
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms  148 ( 1087),  selected  148 , name T0333_D2.pdb
# PARAMETERS: T0333TS168_4-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          2.446
LGA    A     214      A     214          3.501
LGA    I     215      I     215          3.993
LGA    T     216      -       -           -
LGA    M     217      T     216          3.546
LGA    G     218      M     217          1.751
LGA    T     219      G     218          3.632
LGA    I     220      T     219           #
LGA    E     221      I     220           -
LGA    L     222      E     221           #
LGA    Q     223      L     222           #
LGA    A     224      Q     223           -
LGA    F     225      A     224           -
LGA    -       -      F     225           -
LGA    G     226      G     226           #
LGA    I     227      I     227          4.359
LGA    G     228      G     228          4.071
LGA    A     229      A     229          4.686
LGA    V     230      V     230          1.718
LGA    E     231      E     231          0.793
LGA    P     232      P     232          1.470
LGA    I     233      I     233          0.568
LGA    I     234      I     234          1.312
LGA    A     235      A     235          2.110
LGA    A     236      A     236          1.886
LGA    A     237      A     237          2.526
LGA    G     238      G     238          3.482
LGA    E     239      E     239          3.164
LGA    V     240      V     240          2.548
LGA    -       -      D     241           -
LGA    D     241      A     242          1.392
LGA    A     242      D     243          3.282
LGA    D     243      F     244          1.035
LGA    F     244      V     245          1.380
LGA    -       -      L     246           -
LGA    V     245      A     247          3.221
LGA    L     246      L     248          3.192
LGA    A     247      G     249          3.027
LGA    L     248      D     250          4.356
LGA    G     249      L     251           #
LGA    D     250      -       -           -
LGA    L     251      -       -           -
LGA    D     252      D     252          4.705
LGA    I     253      I     253          2.619
LGA    S     254      S     254          3.128
LGA    P     255      P     255          3.668
LGA    L     256      L     256          2.470
LGA    G     257      G     257          4.003
LGA    T     258      T     258          4.758
LGA    L     259      L     259           #
LGA    P     260      P     260          4.428
LGA    R     261      R     261          3.819
LGA    -       -      N     262           -
LGA    N     262      V     263          4.902
LGA    V     263      R     264          2.594
LGA    R     264      A     265          1.974
LGA    A     265      V     266          4.914
LGA    V     266      G     267          3.629
LGA    G     267      -       -           -
LGA    W     268      W     268           #
LGA    T     269      T     269          0.685
LGA    P     270      P     270          3.069
LGA    L     271      L     271          2.841
LGA    H     272      H     272          2.161
LGA    T     273      T     273          2.924
LGA    L     274      L     274          2.661
LGA    L     275      L     275          3.629
LGA    R     276      R     276          4.456
LGA    T     277      T     277          4.094
LGA    C     278      C     278          2.645
LGA    -       -      T     279           -
LGA    T     279      A     280          4.010
LGA    A     280      V     281          4.832
LGA    V     281      V     282           #
LGA    V     282      H     283          0.381
LGA    H     283      H     284          2.016
LGA    H     284      -       -           -
LGA    G     285      -       -           -
LGA    G     286      G     285          4.214
LGA    G     287      G     286          1.877
LGA    G     288      G     287          3.183
LGA    T     289      -       -           -
LGA    V     290      -       -           -
LGA    M     291      G     288          0.526
