
#######################################################
#                                                     #
#                        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 T0333TS393_3-D2
# Molecule2: number of CA atoms  148 ( 1087),  selected  148 , name T0333_D2.pdb
# PARAMETERS: T0333TS393_3-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          1.143
LGA    V     213      A     214          1.233
LGA    A     214      I     215          4.644
LGA    I     215      T     216          1.009
LGA    T     216      M     217          1.745
LGA    M     217      G     218          4.199
LGA    G     218      T     219          3.554
LGA    T     219      I     220           #
LGA    I     220      -       -           -
LGA    E     221      -       -           -
LGA    L     222      E     221           #
LGA    Q     223      L     222          4.162
LGA    A     224      Q     223           -
LGA    F     225      A     224           -
LGA    G     226      F     225          5.963
LGA    -       -      G     226           -
LGA    I     227      I     227          3.420
LGA    G     228      G     228          3.126
LGA    A     229      A     229          3.406
LGA    V     230      V     230          1.147
LGA    E     231      E     231          0.337
LGA    P     232      P     232          0.550
LGA    I     233      I     233          1.250
LGA    I     234      I     234          1.785
LGA    A     235      A     235          2.186
LGA    A     236      A     236          2.424
LGA    A     237      A     237          3.186
LGA    G     238      G     238          3.654
LGA    E     239      E     239          3.333
LGA    V     240      V     240          2.834
LGA    -       -      D     241           -
LGA    D     241      A     242          2.933
LGA    A     242      D     243          2.402
LGA    -       -      F     244           -
LGA    D     243      V     245          2.251
LGA    F     244      L     246          1.713
LGA    V     245      A     247          0.532
LGA    L     246      L     248          1.740
LGA    A     247      G     249          5.288
LGA    L     248      D     250           -
LGA    G     249      L     251          4.762
LGA    D     250      -       -           -
LGA    L     251      -       -           -
LGA    D     252      D     252          3.661
LGA    I     253      I     253          2.024
LGA    S     254      S     254          1.196
LGA    P     255      P     255          3.045
LGA    L     256      L     256          3.442
LGA    G     257      G     257          2.682
LGA    T     258      T     258          2.646
LGA    L     259      L     259          3.073
LGA    -       -      P     260           -
LGA    P     260      R     261          2.237
LGA    R     261      N     262          5.213
LGA    N     262      V     263          4.049
LGA    V     263      R     264          1.419
LGA    R     264      A     265          1.274
LGA    A     265      V     266          4.773
LGA    V     266      G     267          1.708
LGA    G     267      -       -           -
LGA    W     268      W     268          2.548
LGA    T     269      T     269          1.353
LGA    P     270      P     270          3.862
LGA    L     271      L     271          2.655
LGA    H     272      H     272          2.903
LGA    T     273      T     273          3.182
LGA    L     274      L     274          2.502
LGA    L     275      L     275          2.401
LGA    R     276      R     276          2.745
LGA    T     277      T     277          2.833
LGA    C     278      C     278          2.782
LGA    -       -      T     279           -
LGA    T     279      A     280          1.105
LGA    A     280      V     281          1.817
LGA    V     281      V     282          3.768
LGA    V     282      H     283          1.191
LGA    H     283      H     284          2.063
LGA    H     284      G     285           #
LGA    G     285      -       -           -
LGA    G     286      G     286          2.230
