
#######################################################
#                                                     #
#                        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  148 (  148),  selected  148 , name T0333TS168_1-D2
# Molecule2: number of CA atoms  148 ( 1087),  selected  148 , name T0333_D2.pdb
# PARAMETERS: T0333TS168_1-D2.T0333_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      E     212           -
LGA    E     212      V     213          1.510
LGA    V     213      A     214          1.853
LGA    A     214      I     215           #
LGA    I     215      T     216           #
LGA    T     216      -       -           -
LGA    M     217      M     217          4.014
LGA    G     218      G     218          2.517
LGA    T     219      T     219          3.776
LGA    I     220      I     220           #
LGA    E     221      E     221           #
LGA    -       -      L     222           -
LGA    -       -      Q     223           -
LGA    -       -      A     224           -
LGA    -       -      F     225           -
LGA    L     222      G     226          4.603
LGA    Q     223      I     227          2.730
LGA    A     224      G     228          2.682
LGA    F     225      A     229          2.399
LGA    G     226      V     230          1.431
LGA    I     227      E     231          2.010
LGA    G     228      -       -           -
LGA    A     229      P     232          0.472
LGA    V     230      I     233          3.026
LGA    E     231      I     234          2.028
LGA    P     232      A     235          1.678
LGA    I     233      A     236          3.662
LGA    I     234      A     237          2.927
LGA    A     235      G     238          1.170
LGA    A     236      E     239          4.183
LGA    A     237      -       -           -
LGA    G     238      -       -           -
LGA    E     239      V     240          2.703
LGA    V     240      D     241          3.150
LGA    D     241      A     242          2.263
LGA    A     242      D     243          2.743
LGA    D     243      F     244          0.938
LGA    F     244      V     245          3.442
LGA    V     245      L     246          5.061
LGA    L     246      A     247           #
LGA    A     247      L     248          2.446
LGA    L     248      G     249          4.492
LGA    -       -      D     250           -
LGA    G     249      L     251          1.993
LGA    D     250      D     252          3.620
LGA    L     251      I     253          4.314
LGA    D     252      S     254          3.220
LGA    I     253      P     255          4.523
LGA    S     254      L     256          4.660
LGA    P     255      G     257          3.384
LGA    L     256      T     258          3.346
LGA    G     257      L     259          3.140
LGA    T     258      P     260           #
LGA    L     259      R     261          2.628
LGA    P     260      -       -           -
LGA    R     261      N     262           #
LGA    N     262      V     263           #
LGA    V     263      R     264          1.495
LGA    R     264      A     265          1.590
LGA    A     265      V     266          5.134
LGA    V     266      -       -           -
LGA    G     267      -       -           -
LGA    W     268      -       -           -
LGA    T     269      G     267           #
LGA    -       -      W     268           -
LGA    P     270      T     269          1.880
LGA    L     271      P     270          3.310
LGA    -       -      L     271           -
LGA    H     272      H     272          1.063
LGA    T     273      T     273          2.259
LGA    L     274      L     274          2.216
LGA    L     275      L     275          1.309
LGA    R     276      R     276          2.480
LGA    -       -      T     277           -
LGA    T     277      C     278          2.985
LGA    C     278      T     279          4.958
LGA    T     279      A     280          1.722
LGA    A     280      V     281          2.073
LGA    V     281      V     282          1.082
LGA    V     282      H     283          2.060
LGA    H     283      H     284          3.792
LGA    H     284      -       -           -