LGA    T     292      T     289          5.115
LGA    A     293      V     290          5.370
LGA    I     294      M     291          1.284
LGA    D     295      -       -           -
LGA    A     296      T     292          3.513
LGA    G     297      A     293          3.502
LGA    I     298      I     294          3.445
LGA    -       -      D     295           -
LGA    -       -      A     296           -
LGA    -       -      G     297           -
LGA    -       -      I     298           -
LGA    -       -      P     299           -
LGA    P     299      Q     300          3.327
LGA    Q     300      L     301           #
LGA    L     301      L     302          4.798
LGA    L     302      A     303          2.937
LGA    A     303      P     304          2.706
LGA    P     304      D     305          4.909
LGA    D     305      P     306          3.657
LGA    P     306      R     307          3.035
LGA    R     307      D     308           #
LGA    D     308      Q     309          4.725
LGA    Q     309      F     310           #
LGA    F     310      Q     311          0.948
LGA    Q     311      H     312          5.194
LGA    H     312      -       -           -
LGA    T     313      -       -           -
LGA    A     314      T     313          1.737
LGA    R     315      A     314          2.597
LGA    E     316      R     315          3.569
LGA    A     317      E     316          1.397
LGA    V     318      A     317          2.829
LGA    -       -      V     318           -
LGA    -       -      S     319           -
LGA    -       -      R     320           -
LGA    S     319      R     321          2.640
LGA    R     320      G     322          2.645
LGA    R     321      I     323          3.890
LGA    G     322      G     324          3.675
LGA    I     323      L     325           #
LGA    G     324      V     326          3.171
LGA    L     325      S     327          2.524
LGA    V     326      T     328          0.899
LGA    S     327      S     329          4.543
LGA    T     328      D     330           #
LGA    S     329      -       -           -
LGA    D     330      K     331          2.498
LGA    K     331      -       -           -
LGA    V     332      V     332          4.876
LGA    D     333      D     333          4.110
LGA    A     334      A     334          3.391
LGA    D     335      D     335          2.059
LGA    L     336      L     336          1.581
LGA    L     337      L     337          1.741
LGA    R     338      R     338          1.200
LGA    R     339      R     339          1.462
LGA    L     340      L     340          2.014
LGA    I     341      I     341          1.381
LGA    G     342      G     342          2.537
LGA    D     343      D     343           #
LGA    E     344      E     344          4.381
LGA    S     345      S     345          4.775
LGA    L     346      L     346          3.998
LGA    R     347      R     347          2.924
LGA    T     348      T     348          3.149
LGA    A     349      A     349          3.502
LGA    A     350      A     350          2.743
LGA    R     351      R     351          1.915
LGA    E     352      E     352          2.346
LGA    V     353      V     353          2.864
LGA    R     354      R     354          1.951
LGA    E     355      E     355          1.838
LGA    E     356      E     356          2.678
LGA    M     357      M     357          2.665
LGA    V     358      V     358          2.255
LGA    A     359      A     359          2.326

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  148  148    5.0    117    3.19    62.39     42.023     3.554

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.484556 * X  +  -0.670014 * Y  +  -0.562394 * Z  +  29.648060
  Y_new =  -0.340367 * X  +   0.736659 * Y  +  -0.584367 * Z  +  20.014849
  Z_new =   0.805826 * X  +  -0.091738 * Y  +  -0.585003 * Z  +   9.424643 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.986043    0.155550  [ DEG:  -171.0876      8.9124 ]
  Theta =  -0.937069   -2.204523  [ DEG:   -53.6901   -126.3099 ]
