
#######################################################
#                                                     #
#                        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   51 (  204),  selected   51 , name T0347AL333_1-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347AL333_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      D     134           -
LGA    P     135      P     135           -
LGA    F     136      F     136           -
LGA    R     137      R     137           -
LGA    S     138      S     138           -
LGA    L     139      L     139           -
LGA    A     140      A     140           -
LGA    G     141      G     141           -
LGA    A     142      A     142           -
LGA    L     143      L     143           -
LGA    R     144      R     144           -
LGA    M     145      M     145           -
LGA    A     146      A     146           -
LGA    G     147      G     147           -
LGA    G     148      G     148           -
LGA    Y     149      Y     149           -
LGA    A     150      A     150           -
LGA    K     151      K     151           -
LGA    V     152      V     152           -
LGA    I     153      I     153           -
LGA    I     154      I     154           -
LGA    P     155      P     155           -
LGA    F     156      -       -           -
LGA    E     158      F     156          2.168
LGA    F     159      S     157          2.302
LGA    G     160      E     158          1.633
LGA    D     163      F     159          1.091
LGA    F     164      G     160          1.551
LGA    L     165      W     161          1.610
LGA    R     166      A     162          1.390
LGA    R     167      D     163          1.162
LGA    R     168      F     164          1.058
LGA    I     169      L     165          1.093
LGA    D     170      R     166          1.410
LGA    R     171      R     167          0.522
LGA    D     172      R     168          0.715
LGA    L     173      I     169          2.403
LGA    L     174      D     170          3.970
LGA    S     175      R     171          3.283
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     176      D     180          7.283
LGA    S     177      A     181          2.343
LGA    F     178      L     182          3.373
LGA    D     179      A     183          2.907
LGA    -       -      E     184           -
LGA    -       -      A     185           -
LGA    -       -      M     186           -
LGA    D     180      K     187          4.191
LGA    A     181      L     188          3.427
LGA    L     182      A     189          2.753
LGA    A     183      K     190          5.542
LGA    -       -      S     191           -
LGA    -       -      R     192           -
LGA    -       -      E     193           -
LGA    E     184      A     194          1.492
LGA    -       -      R     195           -
LGA    -       -      H     196           -
LGA    A     185      L     197          2.350
LGA    M     186      P     198          2.571
LGA    K     187      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)   51   71    5.0     27    2.85     7.41     26.276     0.914

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.659988 * X  +   0.750315 * Y  +  -0.037999 * Z  +  30.761150
  Y_new =   0.570676 * X  +   0.467794 * Y  +  -0.674906 * Z  +  35.115368
  Z_new =  -0.488616 * X  +  -0.467115 * Y  +  -0.736925 * Z  +  77.469749 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.576640    0.564952  [ DEG:  -147.6306     32.3694 ]
  Theta =   0.510503    2.631090  [ DEG:    29.2496    150.7504 ]
  Phi   =   2.428640   -0.712953  [ DEG:   139.1508    -40.8492 ]
 
# 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: T0347AL333_1-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL333_1-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   51   71   5.0   27   2.85    7.41  26.276
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL333_1-D2
REMARK Aligment from pdb entry: 1cxq_A
ATOM    290  N   ASP   134      28.691  42.649 -14.944  1.00  0.00              
