
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0347AL257_1-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347AL257_1-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D     134      -       -           -
LGA    P     135      -       -           -
LGA    F     136      D     134          3.832
LGA    R     137      P     135          1.627
LGA    S     138      F     136           #
LGA    L     139      R     137           -
LGA    A     140      S     138          6.368
LGA    G     141      L     139          1.309
LGA    A     142      A     140          4.064
LGA    L     143      G     141          4.044
LGA    R     144      A     142          3.616
LGA    M     145      L     143          3.614
LGA    A     146      R     144          2.051
LGA    G     147      M     145          4.645
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    G     148      Y     149          1.945
LGA    Y     149      A     150          2.435
LGA    A     150      K     151          3.104
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    K     151      I     154          4.029
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    V     152      S     157          4.260
LGA    I     153      E     158          2.440
LGA    I     154      F     159          2.479
LGA    D     163      G     160          1.912
LGA    F     164      W     161          1.000
LGA    L     165      A     162          0.709
LGA    R     166      D     163          0.284
LGA    R     167      F     164          1.456
LGA    R     168      L     165          1.950
LGA    I     169      R     166          2.102
LGA    D     170      R     167          2.731
LGA    R     171      R     168          2.883
LGA    D     172      I     169          2.788
LGA    L     173      D     170          4.767
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    L     174      A     181          2.274
LGA    S     175      L     182          1.834
LGA    D     176      A     183          1.636
LGA    S     177      E     184          1.852
LGA    F     178      A     185          1.473
LGA    D     179      M     186          1.305
LGA    -       -      K     187           -
LGA    D     180      L     188          2.472
LGA    A     181      A     189          1.749
LGA    L     182      K     190          3.804
LGA    A     183      S     191          4.102
LGA    E     184      R     192          3.541
LGA    -       -      E     193           -
LGA    A     185      A     194          3.429
LGA    M     186      R     195          4.018
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)   45   71    5.0     41    3.01     9.76     37.849     1.318

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.778875 * X  +  -0.532080 * Y  +  -0.332031 * Z  +  34.937428
  Y_new =   0.553690 * X  +  -0.334686 * Y  +  -0.762504 * Z  +  -0.485554
  Z_new =   0.294587 * X  +  -0.777738 * Y  +   0.555286 * Z  + -40.003479 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.950752    2.190840  [ DEG:   -54.4741    125.5259 ]
  Theta =  -0.299024   -2.842569  [ DEG:   -17.1328   -162.8672 ]
  Phi   =   2.523599   -0.617994  [ DEG:   144.5916    -35.4084 ]
 
# 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: T0347AL257_1-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL257_1-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   71   5.0   41   3.01    9.76  37.849
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL257_1-D2
REMARK Aligment from pdb entry: 1vz0_B
ATOM    469  N   ASP   134       3.429  54.187  -4.696  1.00  0.00              
ATOM    470  CA  ASP   134       2.420  55.038  -4.073  1.00  0.00              
ATOM    471  C   ASP   134       2.753  56.513  -4.283  1.00  0.00              
ATOM    472  O   ASP   134       1.902  57.375  -4.108  1.00  0.00              
ATOM    473  N   PRO   135       3.996  56.800  -4.649  1.00  0.00              
ATOM    474  CA  PRO   135       4.385  58.181  -4.859  1.00  0.00              
ATOM    475  C   PRO   135       4.816  58.857  -3.571  1.00  0.00              
ATOM    476  O   PRO   135       4.935  60.087  -3.513  1.00  0.00              
ATOM    477  N   PHE   136       5.051  58.058  -2.535  1.00  0.00              
ATOM    478  CA  PHE   136       5.478  58.592  -1.254  1.00  0.00              
ATOM    479  C   PHE   136       6.946  59.023  -1.334  1.00  0.00              
ATOM    480  O   PHE   136       7.397  59.836  -0.541  1.00  0.00              
