
#######################################################
#                                                     #
#                        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_5-D2
# Molecule2: number of CA atoms  148 ( 1087),  selected  148 , name T0333_D2.pdb
# PARAMETERS: T0333TS393_5-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          2.214
LGA    V     213      V     213          2.271
LGA    A     214      A     214          2.614
LGA    I     215      I     215          4.549
LGA    T     216      T     216          4.194
LGA    M     217      M     217          1.399
LGA    G     218      G     218          4.039
LGA    T     219      T     219          1.533
LGA    I     220      I     220          3.461
LGA    E     221      E     221           #
LGA    L     222      L     222          4.771
LGA    Q     223      Q     223          3.504
LGA    A     224      A     224          2.200
LGA    F     225      F     225          2.869
LGA    G     226      G     226          3.602
LGA    I     227      I     227          2.111
LGA    G     228      G     228          1.703
LGA    A     229      A     229          2.573
LGA    V     230      V     230          1.223
LGA    E     231      E     231          1.257
LGA    P     232      P     232          1.309
LGA    I     233      I     233          1.560
LGA    I     234      I     234          1.893
LGA    A     235      A     235          1.885
LGA    A     236      A     236          1.690
LGA    A     237      A     237          2.443
LGA    G     238      G     238          2.885
LGA    E     239      E     239          2.245
LGA    V     240      V     240          0.983
LGA    D     241      D     241          2.525
LGA    A     242      A     242          3.970
LGA    -       -      D     243           -
LGA    D     243      F     244          1.526
LGA    F     244      V     245          3.608
LGA    V     245      L     246          1.964
LGA    L     246      A     247          1.271
LGA    A     247      L     248          2.059
LGA    L     248      G     249          1.607
LGA    G     249      D     250          2.794
LGA    D     250      L     251          1.434
LGA    L     251      D     252          2.755
LGA    D     252      -       -           -
LGA    I     253      I     253          1.982
LGA    S     254      S     254          2.041
LGA    P     255      P     255          3.955
LGA    L     256      L     256          2.696
LGA    G     257      G     257          3.961
LGA    T     258      T     258          3.870
LGA    L     259      L     259          4.354
LGA    P     260      P     260           #
LGA    R     261      R     261          3.312
LGA    N     262      N     262          1.648
LGA    V     263      V     263          2.041
LGA    R     264      R     264          3.113
LGA    A     265      A     265          1.991
LGA    V     266      V     266          1.724
LGA    G     267      G     267          1.848
LGA    -       -      W     268           -
LGA    W     268      T     269          5.194
LGA    T     269      P     270           -
LGA    -       -      L     271           -
LGA    -       -      H     272           -
LGA    P     270      T     273          3.765
LGA    L     271      L     274          1.789
LGA    H     272      L     275          4.750
LGA    T     273      R     276          2.379
LGA    L     274      T     277          2.040
LGA    L     275      -       -           -
LGA    R     276      C     278          4.464
LGA    T     277      T     279          2.065
LGA    C     278      A     280          3.185
LGA    T     279      V     281          3.014
LGA    A     280      -       -           -
LGA    V     281      V     282          2.723
LGA    V     282      H     283          2.903
LGA    H     283      H     284          1.677
LGA    H     284      G     285          5.351
LGA    G     285      G     286          2.922
LGA    G     286      -       -           -
LGA    G     287      G     287          3.225
