
#######################################################
#                                                     #
#                        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_2-D2
# Molecule2: number of CA atoms  148 ( 1087),  selected  148 , name T0333_D2.pdb
# PARAMETERS: T0333TS168_2-D2.T0333_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E     212      E     212           #
LGA    V     213      V     213           #
LGA    A     214      A     214          4.169
LGA    I     215      I     215          3.856
LGA    T     216      T     216          1.716
LGA    M     217      M     217          2.306
LGA    G     218      G     218          3.126
LGA    T     219      T     219          2.069
LGA    -       -      I     220           -
LGA    -       -      E     221           -
LGA    I     220      L     222          2.754
LGA    E     221      Q     223           #
LGA    -       -      A     224           -
LGA    -       -      F     225           -
LGA    L     222      G     226          2.990
LGA    Q     223      I     227          4.715
LGA    A     224      G     228          5.051
LGA    F     225      A     229          2.356
LGA    G     226      -       -           -
LGA    I     227      -       -           -
LGA    G     228      -       -           -
LGA    A     229      -       -           -
LGA    V     230      V     230          2.419
LGA    E     231      E     231          2.070
LGA    P     232      P     232          2.329
LGA    I     233      I     233          0.438
LGA    I     234      I     234          1.337
LGA    A     235      A     235          3.105
LGA    A     236      A     236          3.159
LGA    A     237      A     237          3.607
LGA    G     238      G     238          4.592
LGA    E     239      E     239          4.820
LGA    V     240      V     240          4.186
LGA    -       -      D     241           -
LGA    D     241      A     242          0.944
LGA    A     242      D     243          0.670
LGA    D     243      F     244          0.952
LGA    F     244      V     245          1.641
LGA    V     245      L     246          1.377
LGA    L     246      A     247          1.001
LGA    A     247      L     248          0.876
LGA    L     248      G     249          1.634
LGA    G     249      D     250          4.714
LGA    D     250      L     251          3.078
LGA    L     251      D     252          1.535
LGA    D     252      I     253          5.181
LGA    I     253      S     254          1.950
LGA    S     254      P     255          2.683
LGA    P     255      L     256          2.874
LGA    L     256      G     257          3.835
LGA    G     257      T     258          3.303
LGA    T     258      L     259          4.760
LGA    L     259      P     260          2.910
LGA    P     260      R     261          2.133
LGA    R     261      -       -           -
LGA    N     262      N     262          3.895
LGA    V     263      V     263          2.286
LGA    R     264      R     264          2.367
LGA    A     265      A     265          2.380
LGA    V     266      V     266          2.582
LGA    G     267      G     267          2.567
LGA    W     268      W     268          1.746
LGA    T     269      T     269          0.567
LGA    P     270      P     270          2.997
LGA    L     271      L     271          3.447
LGA    H     272      H     272          3.212
LGA    T     273      T     273          3.997
LGA    L     274      L     274          2.610
LGA    L     275      L     275          2.291
LGA    R     276      R     276          3.161
LGA    T     277      T     277          3.027
LGA    -       -      C     278           -
LGA    C     278      T     279           #
LGA    T     279      A     280           #
LGA    A     280      V     281          3.740
LGA    V     281      V     282          0.736
LGA    V     282      H     283          0.784
LGA    H     283      H     284          2.254
LGA    H     284      -       -           -
LGA    G     285      -       -           -
LGA    G     286      -       -           -
