOM    566  CA  ARG   195      24.983  58.230   3.880  1.00  0.00              
ATOM    567  C   ARG   195      25.664  57.839   5.186  1.00  0.00              
ATOM    568  O   ARG   195      26.226  56.750   5.300  1.00  0.00              
ATOM    569  N   HIS   196      25.602  58.725   6.174  1.00  0.00              
ATOM    570  CA  HIS   196      26.206  58.445   7.466  1.00  0.00              
ATOM    571  C   HIS   196      25.572  57.190   8.044  1.00  0.00              
ATOM    572  O   HIS   196      26.266  56.290   8.521  1.00  0.00              
ATOM    573  N   LEU   197      24.245  57.142   7.995  1.00  0.00              
ATOM    574  CA  LEU   197      23.522  55.997   8.513  1.00  0.00              
ATOM    575  C   LEU   197      23.911  54.714   7.814  1.00  0.00              
ATOM    576  O   LEU   197      24.011  53.659   8.443  1.00  0.00              
END