ATOM    291  CA  ASP   134      29.996  42.908 -15.527  1.00  0.00              
ATOM    292  C   ASP   134      30.978  43.518 -14.526  1.00  0.00              
ATOM    293  O   ASP   134      32.190  43.285 -14.625  1.00  0.00              
ATOM    294  N   PRO   135      30.483  44.273 -13.545  1.00  0.00              
ATOM    295  CA  PRO   135      31.382  44.855 -12.538  1.00  0.00              
ATOM    296  C   PRO   135      31.984  43.816 -11.630  1.00  0.00              
ATOM    297  O   PRO   135      32.985  44.085 -10.931  1.00  0.00              
ATOM    298  N   PHE   136      31.361  42.609 -11.601  1.00  0.00              
ATOM    299  CA  PHE   136      31.859  41.538 -10.751  1.00  0.00              
ATOM    300  C   PHE   136      32.628  40.487 -11.527  1.00  0.00              
ATOM    301  O   PHE   136      33.494  39.826 -10.938  1.00  0.00              
ATOM    302  N   ARG   137      32.385  40.359 -12.833  1.00  0.00              
ATOM    303  CA  ARG   137      33.040  39.308 -13.564  1.00  0.00              
ATOM    304  C   ARG   137      34.168  39.809 -14.474  1.00  0.00              
ATOM    305  O   ARG   137      34.776  39.058 -15.224  1.00  0.00              
ATOM    306  N   SER   138      34.456  41.089 -14.415  1.00  0.00              
ATOM    307  CA  SER   138      35.510  41.653 -15.172  1.00  0.00              
ATOM    308  C   SER   138      36.885  41.109 -14.791  1.00  0.00              
ATOM    309  O   SER   138      37.108  40.637 -13.677  1.00  0.00              
ATOM    310  N   LEU   139      38.100  43.043 -11.684  1.00  0.00              
ATOM    311  CA  LEU   139      37.578  42.576 -10.387  1.00  0.00              
ATOM    312  C   LEU   139      38.126  41.237 -10.011  1.00  0.00              
ATOM    313  O   LEU   139      38.458  40.994  -8.827  1.00  0.00              
ATOM    314  N   ALA   140      38.227  40.314 -10.986  1.00  0.00              
ATOM    315  CA  ALA   140      38.803  39.028 -10.675  1.00  0.00              
ATOM    316  C   ALA   140      40.225  39.142 -10.143  1.00  0.00              
ATOM    317  O   ALA   140      40.628  38.477  -9.162  1.00  0.00              
ATOM    318  N   GLY   141      40.997  40.022 -10.741  1.00  0.00              
ATOM    319  CA  GLY   141      42.373  40.245 -10.287  1.00  0.00              
ATOM    320  C   GLY   141      42.426  40.886  -8.896  1.00  0.00              
ATOM    321  O   GLY   141      43.273  40.529  -8.069  1.00  0.00              
ATOM    322  N   ALA   142      41.532  41.825  -8.622  1.00  0.00              
ATOM    323  CA  ALA   142      41.498  42.487  -7.310  1.00  0.00              
ATOM    324  C   ALA   142      41.178  41.485  -6.213  1.00  0.00              
ATOM    325  O   ALA   142      41.806  41.456  -5.160  1.00  0.00              
ATOM    326  N   LEU   143      40.201  40.613  -6.457  1.00  0.00              
ATOM    327  CA  LEU   143      39.860  39.597  -5.464  1.00  0.00              
ATOM    328  C   LEU   143      41.000  38.604  -5.295  1.00  0.00              
ATOM    329  O   LEU   143      41.281  38.162  -4.169  1.00  0.00              
ATOM    330  N   ARG   144      41.691  38.233  -6.378  1.00  0.00              
ATOM    331  CA  ARG   144      42.838  37.334  -6.270  1.00  0.00              
ATOM    332  C   ARG   144      43.964  37.984  -5.466  1.00  0.00              
ATOM    333  O   ARG   144      44.620  37.308  -4.665  1.00  0.00              
ATOM    334  N   MET   145      44.190  39.267  -5.657  1.00  0.00              
ATOM    335  CA  MET   145      45.195  40.023  -4.880  1.00  0.00              
ATOM    336  C   MET   145      44.956  39.916  -3.390  1.00  0.00              
ATOM    337  O   MET   145      45.886  39.825  -2.597  1.00  0.00              
ATOM    338  N   ALA   146      43.680  39.954  -3.000  1.00  0.00              
ATOM    339  CA  ALA   146      43.261  39.836  -1.618  1.00  0.00              
ATOM    340  C   ALA   146      43.156  38.401  -1.135  1.00  0.00              
ATOM    341  O   ALA   146      42.963  38.210   0.083  1.00  0.00              