  Phi   =  -2.529238    0.612355  [ DEG:  -144.9146     35.0854 ]
 
# 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_4-D2                               
REMARK     2: T0333_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0333TS168_4-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   3.19   62.39  42.023
REMARK  ---------------------------------------------------------- 
MOLECULE T0333TS168_4-D2
PFRMAT TS
TARGET T0333
MODEL 4
PARENT N/A
ATOM    212  CA  GLU   212      30.575  11.108 -11.802  1.00 25.00           C
ATOM    213  CA  VAL   213      28.106  11.788  -9.015  1.00 25.00           C
ATOM    214  CA  ALA   214      26.473  13.199  -5.851  1.00 25.00           C
ATOM    215  CA  ILE   215      23.183  15.107  -5.955  1.00 25.00           C
ATOM    216  CA  THR   216      21.004  14.809  -2.864  1.00 25.00           C
ATOM    217  CA  MET   217      22.799  13.533   0.159  1.00 25.00           C
ATOM    218  CA  GLY   218      25.437  14.365   2.751  1.00 25.00           C
ATOM    219  CA  THR   219      22.905  14.078   5.525  1.00 25.00           C
ATOM    220  CA  ILE   220      21.109  10.814   4.491  1.00 25.00           C
ATOM    221  CA  GLU   221      17.421  11.449   4.008  1.00 25.00           C
ATOM    222  CA  LEU   222      18.184  15.077   3.457  1.00 25.00           C
ATOM    223  CA  GLN   223      16.611  18.399   2.315  1.00 25.00           C
ATOM    224  CA  ALA   224      16.724  19.873  -1.205  1.00 25.00           C
ATOM    225  CA  PHE   225      13.891  22.354  -0.429  1.00 25.00           C
ATOM    226  CA  GLY   226      12.100  19.244   0.692  1.00 25.00           C
ATOM    227  CA  ILE   227      12.371  15.498   0.559  1.00 25.00           C
ATOM    228  CA  GLY   228      10.691  15.451  -2.882  1.00 25.00           C
ATOM    229  CA  ALA   229      13.588  17.478  -4.352  1.00 25.00           C
ATOM    230  CA  VAL   230      16.108  15.039  -2.812  1.00 25.00           C
ATOM    231  CA  GLU   231      14.180  12.076  -4.287  1.00 25.00           C
ATOM    232  CA  PRO   232      14.175  13.761  -7.727  1.00 25.00           C
ATOM    233  CA  ILE   233      17.951  14.355  -7.468  1.00 25.00           C
ATOM    234  CA  ILE   234      18.488  10.681  -6.530  1.00 25.00           C
ATOM    235  CA  ALA   235      16.372   9.581  -9.526  1.00 25.00           C
ATOM    236  CA  ALA   236      18.413  11.854 -11.835  1.00 25.00           C
ATOM    237  CA  ALA   237      21.667  10.383 -10.448  1.00 25.00           C
ATOM    238  CA  GLY   238      20.340   6.838 -11.032  1.00 25.00           C
ATOM    239  CA  GLU   239      19.394   7.758 -14.627  1.00 25.00           C
ATOM    240  CA  VAL   240      22.316  10.115 -15.455  1.00 25.00           C
ATOM    241  CA  ASP   241      25.312   7.769 -15.700  1.00 25.00           C
ATOM    242  CA  ALA   242      26.212   7.852 -12.004  1.00 25.00           C
ATOM    243  CA  ASP   243      25.325   6.865  -8.456  1.00 25.00           C
ATOM    244  CA  PHE   244      26.773   6.957  -4.934  1.00 25.00           C
ATOM    245  CA  VAL   245      27.965   9.304  -2.247  1.00 25.00           C
ATOM    246  CA  LEU   246      26.413   9.727   1.138  1.00 25.00           C
ATOM    247  CA  ALA   247      28.211   8.333   4.178  1.00 25.00           C
ATOM    248  CA  LEU   248      28.390   5.053   6.180  1.00 25.00           C
ATOM    249  CA  GLY   249      26.007   2.701   7.951  1.00 25.00           C
ATOM    250  CA  ASP   250      22.305   2.023   7.346  1.00 25.00           C
ATOM    251  CA  LEU   251      18.525   2.428   7.407  1.00 25.00           C
ATOM    252  CA  ASP   252      15.244   1.889   5.560  1.00 25.00           C
ATOM    253  CA  ILE   253      15.026   4.546   2.923  1.00 25.00           C
ATOM    254  CA  SER   254      13.319   2.607   0.096  1.00 25.00           C
ATOM    255  CA  PRO   255      10.641   5.330  -0.188  1.00 25.00           C
ATOM    256  CA  LEU   256      12.713   6.534  -3.149  1.00 25.00           C
ATOM    257  CA  GLY   257      12.558   3.275  -5.193  1.00 25.00           C
