
#######################################################
#                                                     #
#                        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 T0347AL509_1-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347AL509_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           -
LGA    -       -      R     137           -
LGA    -       -      S     138           -
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    -       -      G     141           -
LGA    -       -      A     142           -
LGA    -       -      L     143           -
LGA    -       -      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    F     136      E     158          1.528
LGA    R     137      F     159          1.695
LGA    S     138      G     160          1.669
LGA    L     139      W     161          0.612
LGA    A     140      A     162          0.282
LGA    G     141      D     163          0.875
LGA    A     142      F     164          1.283
LGA    L     143      L     165          1.109
LGA    R     144      R     166          1.095
LGA    M     145      R     167          1.233
LGA    A     146      R     168          1.851
LGA    G     147      I     169          2.680
LGA    Y     149      D     170           -
LGA    A     150      R     171           -
LGA    K     151      D     172           -
LGA    -       -      L     173           -
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    V     152      F     178          3.833
LGA    I     153      D     179          2.134
LGA    D     170      -       -           -
LGA    R     171      -       -           -
LGA    L     173      -       -           -
LGA    L     174      D     180          2.803
LGA    S     175      A     181          1.574
LGA    D     176      L     182          2.490
LGA    S     177      A     183          2.391
LGA    F     178      E     184          1.359
LGA    D     179      A     185          0.868
LGA    D     180      M     186          0.918
LGA    A     181      K     187          2.355
LGA    L     182      L     188          2.410
LGA    A     183      A     189          0.845
LGA    E     184      K     190          1.346
LGA    A     185      S     191          2.770
LGA    -       -      R     192           -
LGA    M     186      E     193          4.973
LGA    K     187      A     194          4.935
LGA    L     188      -       -           -
LGA    A     189      R     195          1.799
LGA    K     190      H     196          4.084
LGA    S     191      L     197          2.076
LGA    R     192      P     198           -
LGA    E     193      G     199           -
LGA    A     194      W     200           -
LGA    R     195      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     31    2.31    16.13     36.130     1.287

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.993566 * X  +   0.019303 * Y  +  -0.111595 * Z  +  36.319248
  Y_new =  -0.094170 * X  +   0.406583 * Y  +   0.908748 * Z  +  37.160046
  Z_new =   0.062914 * X  +   0.913410 * Y  +  -0.402149 * Z  + -26.696014 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.985532   -1.156061  [ DEG:   113.7626    -66.2374 ]
  Theta =  -0.062956   -3.078637  [ DEG:    -3.6071   -176.3929 ]
  Phi   =  -3.047096    0.094497  [ DEG:  -174.5857      5.4143 ]
 
# 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: T0347AL509_1-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL509_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   31   2.31   16.13  36.130
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL509_1-D2
REMARK Aligment from pdb entry: 1vk1_A
ATOM    229  N   PHE   136      16.417  48.893   4.266  1.00  0.00              
ATOM    230  CA  PHE   136      15.824  49.939   3.442  1.00  0.00              
ATOM    231  C   PHE   136      14.618  50.584   4.121  1.00  0.00              
ATOM    232  O   PHE   136      14.334  51.744   3.904  1.00  0.00              
ATOM    233  N   ARG   137      13.881  49.830   4.938  1.00  0.00              
ATOM    234  CA  ARG   137      12.740  50.418   5.617  1.00  0.00              
ATOM    235  C   ARG   137      13.164  51.500   6.613  1.00  0.00              
ATOM    236  O   ARG   137      12.500  52.510   6.757  1.00  0.00              