ATOM    342  N   GLY   147      43.228  37.411  -2.009  1.00  0.00              
ATOM    343  CA  GLY   147      43.045  36.019  -1.626  1.00  0.00              
ATOM    344  C   GLY   147      41.637  35.678  -1.220  1.00  0.00              
ATOM    345  O   GLY   147      41.423  34.816  -0.339  1.00  0.00              
ATOM    346  N   GLY   148      40.650  36.309  -1.826  1.00  0.00              
ATOM    347  CA  GLY   148      39.243  36.083  -1.551  1.00  0.00              
ATOM    348  C   GLY   148      38.617  35.257  -2.681  1.00  0.00              
ATOM    349  O   GLY   148      38.700  35.665  -3.825  1.00  0.00              
ATOM    350  N   TYR   149      38.009  34.133  -2.352  1.00  0.00              
ATOM    351  CA  TYR   149      37.316  33.336  -3.345  1.00  0.00              
ATOM    352  C   TYR   149      36.060  34.039  -3.797  1.00  0.00              
ATOM    353  O   TYR   149      35.383  34.693  -2.990  1.00  0.00              
ATOM    354  N   ALA   150      35.700  33.873  -5.064  1.00  0.00              
ATOM    355  CA  ALA   150      34.540  34.539  -5.646  1.00  0.00              
ATOM    356  C   ALA   150      33.693  33.490  -6.331  1.00  0.00              
ATOM    357  O   ALA   150      34.210  32.674  -7.103  1.00  0.00              
ATOM    358  N   LYS   151      32.380  33.526  -6.066  1.00  0.00              
ATOM    359  CA  LYS   151      31.413  32.675  -6.731  1.00  0.00              
ATOM    360  C   LYS   151      30.263  33.552  -7.222  1.00  0.00              
ATOM    361  O   LYS   151      29.861  34.481  -6.571  1.00  0.00              
ATOM    362  N   VAL   152      29.732  33.144  -8.377  1.00  0.00              
ATOM    363  CA  VAL   152      28.494  33.719  -8.849  1.00  0.00              
ATOM    364  C   VAL   152      27.374  32.683  -8.835  1.00  0.00              
ATOM    365  O   VAL   152      26.293  32.956  -9.325  1.00  0.00              
ATOM    366  N   ILE   153      27.606  31.535  -8.217  1.00  0.00              
ATOM    367  CA  ILE   153      26.621  30.512  -7.972  1.00  0.00              
ATOM    368  C   ILE   153      26.463  29.536  -9.073  1.00  0.00              
ATOM    369  O   ILE   153      27.346  29.327  -9.869  1.00  0.00              
ATOM    370  N   ILE   154      25.280  28.948  -9.114  1.00  0.00              
ATOM    371  CA  ILE   154      25.003  27.849 -10.020  1.00  0.00              
ATOM    372  C   ILE   154      24.479  28.498 -11.288  1.00  0.00              
ATOM    373  O   ILE   154      23.522  29.284 -11.180  1.00  0.00              
ATOM    374  N   PRO   155      25.080  28.271 -12.442  1.00  0.00              
ATOM    375  CA  PRO   155      24.578  28.831 -13.703  1.00  0.00              
ATOM    376  C   PRO   155      23.212  28.283 -14.137  1.00  0.00              
ATOM    377  O   PRO   155      22.633  27.471 -13.399  1.00  0.00              
ATOM    378  N   PHE   156      20.248  32.228  -5.025  1.00  0.00              
ATOM    379  CA  PHE   156      21.364  32.064  -4.131  1.00  0.00              
ATOM    380  C   PHE   156      21.964  33.215  -3.370  1.00  0.00              
ATOM    381  O   PHE   156      23.050  33.067  -2.791  1.00  0.00              
ATOM    382  N   GLU   158      15.611  46.202   3.033  1.00  0.00              
ATOM    383  CA  GLU   158      15.608  46.825   4.376  1.00  0.00              
ATOM    384  C   GLU   158      16.318  48.149   4.332  1.00  0.00              
ATOM    385  O   GLU   158      15.891  49.115   5.011  1.00  0.00              
ATOM    386  N   PHE   159      17.411  48.241   3.602  1.00  0.00              
ATOM    387  CA  PHE   159      18.155  49.490   3.526  1.00  0.00              
ATOM    388  C   PHE   159      17.369  50.565   2.803  1.00  0.00              
ATOM    389  O   PHE   159      17.288  51.697   3.281  1.00  0.00              
ATOM    390  N   GLY   160      16.785  50.255   1.641  1.00  0.00              
ATOM    391  CA  GLY   160      16.021  51.309   0.939  1.00  0.00              
ATOM    392  C   GLY   160      14.829  51.726   1.791  1.00  0.00              