LGA    G     288      G     288          2.738
LGA    T     289      T     289          2.830
LGA    V     290      V     290          3.349
LGA    M     291      M     291          3.291
LGA    T     292      T     292          2.014
LGA    A     293      A     293          2.167
LGA    I     294      I     294          3.126
LGA    D     295      D     295          2.705
LGA    A     296      A     296          1.885
LGA    -       -      G     297           -
LGA    G     297      I     298          2.773
LGA    I     298      P     299          2.413
LGA    P     299      Q     300          2.442
LGA    Q     300      L     301          5.052
LGA    L     301      L     302          2.276
LGA    L     302      A     303           #
LGA    A     303      P     304           #
LGA    P     304      D     305          4.416
LGA    D     305      P     306          2.718
LGA    -       -      R     307           -
LGA    P     306      D     308          3.895
LGA    R     307      Q     309          3.837
LGA    D     308      F     310          0.683
LGA    Q     309      Q     311          5.432
LGA    F     310      -       -           -
LGA    Q     311      -       -           -
LGA    H     312      -       -           -
LGA    T     313      H     312          3.432
LGA    A     314      T     313          2.581
LGA    R     315      A     314          3.919
LGA    E     316      R     315          2.497
LGA    A     317      E     316          1.643
LGA    V     318      A     317          3.701
LGA    S     319      V     318          4.087
LGA    R     320      S     319          2.684
LGA    R     321      R     320           -
LGA    -       -      R     321           -
LGA    -       -      G     322           -
LGA    -       -      I     323           -
LGA    -       -      G     324           -
LGA    G     322      L     325          3.787
LGA    I     323      V     326          3.934
LGA    G     324      S     327          3.676
LGA    L     325      T     328          3.892
LGA    V     326      S     329          2.781
LGA    S     327      D     330          3.203
LGA    T     328      -       -           -
LGA    S     329      -       -           -
LGA    D     330      K     331          2.720
LGA    K     331      -       -           -
LGA    V     332      V     332           #
LGA    D     333      D     333          4.180
LGA    A     334      A     334          3.348
LGA    D     335      D     335          2.406
LGA    L     336      L     336          2.425
LGA    L     337      L     337          2.668
LGA    R     338      R     338          1.944
LGA    R     339      R     339          2.761
LGA    L     340      L     340          3.584
LGA    I     341      I     341          2.984
LGA    G     342      G     342          2.999
LGA    D     343      D     343           #
LGA    E     344      E     344          2.856
LGA    S     345      S     345          3.182
LGA    L     346      L     346          2.911
LGA    R     347      R     347          2.363
LGA    T     348      T     348          2.357
LGA    A     349      A     349          2.558
LGA    A     350      A     350          2.356
LGA    R     351      R     351          2.075
LGA    E     352      E     352          1.990
LGA    V     353      V     353          2.111
LGA    R     354      R     354          1.961
LGA    E     355      E     355          2.007
LGA    E     356      E     356          2.021
LGA    M     357      M     357          1.951
LGA    V     358      V     358          2.348
LGA    A     359      A     359          1.977

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  148  148    5.0    130    2.93    66.92     49.069     4.287

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.098511 * X  +   0.970016 * Y  +  -0.222183 * Z  +  36.785461
  Y_new =   0.990325 * X  +  -0.117488 * Y  +  -0.073846 * Z  +  16.105938
  Z_new =  -0.097735 * X  +  -0.212759 * Y  +  -0.972204 * Z  +   6.223203 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.926147    0.215445  [ DEG:  -167.6559     12.3441 ]