ATOM    481  N   ARG   137       7.687  58.471  -2.294  1.00  0.00              
ATOM    482  CA  ARG   137       9.098  58.836  -2.490  1.00  0.00              
ATOM    483  C   ARG   137       9.332  58.851  -3.992  1.00  0.00              
ATOM    484  O   ARG   137       8.536  58.291  -4.738  1.00  0.00              
ATOM    485  N   SER   138      10.424  59.473  -4.430  1.00  0.00              
ATOM    486  CA  SER   138      10.740  59.569  -5.854  1.00  0.00              
ATOM    487  C   SER   138      11.800  58.573  -6.285  1.00  0.00              
ATOM    488  O   SER   138      12.428  57.920  -5.458  1.00  0.00              
ATOM    489  N   LEU   139      12.011  58.494  -7.595  1.00  0.00              
ATOM    490  CA  LEU   139      13.014  57.610  -8.175  1.00  0.00              
ATOM    491  C   LEU   139      14.393  58.029  -7.662  1.00  0.00              
ATOM    492  O   LEU   139      15.292  57.200  -7.507  1.00  0.00              
ATOM    493  N   ALA   140      14.560  59.325  -7.409  1.00  0.00              
ATOM    494  CA  ALA   140      15.817  59.801  -6.873  1.00  0.00              
ATOM    495  C   ALA   140      16.018  59.251  -5.468  1.00  0.00              
ATOM    496  O   ALA   140      17.125  58.822  -5.134  1.00  0.00              
ATOM    497  N   GLY   141      14.965  59.269  -4.642  1.00  0.00              
ATOM    498  CA  GLY   141      15.054  58.731  -3.276  1.00  0.00              
ATOM    499  C   GLY   141      15.466  57.264  -3.357  1.00  0.00              
ATOM    500  O   GLY   141      16.301  56.788  -2.584  1.00  0.00              
ATOM    501  N   ALA   142      14.851  56.558  -4.303  1.00  0.00              
ATOM    502  CA  ALA   142      15.115  55.148  -4.509  1.00  0.00              
ATOM    503  C   ALA   142      16.592  54.967  -4.835  1.00  0.00              
ATOM    504  O   ALA   142      17.243  54.063  -4.305  1.00  0.00              
ATOM    505  N   LEU   143      17.125  55.831  -5.691  1.00  0.00              
ATOM    506  CA  LEU   143      18.544  55.736  -6.036  1.00  0.00              
ATOM    507  C   LEU   143      19.431  56.037  -4.832  1.00  0.00              
ATOM    508  O   LEU   143      20.521  55.478  -4.707  1.00  0.00              
ATOM    509  N   ARG   144      18.977  56.932  -3.955  1.00  0.00              
ATOM    510  CA  ARG   144      19.751  57.255  -2.765  1.00  0.00              
ATOM    511  C   ARG   144      19.776  56.019  -1.851  1.00  0.00              
ATOM    512  O   ARG   144      20.794  55.710  -1.238  1.00  0.00              
ATOM    513  N   MET   145      18.653  55.310  -1.770  1.00  0.00              
ATOM    514  CA  MET   145      18.576  54.121  -0.929  1.00  0.00              
ATOM    515  C   MET   145      19.483  53.012  -1.440  1.00  0.00              
ATOM    516  O   MET   145      20.023  52.239  -0.650  1.00  0.00              
ATOM    517  N   ALA   146      19.661  52.942  -2.757  1.00  0.00              
ATOM    518  CA  ALA   146      20.520  51.925  -3.347  1.00  0.00              
ATOM    519  C   ALA   146      21.973  52.123  -2.946  1.00  0.00              
ATOM    520  O   ALA   146      22.765  51.193  -3.034  1.00  0.00              
ATOM    521  N   GLY   147      22.313  53.336  -2.519  1.00  0.00              
ATOM    522  CA  GLY   147      23.677  53.649  -2.121  1.00  0.00              
ATOM    523  C   GLY   147      23.953  53.212  -0.692  1.00  0.00              
ATOM    524  O   GLY   147      25.096  53.175  -0.258  1.00  0.00              
ATOM    525  N   GLY   148      22.900  52.869   0.040  1.00  0.00              
ATOM    526  CA  GLY   148      23.062  52.408   1.414  1.00  0.00              
ATOM    527  C   GLY   148      23.268  50.907   1.378  1.00  0.00              
ATOM    528  O   GLY   148      22.827  50.241   0.442  1.00  0.00              
ATOM    529  N   TYR   149      23.956  50.371   2.378  1.00  0.00              
ATOM    530  CA  TYR   149      24.163  48.921   2.443  1.00  0.00              
ATOM    531  C   TYR   149      22.777  48.277   2.589  1.00  0.00              
ATOM    532  O   TYR   149      21.893  48.820   3.250  1.00  0.00              
ATOM    533  N   ALA   150      22.575  47.115   1.971  1.00  0.00              
ATOM    534  CA  ALA   150      21.296  46.405   2.019  1.00  0.00              
ATOM    535  C   ALA   150      20.575  46.428   3.362  1.00  0.00              
ATOM    536  O   ALA   150      19.380  46.734   3.430  1.00  0.00              