LGA    G     287      G     287          1.168
LGA    G     288      G     288          4.069
LGA    T     289      T     289          1.746
LGA    V     290      V     290          2.570
LGA    M     291      M     291          4.275
LGA    T     292      T     292          2.004
LGA    A     293      A     293          2.414
LGA    I     294      I     294          4.343
LGA    D     295      D     295          2.671
LGA    A     296      A     296          1.966
LGA    G     297      G     297          3.359
LGA    I     298      I     298          4.788
LGA    -       -      P     299           -
LGA    P     299      Q     300          1.982
LGA    Q     300      L     301           #
LGA    L     301      L     302          2.138
LGA    L     302      A     303           #
LGA    A     303      P     304          0.833
LGA    P     304      D     305           #
LGA    D     305      P     306          3.532
LGA    P     306      R     307           #
LGA    R     307      D     308          4.202
LGA    D     308      Q     309          3.895
LGA    Q     309      F     310          2.196
LGA    F     310      Q     311          0.760
LGA    Q     311      H     312          4.150
LGA    -       -      T     313           -
LGA    H     312      A     314          1.663
LGA    T     313      R     315          2.331
LGA    A     314      E     316          2.982
LGA    R     315      A     317          1.828
LGA    E     316      V     318          1.290
LGA    A     317      S     319          2.584
LGA    V     318      R     320          3.005
LGA    S     319      R     321          2.721
LGA    R     320      G     322          2.884
LGA    -       -      I     323           -
LGA    R     321      G     324          1.823
LGA    G     322      L     325          2.602
LGA    I     323      V     326          2.480
LGA    G     324      S     327          4.508
LGA    L     325      -       -           -
LGA    V     326      T     328          0.721
LGA    S     327      S     329          3.562
LGA    T     328      D     330          3.640
LGA    S     329      K     331          3.820
LGA    D     330      -       -           -
LGA    K     331      -       -           -
LGA    V     332      V     332          4.645
LGA    D     333      D     333          3.767
LGA    A     334      A     334          2.816
LGA    D     335      D     335          2.718
LGA    L     336      L     336          1.743
LGA    L     337      L     337          1.012
LGA    R     338      R     338          1.953
LGA    R     339      R     339          1.513
LGA    L     340      L     340          2.502
LGA    I     341      I     341          3.428
LGA    G     342      G     342          2.314
LGA    D     343      D     343          6.405
LGA    E     344      E     344          3.892
LGA    S     345      S     345          3.901
LGA    L     346      L     346          3.477
LGA    R     347      R     347          2.815
LGA    T     348      T     348          2.582
LGA    A     349      A     349          2.697
LGA    A     350      A     350          2.321
LGA    R     351      R     351          1.841
LGA    E     352      E     352          1.711
LGA    V     353      V     353          1.929
LGA    R     354      R     354          1.592
LGA    E     355      E     355          1.738
LGA    E     356      E     356          1.974
LGA    M     357      M     357          1.745
LGA    V     358      V     358          2.413
LGA    A     359      A     359          1.337

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  148  148    5.0    129    2.91    61.24     48.602     4.291

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.719793 * X  +   0.666688 * Y  +  -0.193458 * Z  +  31.378044
  Y_new =   0.669255 * X  +   0.592429 * Y  +  -0.448470 * Z  +  18.326715
  Z_new =  -0.184379 * X  +  -0.452279 * Y  +  -0.872610 * Z  +   9.115425 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.663408    0.478184  [ DEG:  -152.6021     27.3979 ]
  Theta =   0.185440    2.956152  [ DEG:    10.6249    169.3751 ]