LGA    G     285      G     285          5.044
LGA    G     286      G     286          4.190
LGA    G     287      -       -           -
LGA    G     288      G     287          2.188
LGA    T     289      -       -           -
LGA    V     290      -       -           -
LGA    M     291      G     288          0.728
LGA    T     292      T     289          3.374
LGA    A     293      V     290          3.878
LGA    I     294      M     291          0.994
LGA    D     295      T     292          2.380
LGA    A     296      A     293          3.728
LGA    G     297      I     294          3.727
LGA    -       -      D     295           -
LGA    -       -      A     296           -
LGA    -       -      G     297           -
LGA    -       -      I     298           -
LGA    I     298      P     299           #
LGA    P     299      Q     300          3.950
LGA    Q     300      L     301           #
LGA    L     301      L     302          3.388
LGA    L     302      A     303          3.871
LGA    A     303      P     304          2.795
LGA    P     304      D     305          1.453
LGA    D     305      P     306          2.353
LGA    P     306      R     307          3.271
LGA    R     307      D     308          2.497
LGA    D     308      Q     309          1.996
LGA    Q     309      F     310          2.921
LGA    F     310      Q     311          2.680
LGA    Q     311      -       -           -
LGA    H     312      -       -           -
LGA    T     313      H     312           #
LGA    A     314      T     313          3.753
LGA    R     315      A     314          1.493
LGA    E     316      R     315          2.564
LGA    A     317      -       -           -
LGA    V     318      E     316          1.141
LGA    S     319      A     317          3.136
LGA    R     320      V     318          3.708
LGA    -       -      S     319           -
LGA    -       -      R     320           -
LGA    -       -      R     321           -
LGA    -       -      G     322           -
LGA    -       -      I     323           -
LGA    R     321      G     324          2.056
LGA    G     322      L     325          2.865
LGA    I     323      V     326          3.613
LGA    G     324      S     327          1.022
LGA    L     325      T     328          3.280
LGA    V     326      S     329          4.712
LGA    S     327      D     330          2.239
LGA    T     328      K     331          2.650
LGA    S     329      -       -           -
LGA    D     330      -       -           -
LGA    K     331      -       -           -
LGA    V     332      V     332          5.002
LGA    D     333      D     333          2.047
LGA    A     334      A     334          1.528
LGA    D     335      D     335          1.683
LGA    L     336      L     336          1.036
LGA    L     337      L     337          1.109
LGA    R     338      R     338          1.654
LGA    R     339      R     339          2.216
LGA    L     340      L     340          2.403
LGA    I     341      I     341          2.627
LGA    G     342      G     342          2.312
LGA    D     343      D     343           #
LGA    E     344      E     344          3.536
LGA    S     345      S     345          3.680
LGA    L     346      L     346          2.641
LGA    R     347      R     347          2.001
LGA    T     348      T     348          2.494
LGA    A     349      A     349          2.312
LGA    A     350      A     350          1.390
LGA    R     351      R     351          1.118
LGA    E     352      E     352          1.285
LGA    V     353      V     353          1.262
LGA    R     354      R     354          0.533
LGA    E     355      E     355          0.586
LGA    E     356      E     356          1.106
LGA    M     357      M     357          0.989
LGA    V     358      V     358          1.180
LGA    A     359      A     359          1.684

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  148  148    5.0    117    2.84    37.61     44.984     3.984

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.607405 * X  +  -0.703638 * Y  +   0.368718 * Z  +  31.268772