LGA    G     287      -       -           -
LGA    G     288      G     285          1.082
LGA    T     289      -       -           -
LGA    V     290      G     286          3.971
LGA    -       -      G     287           -
LGA    -       -      G     288           -
LGA    M     291      T     289          3.150
LGA    T     292      V     290          3.166
LGA    A     293      M     291          3.999
LGA    I     294      -       -           -
LGA    D     295      -       -           -
LGA    A     296      T     292          1.515
LGA    G     297      A     293          3.532
LGA    I     298      I     294          4.739
LGA    -       -      D     295           -
LGA    -       -      A     296           -
LGA    -       -      G     297           -
LGA    -       -      I     298           -
LGA    -       -      P     299           -
LGA    P     299      Q     300          3.770
LGA    Q     300      L     301          1.813
LGA    L     301      L     302          0.834
LGA    L     302      A     303          1.836
LGA    A     303      P     304          2.290
LGA    P     304      D     305          3.509
LGA    D     305      P     306          2.236
LGA    -       -      R     307           -
LGA    P     306      D     308          2.773
LGA    R     307      Q     309          2.347
LGA    D     308      F     310          1.779
LGA    Q     309      Q     311          2.410
LGA    F     310      H     312          2.403
LGA    Q     311      T     313          2.709
LGA    H     312      A     314          2.158
LGA    T     313      R     315          1.395
LGA    A     314      E     316          2.093
LGA    R     315      A     317          1.948
LGA    E     316      V     318          1.752
LGA    A     317      S     319          2.453
LGA    V     318      R     320          2.501
LGA    S     319      R     321          1.746
LGA    R     320      G     322          2.154
LGA    -       -      I     323           -
LGA    R     321      G     324          4.397
LGA    G     322      L     325          1.837
LGA    I     323      V     326          1.373
LGA    G     324      S     327          2.033
LGA    L     325      T     328          1.437
LGA    V     326      S     329           #
LGA    S     327      -       -           -
LGA    T     328      -       -           -
LGA    S     329      -       -           -
LGA    D     330      D     330          3.994
LGA    K     331      K     331          5.067
LGA    V     332      V     332           #
LGA    D     333      D     333          4.178
LGA    A     334      A     334          4.109
LGA    D     335      D     335          3.958
LGA    L     336      L     336          2.492
LGA    L     337      L     337          2.268
LGA    R     338      R     338          3.376
LGA    R     339      R     339          2.893
LGA    L     340      L     340          2.467
LGA    I     341      I     341          3.631
LGA    G     342      G     342          1.763
LGA    D     343      D     343          4.647
LGA    E     344      E     344          3.788
LGA    S     345      S     345          4.013
LGA    L     346      L     346          3.289
LGA    R     347      R     347          2.678
LGA    T     348      T     348          2.958
LGA    A     349      A     349          2.920
LGA    A     350      A     350          2.320
LGA    R     351      R     351          2.007
LGA    E     352      E     352          2.021
LGA    V     353      V     353          2.048
LGA    R     354      R     354          1.665
LGA    E     355      E     355          1.631
LGA    E     356      E     356          1.812
LGA    M     357      M     357          1.670
LGA    V     358      V     358          1.829
LGA    A     359      A     359          0.921

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  148  148    5.0    126    2.87    53.97     47.700     4.238

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.266610 * X  +  -0.935457 * Y  +  -0.232033 * Z  +  31.202784
  Y_new =  -0.825003 * X  +   0.097036 * Y  +   0.556735 * Z  +  17.251812