ATOM    393  O   GLY   160      14.479  52.913   1.829  1.00  0.00              
ATOM    394  N   ASP   163      14.175  50.775   2.462  1.00  0.00              
ATOM    395  CA  ASP   163      13.046  51.191   3.321  1.00  0.00              
ATOM    396  C   ASP   163      13.502  52.111   4.439  1.00  0.00              
ATOM    397  O   ASP   163      12.846  53.098   4.744  1.00  0.00              
ATOM    398  N   PHE   164      14.623  51.770   5.093  1.00  0.00              
ATOM    399  CA  PHE   164      15.146  52.577   6.175  1.00  0.00              
ATOM    400  C   PHE   164      15.580  53.965   5.711  1.00  0.00              
ATOM    401  O   PHE   164      15.323  54.974   6.367  1.00  0.00              
ATOM    402  N   LEU   165      16.243  54.038   4.555  1.00  0.00              
ATOM    403  CA  LEU   165      16.616  55.317   3.973  1.00  0.00              
ATOM    404  C   LEU   165      15.387  56.172   3.796  1.00  0.00              
ATOM    405  O   LEU   165      15.380  57.362   4.132  1.00  0.00              
ATOM    406  N   ARG   166      14.308  55.608   3.231  1.00  0.00              
ATOM    407  CA  ARG   166      13.093  56.359   3.028  1.00  0.00              
ATOM    408  C   ARG   166      12.526  56.894   4.366  1.00  0.00              
ATOM    409  O   ARG   166      12.143  58.052   4.474  1.00  0.00              
ATOM    410  N   ARG   167      12.433  56.018   5.341  1.00  0.00              
ATOM    411  CA  ARG   167      11.879  56.405   6.643  1.00  0.00              
ATOM    412  C   ARG   167      12.704  57.538   7.256  1.00  0.00              
ATOM    413  O   ARG   167      12.164  58.530   7.772  1.00  0.00              
ATOM    414  N   ARG   168      14.034  57.397   7.245  1.00  0.00              
ATOM    415  CA  ARG   168      14.903  58.414   7.852  1.00  0.00              
ATOM    416  C   ARG   168      14.779  59.742   7.095  1.00  0.00              
ATOM    417  O   ARG   168      14.711  60.806   7.673  1.00  0.00              
ATOM    418  N   ILE   169      14.789  59.640   5.756  1.00  0.00              
ATOM    419  CA  ILE   169      14.695  60.836   4.934  1.00  0.00              
ATOM    420  C   ILE   169      13.410  61.579   5.192  1.00  0.00              
ATOM    421  O   ILE   169      13.383  62.793   5.410  1.00  0.00              
ATOM    422  N   ASP   170      12.286  60.850   5.140  1.00  0.00              
ATOM    423  CA  ASP   170      10.989  61.465   5.377  1.00  0.00              
ATOM    424  C   ASP   170      10.918  62.048   6.787  1.00  0.00              
ATOM    425  O   ASP   170      10.342  63.124   7.014  1.00  0.00              
ATOM    426  N   ARG   171      11.534  61.377   7.764  1.00  0.00              
ATOM    427  CA  ARG   171      11.606  61.923   9.111  1.00  0.00              
ATOM    428  C   ARG   171      12.242  63.264   9.183  1.00  0.00              
ATOM    429  O   ARG   171      11.866  64.120   9.979  1.00  0.00              
ATOM    430  N   ASP   172      13.283  63.481   8.342  1.00  0.00              
ATOM    431  CA  ASP   172      13.998  64.741   8.235  1.00  0.00              
ATOM    432  C   ASP   172      13.296  65.731   7.295  1.00  0.00              
ATOM    433  O   ASP   172      13.812  66.823   7.068  1.00  0.00              
ATOM    434  N   LEU   173      12.128  65.381   6.755  1.00  0.00              
ATOM    435  CA  LEU   173      11.372  66.256   5.883  1.00  0.00              
ATOM    436  C   LEU   173      11.765  66.171   4.402  1.00  0.00              
ATOM    437  O   LEU   173      11.303  66.983   3.619  1.00  0.00              
ATOM    438  N   LEU   174      12.554  65.180   4.040  1.00  0.00              
ATOM    439  CA  LEU   174      12.979  64.996   2.644  1.00  0.00              
ATOM    440  C   LEU   174      12.092  63.964   2.020  1.00  0.00              
ATOM    441  O   LEU   174      12.271  62.763   2.252  1.00  0.00              
ATOM    442  N   SER   175      11.122  64.410   1.224  1.00  0.00              