  Y_new =  -0.517087 * X  +   0.702562 * Y  +   0.488904 * Z  +  18.758350
  Z_new =  -0.603059 * X  +   0.106303 * Y  +  -0.790582 * Z  +   8.320759 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.007932   -0.133661  [ DEG:   172.3418     -7.6582 ]
  Theta =   0.647330    2.494262  [ DEG:    37.0893    142.9107 ]
  Phi   =  -2.436341    0.705252  [ DEG:  -139.5921     40.4079 ]
 
# 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: T0333TS168_1-D2                               
REMARK     2: T0333_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0333TS168_1-D2.T0333_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  148  148   5.0  117   2.84   37.61  44.984
REMARK  ---------------------------------------------------------- 
MOLECULE T0333TS168_1-D2
PFRMAT TS
TARGET T0333
MODEL 1
PARENT N/A
ATOM    212  CA  GLU   212      30.032  10.129  -9.859  1.00 25.00           C
ATOM    213  CA  VAL   213      30.128   9.922  -6.041  1.00 25.00           C
ATOM    214  CA  ALA   214      30.351   8.820  -2.439  1.00 25.00           C
ATOM    215  CA  ILE   215      29.013   7.221   0.730  1.00 25.00           C
ATOM    216  CA  THR   216      26.855   8.714   3.490  1.00 25.00           C
ATOM    217  CA  MET   217      25.203  12.132   4.074  1.00 25.00           C
ATOM    218  CA  GLY   218      23.517  15.362   5.025  1.00 25.00           C
ATOM    219  CA  THR   219      20.795  13.687   7.079  1.00 25.00           C
ATOM    220  CA  ILE   220      18.451  16.276   5.477  1.00 25.00           C
ATOM    221  CA  GLU   221      19.222  14.513   2.197  1.00 25.00           C
ATOM    222  CA  LEU   222      16.075  12.387   2.680  1.00 25.00           C
ATOM    223  CA  GLN   223      13.667  15.327   2.486  1.00 25.00           C
ATOM    224  CA  ALA   224      13.081  18.074  -0.096  1.00 25.00           C
ATOM    225  CA  PHE   225      15.737  18.376  -2.743  1.00 25.00           C
ATOM    226  CA  GLY   226      16.655  14.896  -1.583  1.00 25.00           C
ATOM    227  CA  ILE   227      13.714  12.547  -2.311  1.00 25.00           C
ATOM    228  CA  GLY   228      12.177  12.791  -5.810  1.00 25.00           C
ATOM    229  CA  ALA   229      15.039  15.074  -6.934  1.00 25.00           C
ATOM    230  CA  VAL   230      17.600  12.591  -5.541  1.00 25.00           C
ATOM    231  CA  GLU   231      15.868   9.724  -7.397  1.00 25.00           C
ATOM    232  CA  PRO   232      15.926  11.757 -10.643  1.00 25.00           C
ATOM    233  CA  ILE   233      19.657  12.471 -10.156  1.00 25.00           C
ATOM    234  CA  ILE   234      20.320   8.744  -9.576  1.00 25.00           C
ATOM    235  CA  ALA   235      18.377   7.878 -12.761  1.00 25.00           C
ATOM    236  CA  ALA   236      20.407  10.460 -14.731  1.00 25.00           C
ATOM    237  CA  ALA   237      23.664   8.983 -13.359  1.00 25.00           C
ATOM    238  CA  GLY   238      22.521   5.468 -14.361  1.00 25.00           C
ATOM    239  CA  GLU   239      21.679   6.719 -17.882  1.00 25.00           C
ATOM    240  CA  VAL   240      24.533   9.088 -18.364  1.00 25.00           C
ATOM    241  CA  ASP   241      27.374   7.202 -16.695  1.00 25.00           C
ATOM    242  CA  ALA   242      27.493   6.896 -12.918  1.00 25.00           C
ATOM    243  CA  ASP   243      26.259   6.743  -9.310  1.00 25.00           C
ATOM    244  CA  PHE   244      24.821   8.994  -6.621  1.00 25.00           C
ATOM    245  CA  VAL   245      22.935  11.897  -5.056  1.00 25.00           C
ATOM    246  CA  LEU   246      21.315  11.163  -1.723  1.00 25.00           C
ATOM    247  CA  ALA   247      21.366   9.710   1.764  1.00 25.00           C
ATOM    248  CA  LEU   248      21.255   8.876   5.442  1.00 25.00           C
ATOM    249  CA  GLY   249      20.148   8.341   9.059  1.00 25.00           C
ATOM    250  CA  ASP   250      16.642   8.935   7.676  1.00 25.00           C
ATOM    251  CA  LEU   251      16.545   5.144   7.225  1.00 25.00           C
ATOM    252  CA  ASP   252      14.277   2.451   5.728  1.00 25.00           C
ATOM    253  CA  ILE   253      15.272   4.052   2.409  1.00 25.00           C
ATOM    254  CA  SER   254      12.293   2.588   0.500  1.00 25.00           C