  Theta =   0.097891    3.043701  [ DEG:     5.6088    174.3912 ]
  Phi   =   1.471649   -1.669943  [ DEG:    84.3193    -95.6807 ]
 
# 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_5-D2                               
REMARK     2: T0333_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0333TS393_5-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  130   2.93   66.92  49.069
REMARK  ---------------------------------------------------------- 
MOLECULE T0333TS393_5-D2
PFRMAT TS
TARGET T0333
MODEL 5
PARENT N/A
ATOM    212  CA  GLU   212      31.232   7.836  -9.511  1.00 25.00           C
ATOM    213  CA  VAL   213      28.833  10.271  -7.926  1.00 25.00           C
ATOM    214  CA  ALA   214      29.293  11.588  -4.322  1.00 25.00           C
ATOM    215  CA  ILE   215      27.652  13.801  -1.746  1.00 25.00           C
ATOM    216  CA  THR   216      26.993  16.214   1.046  1.00 25.00           C
ATOM    217  CA  MET   217      24.088  13.803   1.795  1.00 25.00           C
ATOM    218  CA  GLY   218      26.826  12.086   3.828  1.00 25.00           C
ATOM    219  CA  THR   219      25.267  13.763   6.918  1.00 25.00           C
ATOM    220  CA  ILE   220      22.035  15.678   7.088  1.00 25.00           C
ATOM    221  CA  GLU   221      20.300  12.575   5.875  1.00 25.00           C
ATOM    222  CA  LEU   222      16.519  12.761   6.543  1.00 25.00           C
ATOM    223  CA  GLN   223      16.152  16.532   6.974  1.00 25.00           C
ATOM    224  CA  ALA   224      17.310  20.118   6.453  1.00 25.00           C
ATOM    225  CA  PHE   225      18.126  18.852   2.977  1.00 25.00           C
ATOM    226  CA  GLY   226      14.345  18.607   2.584  1.00 25.00           C
ATOM    227  CA  ILE   227      14.074  14.856   2.513  1.00 25.00           C
ATOM    228  CA  GLY   228      11.809  15.249  -0.548  1.00 25.00           C
ATOM    229  CA  ALA   229      14.418  17.499  -2.221  1.00 25.00           C
ATOM    230  CA  VAL   230      17.148  14.912  -1.497  1.00 25.00           C
ATOM    231  CA  GLU   231      14.962  12.148  -2.996  1.00 25.00           C
ATOM    232  CA  PRO   232      14.361  14.283  -6.119  1.00 25.00           C
ATOM    233  CA  ILE   233      18.127  14.893  -6.455  1.00 25.00           C
ATOM    234  CA  ILE   234      18.791  11.135  -6.135  1.00 25.00           C
ATOM    235  CA  ALA   235      16.165  10.418  -8.830  1.00 25.00           C
ATOM    236  CA  ALA   236      17.785  13.013 -11.133  1.00 25.00           C
ATOM    237  CA  ALA   237      21.218  11.417 -10.558  1.00 25.00           C
ATOM    238  CA  GLY   238      19.777   7.964 -11.374  1.00 25.00           C
ATOM    239  CA  GLU   239      18.214   9.347 -14.585  1.00 25.00           C
ATOM    240  CA  VAL   240      21.018   9.998 -16.985  1.00 25.00           C
ATOM    241  CA  ASP   241      23.680   7.319 -16.595  1.00 25.00           C
ATOM    242  CA  ALA   242      24.709   9.541 -13.629  1.00 25.00           C
ATOM    243  CA  ASP   243      24.803   7.743 -10.296  1.00 25.00           C
ATOM    244  CA  PHE   244      24.213   8.787  -6.676  1.00 25.00           C
ATOM    245  CA  VAL   245      24.840   9.233  -2.953  1.00 25.00           C
ATOM    246  CA  LEU   246      27.193   8.665  -0.017  1.00 25.00           C
ATOM    247  CA  ALA   247      24.206   7.946   2.132  1.00 25.00           C
ATOM    248  CA  LEU   248      24.444   8.144   5.929  1.00 25.00           C
ATOM    249  CA  GLY   249      23.050   7.772   9.497  1.00 25.00           C
ATOM    250  CA  ASP   250      19.663   7.997   7.878  1.00 25.00           C
ATOM    251  CA  LEU   251      19.356   4.317   8.706  1.00 25.00           C
ATOM    252  CA  ASP   252      16.282   3.907   6.509  1.00 25.00           C
ATOM    253  CA  ILE   253      15.545   5.017   2.972  1.00 25.00           C
ATOM    254  CA  SER   254      13.086   2.115   2.537  1.00 25.00           C
ATOM    255  CA  PRO   255      10.936   4.254   0.198  1.00 25.00           C
ATOM    256  CA  LEU   256      13.933   4.632  -1.999  1.00 25.00           C