ATOM    258  CA  THR   258      11.145   1.747  -8.325  1.00 25.00           C
ATOM    259  CA  LEU   259      14.163  -0.493  -8.776  1.00 25.00           C
ATOM    260  CA  PRO   260      17.941  -0.775  -9.084  1.00 25.00           C
ATOM    261  CA  ARG   261      21.710  -0.508  -9.199  1.00 25.00           C
ATOM    262  CA  ASN   262      23.354   0.128  -5.907  1.00 25.00           C
ATOM    263  CA  VAL   263      21.053   2.418  -3.982  1.00 25.00           C
ATOM    264  CA  ARG   264      22.796   1.445  -0.745  1.00 25.00           C
ATOM    265  CA  ALA   265      23.656  -0.370   2.513  1.00 25.00           C
ATOM    266  CA  VAL   266      26.266  -0.102   5.325  1.00 25.00           C
ATOM    267  CA  GLY   267      30.030   0.421   5.203  1.00 25.00           C
ATOM    268  CA  TRP   268      33.228   2.408   5.757  1.00 25.00           C
ATOM    269  CA  THR   269      32.944   5.851   4.177  1.00 25.00           C
ATOM    270  CA  PRO   270      36.508   7.179   4.586  1.00 25.00           C
ATOM    271  CA  LEU   271      36.086  10.212   2.380  1.00 25.00           C
ATOM    272  CA  HIS   272      39.324  11.630   0.905  1.00 25.00           C
ATOM    273  CA  THR   273      39.523   8.693  -1.545  1.00 25.00           C
ATOM    274  CA  LEU   274      35.883   9.280  -2.583  1.00 25.00           C
ATOM    275  CA  LEU   275      36.616  12.998  -3.136  1.00 25.00           C
ATOM    276  CA  ARG   276      39.463  12.205  -5.513  1.00 25.00           C
ATOM    277  CA  THR   277      37.151   9.765  -7.304  1.00 25.00           C
ATOM    278  CA  CYS   278      33.347  10.176  -6.977  1.00 25.00           C
ATOM    279  CA  THR   279      32.441  13.832  -6.884  1.00 25.00           C
ATOM    280  CA  ALA   280      31.411  12.855  -3.361  1.00 25.00           C
ATOM    281  CA  VAL   281      29.121  15.604  -1.965  1.00 25.00           C
ATOM    282  CA  VAL   282      26.128  17.603  -3.195  1.00 25.00           C
ATOM    283  CA  HIS   283      23.689  18.463  -0.373  1.00 25.00           C
ATOM    284  CA  HIS   284      21.277  20.364   1.872  1.00 25.00           C
ATOM    285  CA  GLY   285      23.029  22.619   4.405  1.00 25.00           C
ATOM    286  CA  GLY   286      26.356  23.984   3.302  1.00 25.00           C
ATOM    287  CA  GLY   287      28.386  21.175   4.817  1.00 25.00           C
ATOM    288  CA  GLY   288      30.958  18.880   6.488  1.00 25.00           C
ATOM    289  CA  THR   289      30.875  16.541   3.457  1.00 25.00           C
ATOM    290  CA  VAL   290      31.396  19.521   1.110  1.00 25.00           C
ATOM    291  CA  MET   291      34.363  20.701   3.227  1.00 25.00           C
ATOM    292  CA  THR   292      35.875  17.185   3.110  1.00 25.00           C
ATOM    293  CA  ALA   293      35.448  17.101  -0.696  1.00 25.00           C
ATOM    294  CA  ILE   294      37.149  20.520  -0.985  1.00 25.00           C
ATOM    295  CA  ASP   295      40.049  19.291   1.191  1.00 25.00           C
ATOM    296  CA  ALA   296      40.406  16.172  -1.004  1.00 25.00           C
ATOM    297  CA  GLY   297      39.152  17.556  -4.351  1.00 25.00           C
ATOM    298  CA  ILE   298      35.669  17.739  -5.700  1.00 25.00           C
ATOM    299  CA  PRO   299      32.397  19.517  -6.445  1.00 25.00           C
ATOM    300  CA  GLN   300      30.858  20.822  -3.236  1.00 25.00           C
ATOM    301  CA  LEU   301      27.570  21.707  -1.516  1.00 25.00           C
ATOM    302  CA  LEU   302      24.180  22.389  -3.072  1.00 25.00           C
ATOM    303  CA  ALA   303      22.756  24.611  -0.338  1.00 25.00           C
ATOM    304  CA  PRO   304      20.515  26.801  -2.447  1.00 25.00           C
ATOM    305  CA  ASP   305      17.688  29.070  -3.511  1.00 25.00           C
ATOM    306  CA  PRO   306      17.357  29.242   0.243  1.00 25.00           C
ATOM    307  CA  ARG   307      19.824  32.119   0.727  1.00 25.00           C
ATOM    308  CA  ASP   308      23.015  34.176   1.099  1.00 25.00           C