  Z_new =  -0.498286 * X  +   0.339859 * Y  +  -0.797626 * Z  +   7.862057 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.738801   -0.402792  [ DEG:   156.9217    -23.0783 ]
  Theta =   0.521621    2.619972  [ DEG:    29.8867    150.1133 ]
  Phi   =  -1.883366    1.258227  [ DEG:  -107.9089     72.0911 ]
 
# 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_2-D2                               
REMARK     2: T0333_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0333TS168_2-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  126   2.87   53.97  47.700
REMARK  ---------------------------------------------------------- 
MOLECULE T0333TS168_2-D2
PFRMAT TS
TARGET T0333
MODEL 2
PARENT N/A
ATOM    212  CA  GLU   212      31.444  11.860 -11.681  1.00 25.00           C
ATOM    213  CA  VAL   213      31.047  13.697  -8.409  1.00 25.00           C
ATOM    214  CA  ALA   214      30.600  13.341  -4.659  1.00 25.00           C
ATOM    215  CA  ILE   215      27.846  12.283  -2.250  1.00 25.00           C
ATOM    216  CA  THR   216      24.755  13.324  -0.223  1.00 25.00           C
ATOM    217  CA  MET   217      26.674  15.453   2.221  1.00 25.00           C
ATOM    218  CA  GLY   218      27.189  13.037   5.107  1.00 25.00           C
ATOM    219  CA  THR   219      23.603  13.980   6.108  1.00 25.00           C
ATOM    220  CA  ILE   220      21.528  15.709   3.430  1.00 25.00           C
ATOM    221  CA  GLU   221      18.670  13.196   3.845  1.00 25.00           C
ATOM    222  CA  LEU   222      15.329  14.544   2.621  1.00 25.00           C
ATOM    223  CA  GLN   223      12.389  16.532   4.024  1.00 25.00           C
ATOM    224  CA  ALA   224      13.838  19.764   2.758  1.00 25.00           C
ATOM    225  CA  PHE   225      14.619  18.937  -0.849  1.00 25.00           C
ATOM    226  CA  GLY   226      10.838  18.706  -1.440  1.00 25.00           C
ATOM    227  CA  ILE   227      11.412  15.012  -1.390  1.00 25.00           C
ATOM    228  CA  GLY   228      10.494  15.260  -5.100  1.00 25.00           C
ATOM    229  CA  ALA   229      13.587  17.425  -5.746  1.00 25.00           C
ATOM    230  CA  VAL   230      15.784  14.872  -3.922  1.00 25.00           C
ATOM    231  CA  GLU   231      14.280  12.042  -6.020  1.00 25.00           C
ATOM    232  CA  PRO   232      14.958  14.025  -9.225  1.00 25.00           C
ATOM    233  CA  ILE   233      18.579  14.614  -8.125  1.00 25.00           C
ATOM    234  CA  ILE   234      18.996  10.874  -7.412  1.00 25.00           C
ATOM    235  CA  ALA   235      17.583  10.032 -10.870  1.00 25.00           C
ATOM    236  CA  ALA   236      20.009  12.512 -12.492  1.00 25.00           C
ATOM    237  CA  ALA   237      22.931  10.940 -10.581  1.00 25.00           C
ATOM    238  CA  GLY   238      21.843   7.455 -11.733  1.00 25.00           C
ATOM    239  CA  GLU   239      21.651   8.685 -15.355  1.00 25.00           C
ATOM    240  CA  VAL   240      24.713  10.112 -17.087  1.00 25.00           C
ATOM    241  CA  ASP   241      26.146   6.657 -16.466  1.00 25.00           C
ATOM    242  CA  ALA   242      26.326   5.101 -12.986  1.00 25.00           C
ATOM    243  CA  ASP   243      25.957   5.880  -9.295  1.00 25.00           C
ATOM    244  CA  PHE   244      25.221   7.176  -5.800  1.00 25.00           C
ATOM    245  CA  VAL   245      24.466   8.492  -2.340  1.00 25.00           C
ATOM    246  CA  LEU   246      26.147   8.666   1.038  1.00 25.00           C
ATOM    247  CA  ALA   247      22.805   9.582   2.528  1.00 25.00           C
ATOM    248  CA  LEU   248      24.147   8.801   6.020  1.00 25.00           C
ATOM    249  CA  GLY   249      21.075   9.381   8.207  1.00 25.00           C
ATOM    250  CA  ASP   250      18.034   7.878   6.452  1.00 25.00           C
ATOM    251  CA  LEU   251      17.616   4.096   6.856  1.00 25.00           C
ATOM    252  CA  ASP   252      13.884   4.885   6.716  1.00 25.00           C
ATOM    253  CA  ILE   253      14.246   5.821   3.021  1.00 25.00           C
ATOM    254  CA  SER   254      10.779   4.961   1.641  1.00 25.00           C
ATOM    255  CA  PRO   255      12.260   4.496  -1.860  1.00 25.00           C