ATOM    257  CA  GLY   257      13.143   2.595  -5.075  1.00 25.00           C
ATOM    258  CA  THR   258      13.590  -0.271  -7.536  1.00 25.00           C
ATOM    259  CA  LEU   259      16.298   1.282  -9.749  1.00 25.00           C
ATOM    260  CA  PRO   260      18.637  -1.229  -8.011  1.00 25.00           C
ATOM    261  CA  ARG   261      21.228  -1.397 -10.791  1.00 25.00           C
ATOM    262  CA  ASN   262      22.233   2.250 -10.370  1.00 25.00           C
ATOM    263  CA  VAL   263      22.610   3.119  -6.692  1.00 25.00           C
ATOM    264  CA  ARG   264      24.000   4.248  -3.312  1.00 25.00           C
ATOM    265  CA  ALA   265      23.289   3.349   0.283  1.00 25.00           C
ATOM    266  CA  VAL   266      26.727   3.365   1.885  1.00 25.00           C
ATOM    267  CA  GLY   267      28.306   3.118   5.343  1.00 25.00           C
ATOM    268  CA  TRP   268      31.653   1.379   4.617  1.00 25.00           C
ATOM    269  CA  THR   269      35.077   1.682   3.079  1.00 25.00           C
ATOM    270  CA  PRO   270      36.722   4.052   0.607  1.00 25.00           C
ATOM    271  CA  LEU   271      35.710   7.151  -1.425  1.00 25.00           C
ATOM    272  CA  HIS   272      39.221   7.932  -2.741  1.00 25.00           C
ATOM    273  CA  THR   273      38.667   5.561  -5.697  1.00 25.00           C
ATOM    274  CA  LEU   274      35.319   7.256  -6.462  1.00 25.00           C
ATOM    275  CA  LEU   275      37.006  10.693  -6.350  1.00 25.00           C
ATOM    276  CA  ARG   276      38.035   9.778  -9.895  1.00 25.00           C
ATOM    277  CA  THR   277      34.699  11.462 -10.727  1.00 25.00           C
ATOM    278  CA  CYS   278      32.920  13.219  -7.860  1.00 25.00           C
ATOM    279  CA  THR   279      30.573  14.485 -10.590  1.00 25.00           C
ATOM    280  CA  ALA   280      27.278  14.949  -8.834  1.00 25.00           C
ATOM    281  CA  VAL   281      25.036  13.739  -6.038  1.00 25.00           C
ATOM    282  CA  VAL   282      23.771  17.000  -4.471  1.00 25.00           C
ATOM    283  CA  HIS   283      23.422  18.902  -1.270  1.00 25.00           C
ATOM    284  CA  HIS   284      23.736  19.809   2.403  1.00 25.00           C
ATOM    285  CA  GLY   285      26.390  20.070   5.099  1.00 25.00           C
ATOM    286  CA  GLY   286      28.322  23.097   6.390  1.00 25.00           C
ATOM    287  CA  GLY   287      29.632  23.185   2.834  1.00 25.00           C
ATOM    288  CA  GLY   288      32.231  20.656   4.066  1.00 25.00           C
ATOM    289  CA  THR   289      30.904  18.051   1.593  1.00 25.00           C
ATOM    290  CA  VAL   290      31.117  20.607  -1.252  1.00 25.00           C
ATOM    291  CA  MET   291      34.720  21.448  -0.259  1.00 25.00           C
ATOM    292  CA  THR   292      35.607  17.722  -0.231  1.00 25.00           C
ATOM    293  CA  ALA   293      34.047  17.298  -3.702  1.00 25.00           C
ATOM    294  CA  ILE   294      36.052  20.293  -4.996  1.00 25.00           C
ATOM    295  CA  ASP   295      39.266  18.800  -3.545  1.00 25.00           C
ATOM    296  CA  ALA   296      38.495  15.445  -5.225  1.00 25.00           C
ATOM    297  CA  GLY   297      36.482  16.802  -8.147  1.00 25.00           C
ATOM    298  CA  ILE   298      33.764  18.971  -9.627  1.00 25.00           C
ATOM    299  CA  PRO   299      31.064  19.751  -7.103  1.00 25.00           C
ATOM    300  CA  GLN   300      28.769  17.790  -4.841  1.00 25.00           C
ATOM    301  CA  LEU   301      26.913  21.069  -4.215  1.00 25.00           C
ATOM    302  CA  LEU   302      26.151  23.125  -1.091  1.00 25.00           C
ATOM    303  CA  ALA   303      24.835  24.729   2.115  1.00 25.00           C
ATOM    304  CA  PRO   304      21.025  25.053   2.006  1.00 25.00           C
ATOM    305  CA  ASP   305      18.709  26.987  -0.330  1.00 25.00           C
ATOM    306  CA  PRO   306      20.472  30.243   0.645  1.00 25.00           C
ATOM    307  CA  ARG   307      23.807  32.104   1.071  1.00 25.00           C
