
#######################################################
#                                                     #
#                        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   74 (   74),  selected   74 , name T0289TS393_1-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS393_1-D2.T0289_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      I     224           -
LGA    I     224      M     225          4.805
LGA    M     225      E     226          2.791
LGA    E     226      K     227          4.947
LGA    K     227      V     228          2.574
LGA    V     228      D     229          4.928
LGA    D     229      Y     230          5.003
LGA    Y     230      P     231          2.143
LGA    P     231      R     232          2.291
LGA    R     232      N     233          3.058
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    N     233      G     236          2.201
LGA    E     234      D     237          3.063
LGA    S     235      V     238          5.354
LGA    G     236      A     239           -
LGA    D     237      A     240           -
LGA    V     238      V     241           -
LGA    A     239      -       -           -
LGA    A     240      I     242           #
LGA    -       -      H     243           -
LGA    -       -      P     244           -
LGA    -       -      N     245           -
LGA    V     241      L     246          3.728
LGA    I     242      Q     247          2.624
LGA    H     243      D     248          3.179
LGA    P     244      -       -           -
LGA    N     245      -       -           -
LGA    L     246      -       -           -
LGA    Q     247      -       -           -
LGA    D     248      -       -           -
LGA    Q     249      -       -           -
LGA    D     250      -       -           -
LGA    W     251      -       -           -
LGA    K     252      -       -           -
LGA    P     253      -       -           -
LGA    L     254      -       -           -
LGA    H     255      -       -           -
LGA    P     256      -       -           -
LGA    G     257      -       -           -
LGA    D     258      -       -           -
LGA    P     259      Q     249          5.363
LGA    V     260      D     250          3.054
LGA    F     261      W     251          2.434
LGA    -       -      K     252           -
LGA    V     262      P     253          3.226
LGA    S     263      L     254          0.873
LGA    L     264      H     255          1.331
LGA    D     265      P     256          3.575
LGA    G     266      G     257          3.352
LGA    -       -      D     258           -
LGA    -       -      P     259           -
LGA    -       -      V     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      S     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    -       -      K     267           -
LGA    -       -      V     268           -
LGA    -       -      I     269           -
LGA    K     267      P     270          3.077
LGA    V     268      L     271          3.716
LGA    I     269      G     272          3.226
LGA    P     270      G     273          4.236
LGA    L     271      -       -           -
LGA    G     272      -       -           -
LGA    G     273      -       -           -
LGA    D     274      -       -           -
LGA    C     275      -       -           -
LGA    T     276      -       -           -
LGA    V     277      -       -           -
LGA    Y     278      D     274           #
LGA    P     279      C     275           -
LGA    V     280      T     276           -
LGA    F     281      V     277           #
LGA    V     282      Y     278           #
LGA    N     283      P     279          2.411
LGA    E     284      V     280          2.438
LGA    A     285      F     281          3.721
LGA    A     286      -       -           -
LGA    Y     287      V     282          1.945
LGA    Y     288      -       -           -
LGA    E     289      -       -           -
LGA    K     290      -       -           -
LGA    K     291      N     283          4.383
LGA    -       -      E     284           -
LGA    -       -      A     285           -
LGA    -       -      A     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      E     289           -
LGA    -       -      K     290           -
LGA    -       -      K     291           -
LGA    -       -      E     292           -
LGA    -       -      A     293           -
LGA    E     292      F     294           #
LGA    A     293      A     295           -
LGA    F     294      K     296           -
LGA    A     295      T     297           -
LGA    K     296      -       -           -
LGA    T     297      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   74   74    5.0     32    3.47     3.12     23.589     0.896

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.164199 * X  +   0.963825 * Y  +   0.209954 * Z  +  31.404701
  Y_new =  -0.984829 * X  +  -0.172288 * Y  +   0.020705 * Z  +  32.021919
  Z_new =   0.056129 * X  +  -0.203369 * Y  +   0.977492 * Z  +  24.681252 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.205126    2.936467  [ DEG:   -11.7529    168.2471 ]
  Theta =  -0.056158   -3.085434  [ DEG:    -3.2176   -176.7824 ]
  Phi   =  -1.736006    1.405587  [ DEG:   -99.4658     80.5342 ]
 
# 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: T0289TS393_1-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS393_1-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   74   74   5.0   32   3.47    3.12  23.589
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS393_1-D2
PFRMAT TS
TARGET T0289
MODEL 1
PARENT N/A
ATOM    224  CA  ILE   224      23.047  29.730  27.126  1.00 25.00           C