ATOM    256  CA  LEU   256      15.982   4.050  -2.702  1.00 25.00           C
ATOM    257  CA  GLY   257      14.871   3.230  -6.251  1.00 25.00           C
ATOM    258  CA  THR   258      12.837   0.807  -8.351  1.00 25.00           C
ATOM    259  CA  LEU   259      15.587   0.959 -11.005  1.00 25.00           C
ATOM    260  CA  PRO   260      18.364  -0.820  -9.161  1.00 25.00           C
ATOM    261  CA  ARG   261      21.585  -2.770  -9.678  1.00 25.00           C
ATOM    262  CA  ASN   262      23.472   0.508  -9.223  1.00 25.00           C
ATOM    263  CA  VAL   263      22.032   2.686  -6.438  1.00 25.00           C
ATOM    264  CA  ARG   264      24.092   2.673  -3.271  1.00 25.00           C
ATOM    265  CA  ALA   265      24.382   3.917   0.263  1.00 25.00           C
ATOM    266  CA  VAL   266      27.250   3.457   2.663  1.00 25.00           C
ATOM    267  CA  GLY   267      26.053   4.061   6.199  1.00 25.00           C
ATOM    268  CA  TRP   268      29.663   5.021   6.797  1.00 25.00           C
ATOM    269  CA  THR   269      32.258   6.324   4.296  1.00 25.00           C
ATOM    270  CA  PRO   270      35.258   7.539   2.375  1.00 25.00           C
ATOM    271  CA  LEU   271      36.997  10.337   0.557  1.00 25.00           C
ATOM    272  CA  HIS   272      39.943  10.719  -1.860  1.00 25.00           C
ATOM    273  CA  THR   273      39.183   7.281  -3.368  1.00 25.00           C
ATOM    274  CA  LEU   274      35.504   8.257  -3.800  1.00 25.00           C
ATOM    275  CA  LEU   275      36.545  11.519  -5.515  1.00 25.00           C
ATOM    276  CA  ARG   276      38.496   9.444  -7.980  1.00 25.00           C
ATOM    277  CA  THR   277      35.050   8.203  -9.025  1.00 25.00           C
ATOM    278  CA  CYS   278      31.952   7.041  -7.141  1.00 25.00           C
ATOM    279  CA  THR   279      29.170   9.484  -7.846  1.00 25.00           C
ATOM    280  CA  ALA   280      26.732  12.277  -7.316  1.00 25.00           C
ATOM    281  CA  VAL   281      26.466  15.842  -6.106  1.00 25.00           C
ATOM    282  CA  VAL   282      26.578  17.345  -2.597  1.00 25.00           C
ATOM    283  CA  HIS   283      23.512  18.173  -0.602  1.00 25.00           C
ATOM    284  CA  HIS   284      22.986  21.171   1.691  1.00 25.00           C
ATOM    285  CA  GLY   285      22.436  21.900   5.349  1.00 25.00           C
ATOM    286  CA  GLY   286      25.734  20.430   6.394  1.00 25.00           C
ATOM    287  CA  GLY   287      27.198  23.313   4.418  1.00 25.00           C
ATOM    288  CA  GLY   288      27.717  22.495   0.712  1.00 25.00           C
ATOM    289  CA  THR   289      31.257  23.950   0.863  1.00 25.00           C
ATOM    290  CA  VAL   290      32.014  21.849   3.975  1.00 25.00           C
ATOM    291  CA  MET   291      30.718  18.712   2.202  1.00 25.00           C
ATOM    292  CA  THR   292      32.918  19.489  -0.835  1.00 25.00           C
ATOM    293  CA  ALA   293      35.956  19.944   1.450  1.00 25.00           C
ATOM    294  CA  ILE   294      35.208  16.596   3.152  1.00 25.00           C
ATOM    295  CA  ASP   295      34.935  14.891  -0.266  1.00 25.00           C
ATOM    296  CA  ALA   296      38.284  16.419  -1.323  1.00 25.00           C
ATOM    297  CA  GLY   297      37.665  19.613  -3.327  1.00 25.00           C
ATOM    298  CA  ILE   298      34.546  17.747  -4.590  1.00 25.00           C
ATOM    299  CA  PRO   299      30.940  18.263  -5.581  1.00 25.00           C
ATOM    300  CA  GLN   300      28.963  19.558  -8.525  1.00 25.00           C
ATOM    301  CA  LEU   301      27.258  21.672  -5.851  1.00 25.00           C
ATOM    302  CA  LEU   302      23.919  21.846  -4.071  1.00 25.00           C
ATOM    303  CA  ALA   303      20.215  21.976  -3.332  1.00 25.00           C
ATOM    304  CA  PRO   304      21.022  25.076  -1.226  1.00 25.00           C
ATOM    305  CA  ASP   305      17.630  26.061   0.124  1.00 25.00           C
ATOM    306  CA  PRO   306      18.906  29.219   1.782  1.00 25.00           C
ATOM    307  CA  ARG   307      20.559  32.544   2.438  1.00 25.00           C