  Phi   =   2.392561   -0.749032  [ DEG:   137.0836    -42.9163 ]
 
# 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: T0333TS393_3-D2                               
REMARK     2: T0333_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0333TS393_3-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  129   2.91   61.24  48.602
REMARK  ---------------------------------------------------------- 
MOLECULE T0333TS393_3-D2
PFRMAT TS
TARGET T0333
MODEL 3
PARENT N/A
ATOM    212  CA  GLU   212      28.849  10.277 -11.035  1.00 25.00           C
ATOM    213  CA  VAL   213      28.586  11.003  -7.354  1.00 25.00           C
ATOM    214  CA  ALA   214      29.616  11.352  -3.757  1.00 25.00           C
ATOM    215  CA  ILE   215      26.692  13.190  -2.069  1.00 25.00           C
ATOM    216  CA  THR   216      26.105  15.594   0.832  1.00 25.00           C
ATOM    217  CA  MET   217      28.563  13.379   2.709  1.00 25.00           C
ATOM    218  CA  GLY   218      27.268  13.254   6.267  1.00 25.00           C
ATOM    219  CA  THR   219      26.251   9.664   5.500  1.00 25.00           C
ATOM    220  CA  ILE   220      22.596   8.799   5.709  1.00 25.00           C
ATOM    221  CA  GLU   221      19.261  10.396   5.105  1.00 25.00           C
ATOM    222  CA  LEU   222      17.819  13.882   4.673  1.00 25.00           C
ATOM    223  CA  GLN   223      16.227  17.372   4.979  1.00 25.00           C
ATOM    224  CA  ALA   224      17.041  18.476   1.448  1.00 25.00           C
ATOM    225  CA  PHE   225      14.097  20.847   0.951  1.00 25.00           C
ATOM    226  CA  GLY   226      11.417  18.447   2.179  1.00 25.00           C
ATOM    227  CA  ILE   227      12.970  15.103   1.237  1.00 25.00           C
ATOM    228  CA  GLY   228      11.344  15.647  -2.187  1.00 25.00           C
ATOM    229  CA  ALA   229      14.356  17.727  -3.315  1.00 25.00           C
ATOM    230  CA  VAL   230      16.734  14.967  -2.132  1.00 25.00           C
ATOM    231  CA  GLU   231      14.694  12.354  -4.050  1.00 25.00           C
ATOM    232  CA  PRO   232      14.823  14.528  -7.199  1.00 25.00           C
ATOM    233  CA  ILE   233      18.616  14.894  -6.821  1.00 25.00           C
ATOM    234  CA  ILE   234      18.969  11.100  -6.436  1.00 25.00           C
ATOM    235  CA  ALA   235      16.852  10.560  -9.581  1.00 25.00           C
ATOM    236  CA  ALA   236      19.033  13.049 -11.507  1.00 25.00           C
ATOM    237  CA  ALA   237      22.191  11.233 -10.327  1.00 25.00           C
ATOM    238  CA  GLY   238      20.711   7.882 -11.444  1.00 25.00           C
ATOM    239  CA  GLU   239      19.866   9.369 -14.870  1.00 25.00           C
ATOM    240  CA  VAL   240      23.029   7.843 -16.183  1.00 25.00           C
ATOM    241  CA  ASP   241      23.845   4.772 -14.081  1.00 25.00           C
ATOM    242  CA  ALA   242      25.611   6.415 -11.081  1.00 25.00           C
ATOM    243  CA  ASP   243      24.916   6.771  -7.402  1.00 25.00           C
ATOM    244  CA  PHE   244      25.548   8.059  -3.900  1.00 25.00           C
ATOM    245  CA  VAL   245      26.306   8.085  -0.176  1.00 25.00           C
ATOM    246  CA  LEU   246      23.528  10.348   1.029  1.00 25.00           C
ATOM    247  CA  ALA   247      22.948  13.023   3.569  1.00 25.00           C
ATOM    248  CA  LEU   248      22.291  13.813   7.201  1.00 25.00           C
ATOM    249  CA  GLY   249      21.407  11.530  10.113  1.00 25.00           C
ATOM    250  CA  ASP   250      18.604   8.941  10.392  1.00 25.00           C
ATOM    251  CA  LEU   251      15.108   8.494   8.856  1.00 25.00           C
ATOM    252  CA  ASP   252      14.379   4.897   7.855  1.00 25.00           C
ATOM    253  CA  ILE   253      16.063   5.317   4.469  1.00 25.00           C
ATOM    254  CA  SER   254      13.147   3.179   3.207  1.00 25.00           C
ATOM    255  CA  PRO   255      12.671   5.540   0.230  1.00 25.00           C
ATOM    256  CA  LEU   256      15.019   4.592  -2.601  1.00 25.00           C