ATOM    443  CA  SER   175      10.140  63.528   0.641  1.00  0.00              
ATOM    444  C   SER   175      10.564  63.008  -0.736  1.00  0.00              
ATOM    445  O   SER   175       9.929  62.088  -1.254  1.00  0.00              
ATOM    446  N   ASP   176      11.623  63.583  -1.283  1.00  0.00              
ATOM    447  CA  ASP   176      12.110  63.160  -2.602  1.00  0.00              
ATOM    448  C   ASP   176      13.617  62.929  -2.469  1.00  0.00              
ATOM    449  O   ASP   176      14.039  62.109  -1.640  1.00  0.00              
ATOM    450  N   SER   177      14.463  63.620  -3.200  1.00  0.00              
ATOM    451  CA  SER   177      15.907  63.372  -3.093  1.00  0.00              
ATOM    452  C   SER   177      16.427  63.988  -1.812  1.00  0.00              
ATOM    453  O   SER   177      16.038  65.097  -1.405  1.00  0.00              
ATOM    454  N   PHE   178      17.358  63.287  -1.152  1.00  0.00              
ATOM    455  CA  PHE   178      18.004  63.840   0.037  1.00  0.00              
ATOM    456  C   PHE   178      19.028  64.858  -0.395  1.00  0.00              
ATOM    457  O   PHE   178      19.850  64.556  -1.289  1.00  0.00              
ATOM    458  N   ASP   179      19.068  66.064   0.178  1.00  0.00              
ATOM    459  CA  ASP   179      20.120  67.020  -0.180  1.00  0.00              
ATOM    460  C   ASP   179      21.491  66.385  -0.063  1.00  0.00              
ATOM    461  O   ASP   179      21.758  65.647   0.884  1.00  0.00              
ATOM    462  N   ASP   180      22.349  66.688  -1.021  1.00  0.00              
ATOM    463  CA  ASP   180      23.638  66.020  -1.107  1.00  0.00              
ATOM    464  C   ASP   180      24.424  66.120   0.180  1.00  0.00              
ATOM    465  O   ASP   180      25.048  65.122   0.605  1.00  0.00              
ATOM    466  N   ALA   181      23.028  60.335   6.627  1.00  0.00              
ATOM    467  CA  ALA   181      21.788  59.578   6.589  1.00  0.00              
ATOM    468  C   ALA   181      22.083  58.124   6.222  1.00  0.00              
ATOM    469  O   ALA   181      21.512  57.201   6.825  1.00  0.00              
ATOM    470  N   LEU   182      22.951  57.898   5.253  1.00  0.00              
ATOM    471  CA  LEU   182      23.318  56.538   4.866  1.00  0.00              
ATOM    472  C   LEU   182      23.974  55.796   6.050  1.00  0.00              
ATOM    473  O   LEU   182      23.671  54.640   6.324  1.00  0.00              
ATOM    474  N   ALA   183      24.887  56.497   6.741  1.00  0.00              
ATOM    475  CA  ALA   183      25.508  55.900   7.916  1.00  0.00              
ATOM    476  C   ALA   183      24.482  55.590   8.990  1.00  0.00              
ATOM    477  O   ALA   183      24.597  54.565   9.689  1.00  0.00              
ATOM    478  N   GLU   184      23.492  56.437   9.155  1.00  0.00              
ATOM    479  CA  GLU   184      22.414  56.194  10.133  1.00  0.00              
ATOM    480  C   GLU   184      21.615  54.965   9.772  1.00  0.00              
ATOM    481  O   GLU   184      21.242  54.180  10.646  1.00  0.00              
ATOM    482  N   ALA   185      21.341  54.781   8.479  1.00  0.00              
ATOM    483  CA  ALA   185      20.618  53.584   8.028  1.00  0.00              
ATOM    484  C   ALA   185      21.437  52.331   8.306  1.00  0.00              
ATOM    485  O   ALA   185      20.876  51.306   8.747  1.00  0.00              
ATOM    486  N   MET   186      22.731  52.371   8.029  1.00  0.00              
ATOM    487  CA  MET   186      23.592  51.254   8.285  1.00  0.00              
ATOM    488  C   MET   186      23.632  50.923   9.787  1.00  0.00              
ATOM    489  O   MET   186      23.529  49.771  10.200  1.00  0.00              
ATOM    490  N   LYS   187      23.117  47.526  14.495  1.00  0.00              
ATOM    491  CA  LYS   187      23.351  47.675  15.941  1.00  0.00              
ATOM    492  C   LYS   187      22.003  47.662  16.636  1.00  0.00              
ATOM    493  O   LYS   187      21.174  48.556  16.415  1.00  0.00              
END