ATOM    537  N   LYS   151      21.307  46.126   4.429  1.00  0.00              
ATOM    538  CA  LYS   151      20.711  46.065   5.748  1.00  0.00              
ATOM    539  C   LYS   151      20.346  47.404   6.384  1.00  0.00              
ATOM    540  O   LYS   151      19.890  47.443   7.528  1.00  0.00              
ATOM    541  N   VAL   152      20.537  48.499   5.658  1.00  0.00              
ATOM    542  CA  VAL   152      20.197  49.811   6.203  1.00  0.00              
ATOM    543  C   VAL   152      19.090  50.466   5.388  1.00  0.00              
ATOM    544  O   VAL   152      18.575  51.516   5.760  1.00  0.00              
ATOM    545  N   ILE   153      18.718  49.834   4.278  1.00  0.00              
ATOM    546  CA  ILE   153      17.711  50.389   3.394  1.00  0.00              
ATOM    547  C   ILE   153      16.350  50.645   4.012  1.00  0.00              
ATOM    548  O   ILE   153      15.736  51.674   3.730  1.00  0.00              
ATOM    549  N   ILE   154      15.874  49.734   4.857  1.00  0.00              
ATOM    550  CA  ILE   154      14.583  49.946   5.504  1.00  0.00              
ATOM    551  C   ILE   154      14.692  51.118   6.468  1.00  0.00              
ATOM    552  O   ILE   154      13.795  51.953   6.552  1.00  0.00              
ATOM    553  N   ASP   163      15.798  51.181   7.203  1.00  0.00              
ATOM    554  CA  ASP   163      15.996  52.282   8.127  1.00  0.00              
ATOM    555  C   ASP   163      15.981  53.599   7.347  1.00  0.00              
ATOM    556  O   ASP   163      15.319  54.557   7.738  1.00  0.00              
ATOM    557  N   PHE   164      16.711  53.639   6.237  1.00  0.00              
ATOM    558  CA  PHE   164      16.769  54.852   5.439  1.00  0.00              
ATOM    559  C   PHE   164      15.423  55.253   4.865  1.00  0.00              
ATOM    560  O   PHE   164      15.102  56.442   4.770  1.00  0.00              
ATOM    561  N   LEU   165      14.637  54.254   4.476  1.00  0.00              
ATOM    562  CA  LEU   165      13.319  54.489   3.912  1.00  0.00              
ATOM    563  C   LEU   165      12.445  55.131   5.001  1.00  0.00              
ATOM    564  O   LEU   165      11.717  56.081   4.730  1.00  0.00              
ATOM    565  N   ARG   166      12.516  54.614   6.230  1.00  0.00              
ATOM    566  CA  ARG   166      11.720  55.175   7.323  1.00  0.00              
ATOM    567  C   ARG   166      12.114  56.626   7.561  1.00  0.00              
ATOM    568  O   ARG   166      11.253  57.472   7.786  1.00  0.00              
ATOM    569  N   ARG   167      13.415  56.906   7.520  1.00  0.00              
ATOM    570  CA  ARG   167      13.901  58.265   7.723  1.00  0.00              
ATOM    571  C   ARG   167      13.285  59.206   6.698  1.00  0.00              
ATOM    572  O   ARG   167      12.704  60.231   7.051  1.00  0.00              
ATOM    573  N   ARG   168      13.403  58.849   5.424  1.00  0.00              
ATOM    574  CA  ARG   168      12.855  59.671   4.359  1.00  0.00              
ATOM    575  C   ARG   168      11.366  59.923   4.558  1.00  0.00              
ATOM    576  O   ARG   168      10.888  61.042   4.366  1.00  0.00              
ATOM    577  N   ILE   169      10.634  58.883   4.944  1.00  0.00              
ATOM    578  CA  ILE   169       9.191  58.999   5.141  1.00  0.00              
ATOM    579  C   ILE   169       8.740  59.825   6.343  1.00  0.00              
ATOM    580  O   ILE   169       7.890  60.699   6.193  1.00  0.00              
ATOM    581  N   ASP   170       9.289  59.568   7.529  1.00  0.00              
ATOM    582  CA  ASP   170       8.859  60.321   8.706  1.00  0.00              
ATOM    583  C   ASP   170       9.260  61.791   8.632  1.00  0.00              
ATOM    584  O   ASP   170       8.448  62.668   8.929  1.00  0.00              
ATOM    585  N   ARG   171      10.503  62.069   8.248  1.00  0.00              
ATOM    586  CA  ARG   171      10.937  63.451   8.082  1.00  0.00              
ATOM    587  C   ARG   171      10.534  63.670   6.634  1.00  0.00              
ATOM    588  O   ARG   171      10.133  62.720   5.972  1.00  0.00              
ATOM    589  N   ASP   172      10.606  64.884   6.117  1.00  0.00              
ATOM    590  CA  ASP   172      10.209  65.050   4.724  1.00  0.00              
ATOM    591  C   ASP   172      11.420  65.170   3.828  1.00  0.00              
ATOM    592  O   ASP   172      11.454  66.007   2.928  1.00  0.00              