ATOM    257  CA  GLY   257      12.239   2.199  -3.682  1.00 25.00           C
ATOM    258  CA  THR   258      13.640  -0.845  -5.416  1.00 25.00           C
ATOM    259  CA  LEU   259      17.229   0.352  -5.151  1.00 25.00           C
ATOM    260  CA  PRO   260      18.461  -0.022  -8.736  1.00 25.00           C
ATOM    261  CA  ARG   261      21.640  -2.048  -9.469  1.00 25.00           C
ATOM    262  CA  ASN   262      23.221   0.520  -7.212  1.00 25.00           C
ATOM    263  CA  VAL   263      23.146   3.133  -4.455  1.00 25.00           C
ATOM    264  CA  ARG   264      24.153   3.146  -0.748  1.00 25.00           C
ATOM    265  CA  ALA   265      22.844   5.047   2.275  1.00 25.00           C
ATOM    266  CA  VAL   266      25.916   4.385   4.461  1.00 25.00           C
ATOM    267  CA  GLY   267      26.091   5.107   8.192  1.00 25.00           C
ATOM    268  CA  TRP   268      29.837   5.763   7.877  1.00 25.00           C
ATOM    269  CA  THR   269      31.510   6.852   4.688  1.00 25.00           C
ATOM    270  CA  PRO   270      34.530   6.336   2.471  1.00 25.00           C
ATOM    271  CA  LEU   271      35.581   9.608   0.773  1.00 25.00           C
ATOM    272  CA  HIS   272      39.165   9.250  -0.529  1.00 25.00           C
ATOM    273  CA  THR   273      38.182   6.073  -2.429  1.00 25.00           C
ATOM    274  CA  LEU   274      35.179   7.888  -3.963  1.00 25.00           C
ATOM    275  CA  LEU   275      37.443  10.789  -5.025  1.00 25.00           C
ATOM    276  CA  ARG   276      38.902   8.744  -7.795  1.00 25.00           C
ATOM    277  CA  THR   277      35.420   8.039  -9.136  1.00 25.00           C
ATOM    278  CA  CYS   278      33.450  11.120  -8.131  1.00 25.00           C
ATOM    279  CA  THR   279      31.903  14.093  -9.953  1.00 25.00           C
ATOM    280  CA  ALA   280      29.085  15.924  -8.196  1.00 25.00           C
ATOM    281  CA  VAL   281      29.317  16.696  -4.483  1.00 25.00           C
ATOM    282  CA  VAL   282      25.572  16.997  -4.081  1.00 25.00           C
ATOM    283  CA  HIS   283      23.361  18.423  -1.371  1.00 25.00           C
ATOM    284  CA  HIS   284      22.845  19.761   2.118  1.00 25.00           C
ATOM    285  CA  GLY   285      25.471  18.850   4.739  1.00 25.00           C
ATOM    286  CA  GLY   286      27.279  22.174   4.250  1.00 25.00           C
ATOM    287  CA  GLY   287      31.083  22.092   3.924  1.00 25.00           C
ATOM    288  CA  GLY   288      31.249  18.373   3.024  1.00 25.00           C
ATOM    289  CA  THR   289      30.983  19.237  -0.698  1.00 25.00           C
ATOM    290  CA  VAL   290      33.800  21.805  -0.328  1.00 25.00           C
ATOM    291  CA  MET   291      35.977  19.199   1.442  1.00 25.00           C
ATOM    292  CA  THR   292      35.294  16.685  -1.366  1.00 25.00           C
ATOM    293  CA  ALA   293      36.243  19.314  -3.983  1.00 25.00           C
ATOM    294  CA  ILE   294      39.486  20.065  -2.090  1.00 25.00           C
ATOM    295  CA  ASP   295      40.300  16.325  -1.953  1.00 25.00           C
ATOM    296  CA  ALA   296      39.664  16.023  -5.717  1.00 25.00           C
ATOM    297  CA  GLY   297      37.233  17.516  -8.267  1.00 25.00           C
ATOM    298  CA  ILE   298      33.883  16.569  -6.705  1.00 25.00           C
ATOM    299  CA  PRO   299      32.434  19.658  -8.440  1.00 25.00           C
ATOM    300  CA  GLN   300      30.708  21.473  -5.525  1.00 25.00           C
ATOM    301  CA  LEU   301      27.165  21.771  -4.162  1.00 25.00           C
ATOM    302  CA  LEU   302      25.974  22.628  -0.659  1.00 25.00           C
ATOM    303  CA  ALA   303      22.353  23.335  -1.671  1.00 25.00           C
ATOM    304  CA  PRO   304      21.292  25.830   0.961  1.00 25.00           C
ATOM    305  CA  ASP   305      18.864  28.366  -0.493  1.00 25.00           C
ATOM    306  CA  PRO   306      21.118  31.264   0.521  1.00 25.00           C
ATOM    307  CA  ARG   307      21.056  30.481   4.257  1.00 25.00           C
ATOM    308  CA  ASP   308      24.628  31.707   4.286  1.00 25.00           C