ATOM    308  CA  ASP   308      24.002  31.446   3.611  1.00 25.00           C
ATOM    309  CA  GLN   309      24.432  28.302   1.571  1.00 25.00           C
ATOM    310  CA  PHE   310      24.366  30.711  -1.326  1.00 25.00           C
ATOM    311  CA  GLN   311      28.125  30.985  -0.646  1.00 25.00           C
ATOM    312  CA  HIS   312      28.726  27.685  -2.494  1.00 25.00           C
ATOM    313  CA  THR   313      26.665  28.947  -5.466  1.00 25.00           C
ATOM    314  CA  ALA   314      28.688  32.199  -5.519  1.00 25.00           C
ATOM    315  CA  ARG   315      31.953  30.198  -5.462  1.00 25.00           C
ATOM    316  CA  GLU   316      30.703  28.031  -8.363  1.00 25.00           C
ATOM    317  CA  ALA   317      29.780  31.174 -10.346  1.00 25.00           C
ATOM    318  CA  VAL   318      33.257  32.639  -9.691  1.00 25.00           C
ATOM    319  CA  SER   319      34.881  29.377 -10.870  1.00 25.00           C
ATOM    320  CA  ARG   320      32.487  27.815 -13.431  1.00 25.00           C
ATOM    321  CA  ARG   321      29.097  26.026 -13.284  1.00 25.00           C
ATOM    322  CA  GLY   322      27.622  23.996 -10.457  1.00 25.00           C
ATOM    323  CA  ILE   323      24.705  25.634  -8.751  1.00 25.00           C
ATOM    324  CA  GLY   324      22.350  22.661  -8.786  1.00 25.00           C
ATOM    325  CA  LEU   325      18.858  23.339  -7.513  1.00 25.00           C
ATOM    326  CA  VAL   326      18.371  26.463  -5.412  1.00 25.00           C
ATOM    327  CA  SER   327      15.094  24.899  -4.221  1.00 25.00           C
ATOM    328  CA  THR   328      13.999  24.919  -7.891  1.00 25.00           C
ATOM    329  CA  SER   329      11.195  23.457 -10.098  1.00 25.00           C
ATOM    330  CA  ASP   330      13.340  20.314 -10.168  1.00 25.00           C
ATOM    331  CA  LYS   331      13.088  20.709 -13.969  1.00 25.00           C
ATOM    332  CA  VAL   332      15.933  23.272 -13.916  1.00 25.00           C
ATOM    333  CA  ASP   333      18.079  20.884 -11.829  1.00 25.00           C
ATOM    334  CA  ALA   334      17.370  18.047 -14.302  1.00 25.00           C
ATOM    335  CA  ASP   335      18.353  20.317 -17.226  1.00 25.00           C
ATOM    336  CA  LEU   336      21.602  21.263 -15.433  1.00 25.00           C
ATOM    337  CA  LEU   337      22.374  17.560 -14.827  1.00 25.00           C
ATOM    338  CA  ARG   338      21.738  16.798 -18.526  1.00 25.00           C
ATOM    339  CA  ARG   339      24.069  19.661 -19.543  1.00 25.00           C
ATOM    340  CA  LEU   340      26.777  18.325 -17.185  1.00 25.00           C
ATOM    341  CA  ILE   341      26.387  14.823 -18.683  1.00 25.00           C
ATOM    342  CA  GLY   342      28.814  15.167 -21.630  1.00 25.00           C
ATOM    343  CA  ASP   343      32.447  14.804 -22.691  1.00 25.00           C
ATOM    344  CA  GLU   344      36.194  15.119 -22.167  1.00 25.00           C
ATOM    345  CA  SER   345      36.711  18.909 -21.975  1.00 25.00           C
ATOM    346  CA  LEU   346      35.255  18.952 -18.433  1.00 25.00           C
ATOM    347  CA  ARG   347      37.593  16.097 -17.410  1.00 25.00           C
ATOM    348  CA  THR   348      40.586  17.994 -18.861  1.00 25.00           C
ATOM    349  CA  ALA   349      39.557  21.140 -16.935  1.00 25.00           C
ATOM    350  CA  ALA   350      39.270  19.099 -13.707  1.00 25.00           C
ATOM    351  CA  ARG   351      42.747  17.611 -14.310  1.00 25.00           C
ATOM    352  CA  GLU   352      44.175  21.117 -14.883  1.00 25.00           C
ATOM    353  CA  VAL   353      42.551  22.337 -11.636  1.00 25.00           C
ATOM    354  CA  ARG   354      44.035  19.355  -9.745  1.00 25.00           C
ATOM    355  CA  GLU   355      47.493  20.121 -11.203  1.00 25.00           C
ATOM    356  CA  GLU   356      47.157  23.785 -10.142  1.00 25.00           C
ATOM    357  CA  MET   357      46.164  22.696  -6.607  1.00 25.00           C
ATOM    358  CA  VAL   358      49.194  20.358  -6.450  1.00 25.00           C
ATOM    359  CA  ALA   359      51.108  23.478  -5.311  1.00 25.00           C
TER
END