ATOM    308  CA  ASP   308      25.221  29.541   3.508  1.00 25.00           C
ATOM    309  CA  GLN   309      28.645  28.008   4.100  1.00 25.00           C
ATOM    310  CA  PHE   310      29.422  30.827   1.635  1.00 25.00           C
ATOM    311  CA  GLN   311      32.607  29.446   0.018  1.00 25.00           C
ATOM    312  CA  HIS   312      30.522  26.985  -2.046  1.00 25.00           C
ATOM    313  CA  THR   313      28.229  29.837  -3.176  1.00 25.00           C
ATOM    314  CA  ALA   314      31.280  31.923  -4.182  1.00 25.00           C
ATOM    315  CA  ARG   315      32.682  28.963  -6.165  1.00 25.00           C
ATOM    316  CA  GLU   316      29.313  28.522  -7.933  1.00 25.00           C
ATOM    317  CA  ALA   317      29.250  32.251  -8.798  1.00 25.00           C
ATOM    318  CA  VAL   318      32.810  32.014 -10.192  1.00 25.00           C
ATOM    319  CA  SER   319      31.806  28.982 -12.306  1.00 25.00           C
ATOM    320  CA  ARG   320      28.071  28.455 -12.538  1.00 25.00           C
ATOM    321  CA  ARG   321      24.954  28.004 -10.413  1.00 25.00           C
ATOM    322  CA  GLY   322      26.671  24.958  -8.903  1.00 25.00           C
ATOM    323  CA  ILE   323      24.007  24.822  -6.171  1.00 25.00           C
ATOM    324  CA  GLY   324      23.633  21.575  -8.065  1.00 25.00           C
ATOM    325  CA  LEU   325      20.126  20.293  -7.650  1.00 25.00           C
ATOM    326  CA  VAL   326      18.595  23.093  -5.645  1.00 25.00           C
ATOM    327  CA  SER   327      15.031  23.249  -4.393  1.00 25.00           C
ATOM    328  CA  THR   328      13.057  24.151  -7.490  1.00 25.00           C
ATOM    329  CA  SER   329      11.753  21.131  -9.458  1.00 25.00           C
ATOM    330  CA  ASP   330      15.003  19.434 -10.309  1.00 25.00           C
ATOM    331  CA  LYS   331      14.417  18.961 -14.065  1.00 25.00           C
ATOM    332  CA  VAL   332      16.501  22.087 -14.808  1.00 25.00           C
ATOM    333  CA  ASP   333      19.319  20.770 -12.574  1.00 25.00           C
ATOM    334  CA  ALA   334      19.212  17.397 -14.385  1.00 25.00           C
ATOM    335  CA  ASP   335      19.388  19.182 -17.769  1.00 25.00           C
ATOM    336  CA  LEU   336      22.389  21.230 -16.562  1.00 25.00           C
ATOM    337  CA  LEU   337      24.128  18.030 -15.376  1.00 25.00           C
ATOM    338  CA  ARG   338      23.477  16.389 -18.775  1.00 25.00           C
ATOM    339  CA  ARG   339      24.921  19.454 -20.559  1.00 25.00           C
ATOM    340  CA  LEU   340      28.025  19.326 -18.320  1.00 25.00           C
ATOM    341  CA  ILE   341      28.459  15.600 -19.092  1.00 25.00           C
ATOM    342  CA  GLY   342      28.544  15.717 -22.852  1.00 25.00           C
ATOM    343  CA  ASP   343      32.088  15.070 -23.950  1.00 25.00           C
ATOM    344  CA  GLU   344      35.471  16.546 -23.008  1.00 25.00           C
ATOM    345  CA  SER   345      35.829  20.317 -22.445  1.00 25.00           C
ATOM    346  CA  LEU   346      34.473  19.939 -18.883  1.00 25.00           C
ATOM    347  CA  ARG   347      36.960  17.104 -18.210  1.00 25.00           C
ATOM    348  CA  THR   348      39.826  19.273 -19.534  1.00 25.00           C
ATOM    349  CA  ALA   349      38.718  22.160 -17.274  1.00 25.00           C
ATOM    350  CA  ALA   350      38.611  19.794 -14.264  1.00 25.00           C
ATOM    351  CA  ARG   351      42.130  18.534 -15.096  1.00 25.00           C
ATOM    352  CA  GLU   352      43.390  22.143 -15.345  1.00 25.00           C
ATOM    353  CA  VAL   353      41.806  22.955 -11.954  1.00 25.00           C
ATOM    354  CA  ARG   354      43.471  19.870 -10.411  1.00 25.00           C
ATOM    355  CA  GLU   355      46.850  20.934 -11.866  1.00 25.00           C
ATOM    356  CA  GLU   356      46.386  24.455 -10.431  1.00 25.00           C
ATOM    357  CA  MET   357      45.542  22.974  -7.002  1.00 25.00           C
ATOM    358  CA  VAL   358      48.673  20.773  -7.156  1.00 25.00           C
ATOM    359  CA  ALA   359      52.147  21.003  -5.611  1.00 25.00           C
TER
END