ATOM    237  N   SER   138      14.285  51.286   7.284  1.00  0.00              
ATOM    238  CA  SER   138      14.820  52.294   8.177  1.00  0.00              
ATOM    239  C   SER   138      15.308  53.520   7.387  1.00  0.00              
ATOM    240  O   SER   138      15.055  54.648   7.773  1.00  0.00              
ATOM    241  N   LEU   139      15.994  53.272   6.276  1.00  0.00              
ATOM    242  CA  LEU   139      16.452  54.367   5.426  1.00  0.00              
ATOM    243  C   LEU   139      15.239  55.194   4.935  1.00  0.00              
ATOM    244  O   LEU   139      15.228  56.403   5.024  1.00  0.00              
ATOM    245  N   ALA   140      14.208  54.509   4.443  1.00  0.00              
ATOM    246  CA  ALA   140      13.017  55.211   3.937  1.00  0.00              
ATOM    247  C   ALA   140      12.357  56.029   5.030  1.00  0.00              
ATOM    248  O   ALA   140      11.964  57.153   4.800  1.00  0.00              
ATOM    249  N   GLY   141      12.225  55.470   6.243  1.00  0.00              
ATOM    250  CA  GLY   141      11.641  56.243   7.346  1.00  0.00              
ATOM    251  C   GLY   141      12.431  57.534   7.604  1.00  0.00              
ATOM    252  O   GLY   141      11.862  58.595   7.786  1.00  0.00              
ATOM    253  N   ALA   142      13.761  57.430   7.600  1.00  0.00              
ATOM    254  CA  ALA   142      14.598  58.590   7.834  1.00  0.00              
ATOM    255  C   ALA   142      14.495  59.611   6.701  1.00  0.00              
ATOM    256  O   ALA   142      14.508  60.804   6.939  1.00  0.00              
ATOM    257  N   LEU   143      14.389  59.128   5.468  1.00  0.00              
ATOM    258  CA  LEU   143      14.185  60.025   4.319  1.00  0.00              
ATOM    259  C   LEU   143      12.865  60.773   4.453  1.00  0.00              
ATOM    260  O   LEU   143      12.807  61.986   4.278  1.00  0.00              
ATOM    261  N   ARG   144      11.807  60.053   4.813  1.00  0.00              
ATOM    262  CA  ARG   144      10.491  60.695   4.948  1.00  0.00              
ATOM    263  C   ARG   144      10.498  61.715   6.083  1.00  0.00              
ATOM    264  O   ARG   144       9.876  62.764   5.971  1.00  0.00              
ATOM    265  N   MET   145      11.248  61.433   7.151  1.00  0.00              
ATOM    266  CA  MET   145      11.363  62.365   8.277  1.00  0.00              
ATOM    267  C   MET   145      12.020  63.687   7.877  1.00  0.00              
ATOM    268  O   MET   145      11.839  64.696   8.550  1.00  0.00              
ATOM    269  N   ALA   146      12.788  63.676   6.787  1.00  0.00              
ATOM    270  CA  ALA   146      13.416  64.890   6.276  1.00  0.00              
ATOM    271  C   ALA   146      12.556  65.626   5.248  1.00  0.00              
ATOM    272  O   ALA   146      13.011  66.601   4.644  1.00  0.00              
ATOM    273  N   GLY   147      11.327  65.162   5.050  1.00  0.00              
ATOM    274  CA  GLY   147      10.381  65.810   4.147  1.00  0.00              
ATOM    275  C   GLY   147      10.417  65.301   2.720  1.00  0.00              
ATOM    276  O   GLY   147       9.817  65.904   1.837  1.00  0.00              
ATOM    277  N   TYR   149      17.212  60.499 -16.515  1.00  0.00              
ATOM    278  CA  TYR   149      16.780  61.621 -17.348  1.00  0.00              
ATOM    279  C   TYR   149      16.800  62.936 -16.579  1.00  0.00              
ATOM    280  O   TYR   149      16.500  63.979 -17.131  1.00  0.00              
ATOM    281  N   ALA   150      17.161  62.896 -15.297  1.00  0.00              
ATOM    282  CA  ALA   150      17.201  64.095 -14.476  1.00  0.00              
ATOM    283  C   ALA   150      15.845  64.599 -14.034  1.00  0.00              
ATOM    284  O   ALA   150      15.701  65.756 -13.676  1.00  0.00              
ATOM    285  N   LYS   151      14.851  63.715 -13.998  1.00  0.00              
ATOM    286  CA  LYS   151      13.472  64.103 -13.669  1.00  0.00              
ATOM    287  C   LYS   151      13.138  64.006 -12.202  1.00  0.00              
ATOM    288  O   LYS   151      12.180  64.591 -11.761  1.00  0.00              
ATOM    289  N   VAL   152      13.914  63.209 -11.468  1.00  0.00              