ATOM    225  CA  MET   225      19.980  31.050  25.302  1.00 25.00           C
ATOM    226  CA  GLU   226      17.553  32.859  27.642  1.00 25.00           C
ATOM    227  CA  LYS   227      19.399  36.197  28.127  1.00 25.00           C
ATOM    228  CA  VAL   228      19.432  34.780  31.656  1.00 25.00           C
ATOM    229  CA  ASP   229      21.802  37.664  32.397  1.00 25.00           C
ATOM    230  CA  TYR   230      19.041  40.234  32.848  1.00 25.00           C
ATOM    231  CA  PRO   231      17.498  42.741  35.289  1.00 25.00           C
ATOM    232  CA  ARG   232      14.240  44.258  34.134  1.00 25.00           C
ATOM    233  CA  ASN   233      11.680  46.668  32.711  1.00 25.00           C
ATOM    234  CA  GLU   234      11.159  49.295  30.003  1.00 25.00           C
ATOM    235  CA  SER   235      13.761  48.106  27.440  1.00 25.00           C
ATOM    236  CA  GLY   236      15.089  46.112  24.535  1.00 25.00           C
ATOM    237  CA  ASP   237      17.630  43.289  24.562  1.00 25.00           C
ATOM    238  CA  VAL   238      20.138  40.416  24.104  1.00 25.00           C
ATOM    239  CA  ALA   239      23.714  39.166  23.758  1.00 25.00           C
ATOM    240  CA  ALA   240      26.136  41.226  25.891  1.00 25.00           C
ATOM    241  CA  VAL   241      29.817  42.037  26.399  1.00 25.00           C
ATOM    242  CA  ILE   242      33.120  43.897  25.954  1.00 25.00           C
ATOM    243  CA  HIS   243      32.327  47.400  24.839  1.00 25.00           C
ATOM    244  CA  PRO   244      32.391  51.177  25.029  1.00 25.00           C
ATOM    245  CA  ASN   245      31.273  54.237  27.049  1.00 25.00           C
ATOM    246  CA  LEU   246      29.386  57.290  28.100  1.00 25.00           C
ATOM    247  CA  GLN   247      32.462  59.431  28.702  1.00 25.00           C
ATOM    248  CA  ASP   248      34.185  61.694  26.195  1.00 25.00           C
ATOM    249  CA  GLN   249      36.044  63.304  23.278  1.00 25.00           C
ATOM    250  CA  ASP   250      36.404  63.434  19.506  1.00 25.00           C
ATOM    251  CA  TRP   251      36.435  60.022  17.836  1.00 25.00           C
ATOM    252  CA  LYS   252      34.929  60.879  14.479  1.00 25.00           C
ATOM    253  CA  PRO   253      35.121  60.965  10.707  1.00 25.00           C
ATOM    254  CA  LEU   254      35.583  57.620   9.025  1.00 25.00           C
ATOM    255  CA  HIS   255      37.264  55.129  11.382  1.00 25.00           C
ATOM    256  CA  PRO   256      35.186  52.164  12.584  1.00 25.00           C
ATOM    257  CA  GLY   257      36.212  49.074  14.583  1.00 25.00           C
ATOM    258  CA  ASP   258      35.639  45.440  15.633  1.00 25.00           C
ATOM    259  CA  PRO   259      35.534  42.492  18.053  1.00 25.00           C
ATOM    260  CA  VAL   260      35.589  41.992  21.848  1.00 25.00           C
ATOM    261  CA  PHE   261      35.713  38.197  22.442  1.00 25.00           C
ATOM    262  CA  VAL   262      35.922  37.438  26.169  1.00 25.00           C
ATOM    263  CA  SER   263      35.646  35.816  29.591  1.00 25.00           C
ATOM    264  CA  LEU   264      36.752  32.881  31.782  1.00 25.00           C
ATOM    265  CA  ASP   265      36.366  34.143  35.322  1.00 25.00           C
ATOM    266  CA  GLY   266      35.197  37.751  35.093  1.00 25.00           C
ATOM    267  CA  LYS   267      31.669  36.332  35.299  1.00 25.00           C
ATOM    268  CA  VAL   268      30.316  32.886  36.235  1.00 25.00           C
ATOM    269  CA  ILE   269      28.219  29.744  36.251  1.00 25.00           C
ATOM    270  CA  PRO   270      24.509  29.350  36.698  1.00 25.00           C
ATOM    271  CA  LEU   271      22.874  26.567  34.753  1.00 25.00           C
ATOM    272  CA  GLY   272      22.661  22.971  35.903  1.00 25.00           C
ATOM    273  CA  GLY   273      23.075  21.856  32.312  1.00 25.00           C
ATOM    274  CA  ASP   274      24.271  21.050  28.762  1.00 25.00           C
ATOM    275  CA  CYS   275      26.010  24.388  28.760  1.00 25.00           C
ATOM    276  CA  THR   276      29.102  23.163  30.521  1.00 25.00           C
ATOM    277  CA  VAL   277      27.594  24.591  33.663  1.00 25.00           C
ATOM    278  CA  TYR   278      27.551  28.006  31.979  1.00 25.00           C
ATOM    279  CA  PRO   279      26.892  31.753  31.816  1.00 25.00           C
ATOM    280  CA  VAL   280      28.796  34.936  31.143  1.00 25.00           C
ATOM    281  CA  PHE   281      31.035  36.963  28.929  1.00 25.00           C
ATOM    282  CA  VAL   282      31.789  38.840  25.743  1.00 25.00           C
ATOM    283  CA  ASN   283      29.312  38.070  22.941  1.00 25.00           C
ATOM    284  CA  GLU   284      31.154  38.476  19.700  1.00 25.00           C
ATOM    285  CA  ALA   285      29.461  40.790  17.159  1.00 25.00           C
ATOM    286  CA  ALA   286      26.805  41.734  19.752  1.00 25.00           C
ATOM    287  CA  TYR   287      29.544  42.487  22.321  1.00 25.00           C
ATOM    288  CA  TYR   288      31.374  44.675  19.765  1.00 25.00           C
ATOM    289  CA  GLU   289      28.123  46.556  19.014  1.00 25.00           C
ATOM    290  CA  LYS   290      27.547  47.108  22.758  1.00 25.00           C
ATOM    291  CA  LYS   291      27.283  46.525  26.516  1.00 25.00           C
ATOM    292  CA  GLU   292      29.205  44.589  29.118  1.00 25.00           C
ATOM    293  CA  ALA   293      31.531  42.060  30.645  1.00 25.00           C
ATOM    294  CA  PHE   294      34.728  40.029  30.620  1.00 25.00           C
ATOM    295  CA  ALA   295      38.446  40.298  31.464  1.00 25.00           C
ATOM    296  CA  LYS   296      41.349  42.824  31.468  1.00 25.00           C
ATOM    297  CA  THR   297      45.106  42.711  31.111  1.00 25.00           C
TER
END