ATOM    309  CA  GLN   309      25.784  28.151   3.919  1.00 25.00           C
ATOM    310  CA  PHE   310      26.010  28.468   0.170  1.00 25.00           C
ATOM    311  CA  GLN   311      29.220  30.525  -0.193  1.00 25.00           C
ATOM    312  CA  HIS   312      30.924  27.595  -1.975  1.00 25.00           C
ATOM    313  CA  THR   313      27.934  27.264  -4.345  1.00 25.00           C
ATOM    314  CA  ALA   314      28.080  31.017  -5.092  1.00 25.00           C
ATOM    315  CA  ARG   315      31.832  30.753  -5.815  1.00 25.00           C
ATOM    316  CA  GLU   316      31.194  27.800  -8.168  1.00 25.00           C
ATOM    317  CA  ALA   317      28.476  29.798  -9.980  1.00 25.00           C
ATOM    318  CA  VAL   318      30.869  32.766 -10.349  1.00 25.00           C
ATOM    319  CA  SER   319      33.569  30.445 -11.762  1.00 25.00           C
ATOM    320  CA  ARG   320      31.536  27.705 -13.390  1.00 25.00           C
ATOM    321  CA  ARG   321      30.688  24.234 -12.146  1.00 25.00           C
ATOM    322  CA  GLY   322      27.694  24.311  -9.755  1.00 25.00           C
ATOM    323  CA  ILE   323      24.594  24.378  -7.622  1.00 25.00           C
ATOM    324  CA  GLY   324      23.588  20.753  -7.538  1.00 25.00           C
ATOM    325  CA  LEU   325      20.039  20.225  -6.393  1.00 25.00           C
ATOM    326  CA  VAL   326      19.133  23.848  -5.642  1.00 25.00           C
ATOM    327  CA  SER   327      15.689  22.573  -4.640  1.00 25.00           C
ATOM    328  CA  THR   328      14.098  24.205  -7.642  1.00 25.00           C
ATOM    329  CA  SER   329      12.055  21.778  -9.633  1.00 25.00           C
ATOM    330  CA  ASP   330      14.871  19.582 -10.851  1.00 25.00           C
ATOM    331  CA  LYS   331      14.806  20.351 -14.601  1.00 25.00           C
ATOM    332  CA  VAL   332      17.929  22.535 -14.233  1.00 25.00           C
ATOM    333  CA  ASP   333      19.702  19.725 -12.330  1.00 25.00           C
ATOM    334  CA  ALA   334      18.754  17.232 -15.079  1.00 25.00           C
ATOM    335  CA  ASP   335      20.102  19.626 -17.748  1.00 25.00           C
ATOM    336  CA  LEU   336      23.373  20.003 -15.792  1.00 25.00           C
ATOM    337  CA  LEU   337      23.680  16.195 -15.522  1.00 25.00           C
ATOM    338  CA  ARG   338      23.095  15.857 -19.291  1.00 25.00           C
ATOM    339  CA  ARG   339      25.782  18.499 -19.972  1.00 25.00           C
ATOM    340  CA  LEU   340      28.226  16.636 -17.686  1.00 25.00           C
ATOM    341  CA  ILE   341      27.480  13.358 -19.519  1.00 25.00           C
ATOM    342  CA  GLY   342      29.712  14.219 -22.497  1.00 25.00           C
ATOM    343  CA  ASP   343      33.284  13.205 -23.025  1.00 25.00           C
ATOM    344  CA  GLU   344      36.453  15.260 -22.514  1.00 25.00           C
ATOM    345  CA  SER   345      36.390  19.072 -22.153  1.00 25.00           C
ATOM    346  CA  LEU   346      35.019  18.736 -18.592  1.00 25.00           C
ATOM    347  CA  ARG   347      37.785  16.230 -17.736  1.00 25.00           C
ATOM    348  CA  THR   348      40.424  18.626 -19.140  1.00 25.00           C
ATOM    349  CA  ALA   349      38.968  21.489 -17.055  1.00 25.00           C
ATOM    350  CA  ALA   350      39.063  19.289 -13.922  1.00 25.00           C
ATOM    351  CA  ARG   351      42.713  18.380 -14.642  1.00 25.00           C
ATOM    352  CA  GLU   352      43.577  22.085 -15.071  1.00 25.00           C
ATOM    353  CA  VAL   353      41.855  22.898 -11.748  1.00 25.00           C
ATOM    354  CA  ARG   354      43.816  20.099 -10.019  1.00 25.00           C
ATOM    355  CA  GLU   355      47.085  21.448 -11.489  1.00 25.00           C
ATOM    356  CA  GLU   356      46.216  24.967 -10.254  1.00 25.00           C
ATOM    357  CA  MET   357      45.476  23.586  -6.760  1.00 25.00           C
ATOM    358  CA  VAL   358      48.830  21.736  -6.754  1.00 25.00           C
ATOM    359  CA  ALA   359      52.390  22.778  -6.083  1.00 25.00           C
TER
END