ATOM    290  CA  VAL   152      13.752  63.048 -10.029  1.00  0.00              
ATOM    291  C   VAL   152      15.118  63.139  -9.406  1.00  0.00              
ATOM    292  O   VAL   152      16.122  63.096 -10.102  1.00  0.00              
ATOM    293  N   ILE   153      15.158  63.256  -8.090  1.00  0.00              
ATOM    294  CA  ILE   153      16.406  63.431  -7.367  1.00  0.00              
ATOM    295  C   ILE   153      17.260  62.158  -7.396  1.00  0.00              
ATOM    296  O   ILE   153      18.455  62.195  -7.742  1.00  0.00              
ATOM    297  N   ASP   170      15.446  45.276  -4.285  1.00  0.00              
ATOM    298  CA  ASP   170      14.329  44.337  -4.476  1.00  0.00              
ATOM    299  C   ASP   170      13.124  45.066  -5.049  1.00  0.00              
ATOM    300  O   ASP   170      12.449  44.540  -5.954  1.00  0.00              
ATOM    301  N   ARG   171      12.865  46.275  -4.528  1.00  0.00              
ATOM    302  CA  ARG   171      11.841  47.167  -5.040  1.00  0.00              
ATOM    303  C   ARG   171      12.505  48.384  -5.726  1.00  0.00              
ATOM    304  O   ARG   171      13.725  48.608  -5.607  1.00  0.00              
ATOM    305  N   LEU   173      18.124  69.157  -7.047  1.00  0.00              
ATOM    306  CA  LEU   173      19.354  69.351  -6.292  1.00  0.00              
ATOM    307  C   LEU   173      19.175  69.337  -4.784  1.00  0.00              
ATOM    308  O   LEU   173      19.919  68.679  -4.064  1.00  0.00              
ATOM    309  N   LEU   174      18.207  70.071  -4.302  1.00  0.00              
ATOM    310  CA  LEU   174      18.017  70.193  -2.859  1.00  0.00              
ATOM    311  C   LEU   174      17.600  68.862  -2.243  1.00  0.00              
ATOM    312  O   LEU   174      18.057  68.505  -1.154  1.00  0.00              
ATOM    313  N   SER   175      16.763  68.117  -2.945  1.00  0.00              
ATOM    314  CA  SER   175      16.356  66.803  -2.478  1.00  0.00              
ATOM    315  C   SER   175      17.530  65.824  -2.497  1.00  0.00              
ATOM    316  O   SER   175      17.658  64.990  -1.599  1.00  0.00              
ATOM    317  N   ASP   176      18.400  65.931  -3.496  1.00  0.00              
ATOM    318  CA  ASP   176      19.610  65.093  -3.504  1.00  0.00              
ATOM    319  C   ASP   176      20.452  65.385  -2.248  1.00  0.00              
ATOM    320  O   ASP   176      21.007  64.474  -1.625  1.00  0.00              
ATOM    321  N   SER   177      20.556  66.660  -1.886  1.00  0.00              
ATOM    322  CA  SER   177      21.285  67.009  -0.681  1.00  0.00              
ATOM    323  C   SER   177      20.641  66.436   0.596  1.00  0.00              
ATOM    324  O   SER   177      21.345  66.000   1.499  1.00  0.00              
ATOM    325  N   PHE   178      19.321  66.438   0.655  1.00  0.00              
ATOM    326  CA  PHE   178      18.604  65.865   1.802  1.00  0.00              
ATOM    327  C   PHE   178      18.839  64.356   1.896  1.00  0.00              
ATOM    328  O   PHE   178      19.080  63.828   2.967  1.00  0.00              
ATOM    329  N   ASP   179      18.775  63.665   0.768  1.00  0.00              
ATOM    330  CA  ASP   179      19.067  62.236   0.741  1.00  0.00              
ATOM    331  C   ASP   179      20.479  61.986   1.256  1.00  0.00              
ATOM    332  O   ASP   179      20.695  61.142   2.129  1.00  0.00              
ATOM    333  N   ASP   180      21.447  62.724   0.732  1.00  0.00              
ATOM    334  CA  ASP   180      22.841  62.523   1.103  1.00  0.00              
ATOM    335  C   ASP   180      23.110  62.815   2.570  1.00  0.00              
ATOM    336  O   ASP   180      23.905  62.131   3.191  1.00  0.00              
ATOM    337  N   ALA   181      22.440  63.816   3.129  1.00  0.00              
ATOM    338  CA  ALA   181      22.564  64.144   4.550  1.00  0.00              
ATOM    339  C   ALA   181      22.091  62.963   5.411  1.00  0.00              
ATOM    340  O   ALA   181      22.760  62.571   6.360  1.00  0.00              
ATOM    341  N   LEU   182      20.942  62.396   5.070  1.00  0.00              
ATOM    342  CA  LEU   182      20.426  61.225   5.778  1.00  0.00              
ATOM    343  C   LEU   182      21.420  60.066   5.693  1.00  0.00              