ATOM    309  CA  GLN   309      24.600  32.374  -1.872  1.00 25.00           C
ATOM    310  CA  PHE   310      25.240  29.308   0.325  1.00 25.00           C
ATOM    311  CA  GLN   311      29.039  29.273   0.816  1.00 25.00           C
ATOM    312  CA  HIS   312      29.380  26.535  -1.841  1.00 25.00           C
ATOM    313  CA  THR   313      27.233  28.582  -4.262  1.00 25.00           C
ATOM    314  CA  ALA   314      29.406  31.669  -3.618  1.00 25.00           C
ATOM    315  CA  ARG   315      32.568  29.611  -4.274  1.00 25.00           C
ATOM    316  CA  GLU   316      31.066  28.299  -7.543  1.00 25.00           C
ATOM    317  CA  ALA   317      30.194  31.873  -8.606  1.00 25.00           C
ATOM    318  CA  VAL   318      33.767  33.005  -7.821  1.00 25.00           C
ATOM    319  CA  SER   319      35.168  30.098  -9.884  1.00 25.00           C
ATOM    320  CA  ARG   320      33.070  28.367 -12.563  1.00 25.00           C
ATOM    321  CA  ARG   321      31.507  25.089 -11.354  1.00 25.00           C
ATOM    322  CA  GLY   322      29.040  23.362  -8.968  1.00 25.00           C
ATOM    323  CA  ILE   323      25.807  24.680  -7.445  1.00 25.00           C
ATOM    324  CA  GLY   324      23.092  27.019  -8.700  1.00 25.00           C
ATOM    325  CA  LEU   325      19.522  25.651  -8.792  1.00 25.00           C
ATOM    326  CA  VAL   326      18.801  23.489  -5.778  1.00 25.00           C
ATOM    327  CA  SER   327      15.007  23.351  -5.967  1.00 25.00           C
ATOM    328  CA  THR   328      14.503  25.583  -9.012  1.00 25.00           C
ATOM    329  CA  SER   329      12.436  22.657 -10.330  1.00 25.00           C
ATOM    330  CA  ASP   330      14.824  19.731 -10.212  1.00 25.00           C
ATOM    331  CA  LYS   331      14.427  18.990 -13.948  1.00 25.00           C
ATOM    332  CA  VAL   332      16.837  21.844 -14.796  1.00 25.00           C
ATOM    333  CA  ASP   333      19.377  20.482 -12.274  1.00 25.00           C
ATOM    334  CA  ALA   334      19.066  16.988 -13.811  1.00 25.00           C
ATOM    335  CA  ASP   335      19.614  18.451 -17.307  1.00 25.00           C
ATOM    336  CA  LEU   336      22.714  20.324 -16.064  1.00 25.00           C
ATOM    337  CA  LEU   337      24.070  17.098 -14.508  1.00 25.00           C
ATOM    338  CA  ARG   338      23.479  15.233 -17.799  1.00 25.00           C
ATOM    339  CA  ARG   339      25.309  17.994 -19.722  1.00 25.00           C
ATOM    340  CA  LEU   340      28.244  17.788 -17.271  1.00 25.00           C
ATOM    341  CA  ILE   341      28.376  13.986 -17.709  1.00 25.00           C
ATOM    342  CA  GLY   342      28.250  13.504 -21.433  1.00 25.00           C
ATOM    343  CA  ASP   343      31.904  13.232 -22.312  1.00 25.00           C
ATOM    344  CA  GLU   344      35.488  14.415 -22.547  1.00 25.00           C
ATOM    345  CA  SER   345      35.857  18.225 -22.645  1.00 25.00           C
ATOM    346  CA  LEU   346      34.130  18.504 -19.238  1.00 25.00           C
ATOM    347  CA  ARG   347      36.479  15.842 -17.802  1.00 25.00           C
ATOM    348  CA  THR   348      39.509  17.733 -19.186  1.00 25.00           C
ATOM    349  CA  ALA   349      38.225  20.984 -17.620  1.00 25.00           C
ATOM    350  CA  ALA   350      37.760  19.209 -14.258  1.00 25.00           C
ATOM    351  CA  ARG   351      41.323  17.820 -14.470  1.00 25.00           C
ATOM    352  CA  GLU   352      42.669  21.323 -15.236  1.00 25.00           C
ATOM    353  CA  VAL   353      40.757  22.741 -12.236  1.00 25.00           C
ATOM    354  CA  ARG   354      42.193  19.992  -9.990  1.00 25.00           C
ATOM    355  CA  GLU   355      45.725  20.774 -11.249  1.00 25.00           C
ATOM    356  CA  GLU   356      45.181  24.497 -10.536  1.00 25.00           C
ATOM    357  CA  MET   357      43.957  23.668  -7.004  1.00 25.00           C
ATOM    358  CA  VAL   358      47.044  21.478  -6.421  1.00 25.00           C
ATOM    359  CA  ALA   359      49.420  23.777  -4.583  1.00 25.00           C
TER
END