ATOM    255  CA  PRO   255      14.673   0.526  -1.681  1.00 25.00           C
ATOM    256  CA  LEU   256      16.304   2.640  -4.423  1.00 25.00           C
ATOM    257  CA  GLY   257      13.597   1.677  -6.975  1.00 25.00           C
ATOM    258  CA  THR   258      13.518  -1.863  -8.378  1.00 25.00           C
ATOM    259  CA  LEU   259      17.155  -1.201  -9.244  1.00 25.00           C
ATOM    260  CA  PRO   260      20.637  -2.388 -10.294  1.00 25.00           C
ATOM    261  CA  ARG   261      24.247  -3.329 -10.888  1.00 25.00           C
ATOM    262  CA  ASN   262      25.386  -0.311  -8.878  1.00 25.00           C
ATOM    263  CA  VAL   263      24.219   2.369  -6.436  1.00 25.00           C
ATOM    264  CA  ARG   264      23.810   3.906  -2.966  1.00 25.00           C
ATOM    265  CA  ALA   265      24.454   7.262  -1.355  1.00 25.00           C
ATOM    266  CA  VAL   266      25.897  10.720  -1.084  1.00 25.00           C
ATOM    267  CA  GLY   267      28.661  12.220   0.993  1.00 25.00           C
ATOM    268  CA  TRP   268      30.368  12.355   4.364  1.00 25.00           C
ATOM    269  CA  THR   269      31.656   8.845   4.938  1.00 25.00           C
ATOM    270  CA  PRO   270      33.925   6.456   2.980  1.00 25.00           C
ATOM    271  CA  LEU   271      34.737   9.618   1.106  1.00 25.00           C
ATOM    272  CA  HIS   272      38.182  10.789  -0.087  1.00 25.00           C
ATOM    273  CA  THR   273      38.985   7.254  -1.321  1.00 25.00           C
ATOM    274  CA  LEU   274      35.648   7.123  -3.194  1.00 25.00           C
ATOM    275  CA  LEU   275      36.390  10.517  -4.805  1.00 25.00           C
ATOM    276  CA  ARG   276      39.144   9.356  -7.092  1.00 25.00           C
ATOM    277  CA  THR   277      36.564   9.411  -9.836  1.00 25.00           C
ATOM    278  CA  CYS   278      36.742  13.195  -9.433  1.00 25.00           C
ATOM    279  CA  THR   279      33.082  14.090  -9.978  1.00 25.00           C
ATOM    280  CA  ALA   280      29.541  15.291  -9.498  1.00 25.00           C
ATOM    281  CA  VAL   281      27.387  15.453  -6.440  1.00 25.00           C
ATOM    282  CA  VAL   282      24.713  17.283  -4.505  1.00 25.00           C
ATOM    283  CA  HIS   283      24.605  16.211  -0.841  1.00 25.00           C
ATOM    284  CA  HIS   284      24.418  19.051   1.602  1.00 25.00           C
ATOM    285  CA  GLY   285      23.866  22.542   3.028  1.00 25.00           C
ATOM    286  CA  GLY   286      25.715  21.529   6.153  1.00 25.00           C
ATOM    287  CA  GLY   287      28.759  23.040   4.545  1.00 25.00           C
ATOM    288  CA  GLY   288      30.484  19.798   5.631  1.00 25.00           C
ATOM    289  CA  THR   289      29.554  18.157   2.299  1.00 25.00           C
ATOM    290  CA  VAL   290      30.956  21.170   0.396  1.00 25.00           C
ATOM    291  CA  MET   291      34.203  20.966   2.416  1.00 25.00           C
ATOM    292  CA  THR   292      34.478  17.225   1.643  1.00 25.00           C
ATOM    293  CA  ALA   293      33.939  17.930  -2.082  1.00 25.00           C
ATOM    294  CA  ILE   294      36.656  20.628  -1.989  1.00 25.00           C
ATOM    295  CA  ASP   295      39.055  18.187  -0.270  1.00 25.00           C
ATOM    296  CA  ALA   296      38.309  15.539  -2.934  1.00 25.00           C
ATOM    297  CA  GLY   297      36.079  16.660  -5.784  1.00 25.00           C
ATOM    298  CA  ILE   298      32.284  17.055  -5.986  1.00 25.00           C
ATOM    299  CA  PRO   299      33.020  20.770  -6.666  1.00 25.00           C
ATOM    300  CA  GLN   300      30.352  22.278  -4.460  1.00 25.00           C
ATOM    301  CA  LEU   301      27.005  21.497  -2.899  1.00 25.00           C
ATOM    302  CA  LEU   302      23.537  22.800  -2.004  1.00 25.00           C
ATOM    303  CA  ALA   303      20.683  20.349  -1.568  1.00 25.00           C
ATOM    304  CA  PRO   304      19.172  23.151   0.469  1.00 25.00           C
ATOM    305  CA  ASP   305      16.110  25.445   0.232  1.00 25.00           C
ATOM    306  CA  PRO   306      18.648  28.231  -0.084  1.00 25.00           C