ATOM    344  O   LEU   182      21.738  59.443   6.709  1.00  0.00              
ATOM    345  N   ALA   183      21.920  59.788   4.496  1.00  0.00              
ATOM    346  CA  ALA   183      22.884  58.718   4.352  1.00  0.00              
ATOM    347  C   ALA   183      24.161  58.919   5.166  1.00  0.00              
ATOM    348  O   ALA   183      24.657  57.983   5.778  1.00  0.00              
ATOM    349  N   GLU   184      24.674  60.139   5.193  1.00  0.00              
ATOM    350  CA  GLU   184      25.874  60.447   5.961  1.00  0.00              
ATOM    351  C   GLU   184      25.597  60.231   7.464  1.00  0.00              
ATOM    352  O   GLU   184      26.416  59.663   8.185  1.00  0.00              
ATOM    353  N   ALA   185      24.444  60.678   7.944  1.00  0.00              
ATOM    354  CA  ALA   185      24.091  60.477   9.336  1.00  0.00              
ATOM    355  C   ALA   185      23.975  59.005   9.698  1.00  0.00              
ATOM    356  O   ALA   185      24.486  58.583  10.740  1.00  0.00              
ATOM    357  N   MET   186      23.341  58.219   8.830  1.00  0.00              
ATOM    358  CA  MET   186      23.170  56.798   9.088  1.00  0.00              
ATOM    359  C   MET   186      24.500  56.052   8.995  1.00  0.00              
ATOM    360  O   MET   186      24.729  55.108   9.730  1.00  0.00              
ATOM    361  N   LYS   187      25.381  56.506   8.098  1.00  0.00              
ATOM    362  CA  LYS   187      26.754  56.005   7.964  1.00  0.00              
ATOM    363  C   LYS   187      27.508  56.241   9.278  1.00  0.00              
ATOM    364  O   LYS   187      28.096  55.329   9.852  1.00  0.00              
ATOM    365  N   LEU   188      27.482  57.466   9.756  1.00  0.00              
ATOM    366  CA  LEU   188      28.177  57.812  10.992  1.00  0.00              
ATOM    367  C   LEU   188      27.656  57.041  12.207  1.00  0.00              
ATOM    368  O   LEU   188      28.431  56.684  13.086  1.00  0.00              
ATOM    369  N   ALA   189      26.350  56.794  12.246  1.00  0.00              
ATOM    370  CA  ALA   189      25.706  56.052  13.334  1.00  0.00              
ATOM    371  C   ALA   189      25.873  54.560  13.183  1.00  0.00              
ATOM    372  O   ALA   189      25.448  53.808  14.055  1.00  0.00              
ATOM    373  N   LYS   190      26.467  54.116  12.080  1.00  0.00              
ATOM    374  CA  LYS   190      26.649  52.705  11.798  1.00  0.00              
ATOM    375  C   LYS   190      25.310  51.948  11.681  1.00  0.00              
ATOM    376  O   LYS   190      25.252  50.731  11.851  1.00  0.00              
ATOM    377  N   SER   191      24.248  52.672  11.321  1.00  0.00              
ATOM    378  CA  SER   191      22.964  52.050  11.059  1.00  0.00              
ATOM    379  C   SER   191      22.975  51.336   9.720  1.00  0.00              
ATOM    380  O   SER   191      22.283  50.345   9.541  1.00  0.00              
ATOM    381  N   ARG   192      26.798  49.202 -12.890  1.00  0.00              
ATOM    382  CA  ARG   192      26.820  47.753 -13.160  1.00  0.00              
ATOM    383  C   ARG   192      27.458  46.989 -12.020  1.00  0.00              
ATOM    384  O   ARG   192      27.011  45.898 -11.671  1.00  0.00              
ATOM    385  N   GLU   193      28.515  47.559 -11.444  1.00  0.00              
ATOM    386  CA  GLU   193      29.187  46.960 -10.286  1.00  0.00              
ATOM    387  C   GLU   193      28.278  46.925  -9.059  1.00  0.00              
ATOM    388  O   GLU   193      28.225  45.933  -8.355  1.00  0.00              
ATOM    389  N   ALA   194      27.568  48.023  -8.799  1.00  0.00              
ATOM    390  CA  ALA   194      26.612  48.064  -7.701  1.00  0.00              
ATOM    391  C   ALA   194      25.548  46.979  -7.875  1.00  0.00              
ATOM    392  O   ALA   194      25.225  46.252  -6.940  1.00  0.00              
ATOM    393  N   ARG   195      25.017  46.880  -9.092  1.00  0.00              
ATOM    394  CA  ARG   195      23.983  45.888  -9.391  1.00  0.00              
ATOM    395  C   ARG   195      24.511  44.453  -9.252  1.00  0.00              
ATOM    396  O   ARG   195      23.814  43.592  -8.724  1.00  0.00              
END