ATOM    593  N   LEU   173      12.405  64.311   4.064  1.00  0.00              
ATOM    594  CA  LEU   173      13.652  64.369   3.323  1.00  0.00              
ATOM    595  C   LEU   173      13.560  64.473   1.804  1.00  0.00              
ATOM    596  O   LEU   173      12.779  63.778   1.147  1.00  0.00              
ATOM    597  N   LEU   174      14.372  65.376   1.268  1.00  0.00              
ATOM    598  CA  LEU   174      14.463  65.603  -0.165  1.00  0.00              
ATOM    599  C   LEU   174      15.482  64.587  -0.659  1.00  0.00              
ATOM    600  O   LEU   174      16.114  63.912   0.150  1.00  0.00              
ATOM    601  N   SER   175      15.651  64.463  -1.971  1.00  0.00              
ATOM    602  CA  SER   175      16.636  63.514  -2.465  1.00  0.00              
ATOM    603  C   SER   175      18.021  63.857  -1.917  1.00  0.00              
ATOM    604  O   SER   175      18.735  62.983  -1.408  1.00  0.00              
ATOM    605  N   ASP   176      18.401  65.127  -2.020  1.00  0.00              
ATOM    606  CA  ASP   176      19.703  65.578  -1.516  1.00  0.00              
ATOM    607  C   ASP   176      19.856  65.144  -0.050  1.00  0.00              
ATOM    608  O   ASP   176      20.923  64.686   0.364  1.00  0.00              
ATOM    609  N   SER   177      18.786  65.287   0.729  1.00  0.00              
ATOM    610  CA  SER   177      18.826  64.896   2.130  1.00  0.00              
ATOM    611  C   SER   177      19.038  63.389   2.289  1.00  0.00              
ATOM    612  O   SER   177      19.759  62.957   3.186  1.00  0.00              
ATOM    613  N   PHE   178      18.428  62.591   1.417  1.00  0.00              
ATOM    614  CA  PHE   178      18.591  61.145   1.505  1.00  0.00              
ATOM    615  C   PHE   178      20.021  60.755   1.129  1.00  0.00              
ATOM    616  O   PHE   178      20.538  59.745   1.592  1.00  0.00              
ATOM    617  N   ASP   179      20.661  61.567   0.298  1.00  0.00              
ATOM    618  CA  ASP   179      22.031  61.304  -0.095  1.00  0.00              
ATOM    619  C   ASP   179      22.894  61.448   1.150  1.00  0.00              
ATOM    620  O   ASP   179      23.887  60.733   1.330  1.00  0.00              
ATOM    621  N   ASP   180      22.492  62.378   2.009  1.00  0.00              
ATOM    622  CA  ASP   180      23.191  62.647   3.252  1.00  0.00              
ATOM    623  C   ASP   180      22.844  61.590   4.294  1.00  0.00              
ATOM    624  O   ASP   180      23.243  61.701   5.448  1.00  0.00              
ATOM    625  N   ALA   181      22.093  60.570   3.894  1.00  0.00              
ATOM    626  CA  ALA   181      21.728  59.511   4.826  1.00  0.00              
ATOM    627  C   ALA   181      22.728  58.379   4.749  1.00  0.00              
ATOM    628  O   ALA   181      22.451  57.280   5.221  1.00  0.00              
ATOM    629  N   LEU   182      23.886  58.628   4.152  1.00  0.00              
ATOM    630  CA  LEU   182      24.891  57.581   4.053  1.00  0.00              
ATOM    631  C   LEU   182      26.060  57.900   4.976  1.00  0.00              
ATOM    632  O   LEU   182      26.475  57.064   5.770  1.00  0.00              
ATOM    633  N   ALA   183      26.577  59.120   4.872  1.00  0.00              
ATOM    634  CA  ALA   183      27.687  59.570   5.708  1.00  0.00              
ATOM    635  C   ALA   183      27.232  59.715   7.161  1.00  0.00              
ATOM    636  O   ALA   183      28.047  59.876   8.069  1.00  0.00              
ATOM    637  N   GLU   184      25.924  59.663   7.377  1.00  0.00              
ATOM    638  CA  GLU   184      25.381  59.785   8.721  1.00  0.00              
ATOM    639  C   GLU   184      25.379  58.428   9.418  1.00  0.00              
ATOM    640  O   GLU   184      25.315  58.354  10.646  1.00  0.00              
ATOM    641  N   ALA   185      25.455  57.357   8.636  1.00  0.00              
ATOM    642  CA  ALA   185      25.455  56.016   9.198  1.00  0.00              
ATOM    643  C   ALA   185      26.833  55.528   9.624  1.00  0.00              
ATOM    644  O   ALA   185      27.091  54.324   9.649  1.00  0.00              
ATOM    645  N   MET   186      27.716  56.462   9.963  1.00  0.00              
ATOM    646  CA  MET   186      29.058  56.107  10.413  1.00  0.00              
ATOM    647  C   MET   186      29.434  56.938  11.633  1.00  0.00              
ATOM    648  O   MET   186      30.600  57.384  11.694  1.00  0.00              
END