ATOM    307  CA  ARG   307      19.200  28.820   3.618  1.00 25.00           C
ATOM    308  CA  ASP   308      22.244  30.679   4.841  1.00 25.00           C
ATOM    309  CA  GLN   309      23.004  31.024   1.134  1.00 25.00           C
ATOM    310  CA  PHE   310      24.351  27.516   1.470  1.00 25.00           C
ATOM    311  CA  GLN   311      27.786  29.209   1.450  1.00 25.00           C
ATOM    312  CA  HIS   312      29.205  26.360  -0.681  1.00 25.00           C
ATOM    313  CA  THR   313      26.281  26.702  -3.129  1.00 25.00           C
ATOM    314  CA  ALA   314      26.882  30.478  -3.358  1.00 25.00           C
ATOM    315  CA  ARG   315      30.601  29.870  -4.038  1.00 25.00           C
ATOM    316  CA  GLU   316      29.713  27.351  -6.783  1.00 25.00           C
ATOM    317  CA  ALA   317      27.305  29.879  -8.357  1.00 25.00           C
ATOM    318  CA  VAL   318      30.034  32.565  -8.275  1.00 25.00           C
ATOM    319  CA  SER   319      32.497  30.150  -9.937  1.00 25.00           C
ATOM    320  CA  ARG   320      30.259  27.753 -11.791  1.00 25.00           C
ATOM    321  CA  ARG   321      30.678  24.144 -10.553  1.00 25.00           C
ATOM    322  CA  GLY   322      27.037  23.699  -9.428  1.00 25.00           C
ATOM    323  CA  ILE   323      23.983  22.975  -7.322  1.00 25.00           C
ATOM    324  CA  GLY   324      22.209  25.105  -9.856  1.00 25.00           C
ATOM    325  CA  LEU   325      19.396  26.736  -7.907  1.00 25.00           C
ATOM    326  CA  VAL   326      17.717  24.987  -5.008  1.00 25.00           C
ATOM    327  CA  SER   327      15.919  22.545  -7.292  1.00 25.00           C
ATOM    328  CA  THR   328      13.666  23.438 -10.247  1.00 25.00           C
ATOM    329  CA  SER   329      11.734  20.301 -11.287  1.00 25.00           C
ATOM    330  CA  ASP   330      13.657  16.959 -11.364  1.00 25.00           C
ATOM    331  CA  LYS   331      13.566  17.275 -15.179  1.00 25.00           C
ATOM    332  CA  VAL   332      15.694  20.453 -14.993  1.00 25.00           C
ATOM    333  CA  ASP   333      18.215  18.661 -12.733  1.00 25.00           C
ATOM    334  CA  ALA   334      18.378  15.733 -15.196  1.00 25.00           C
ATOM    335  CA  ASP   335      18.969  18.170 -18.091  1.00 25.00           C
ATOM    336  CA  LEU   336      21.768  19.879 -16.113  1.00 25.00           C
ATOM    337  CA  LEU   337      23.373  16.477 -15.396  1.00 25.00           C
ATOM    338  CA  ARG   338      23.185  15.576 -19.113  1.00 25.00           C
ATOM    339  CA  ARG   339      24.813  18.918 -20.031  1.00 25.00           C
ATOM    340  CA  LEU   340      27.603  18.286 -17.485  1.00 25.00           C
ATOM    341  CA  ILE   341      28.174  14.791 -18.943  1.00 25.00           C
ATOM    342  CA  GLY   342      29.350  15.109 -22.548  1.00 25.00           C
ATOM    343  CA  ASP   343      32.945  13.938 -23.180  1.00 25.00           C
ATOM    344  CA  GLU   344      35.992  15.118 -21.236  1.00 25.00           C
ATOM    345  CA  SER   345      36.625  18.894 -21.316  1.00 25.00           C
ATOM    346  CA  LEU   346      35.073  19.252 -17.833  1.00 25.00           C
ATOM    347  CA  ARG   347      37.288  16.415 -16.527  1.00 25.00           C
ATOM    348  CA  THR   348      40.380  18.105 -18.027  1.00 25.00           C
ATOM    349  CA  ALA   349      39.400  21.419 -16.376  1.00 25.00           C
ATOM    350  CA  ALA   350      38.957  19.641 -13.013  1.00 25.00           C
ATOM    351  CA  ARG   351      42.400  18.007 -13.395  1.00 25.00           C
ATOM    352  CA  GLU   352      43.956  21.415 -14.189  1.00 25.00           C
ATOM    353  CA  VAL   353      42.283  22.927 -11.095  1.00 25.00           C
ATOM    354  CA  ARG   354      43.617  20.057  -8.939  1.00 25.00           C
ATOM    355  CA  GLU   355      47.137  20.604 -10.346  1.00 25.00           C
ATOM    356  CA  GLU   356      46.889  24.347  -9.576  1.00 25.00           C
ATOM    357  CA  MET   357      45.764  23.562  -6.001  1.00 25.00           C
ATOM    358  CA  VAL   358      48.712  21.155  -5.576  1.00 25.00           C
ATOM    359  CA  ALA   359      52.055  22.503  -4.383  1.00 25.00           C
TER
END
