
#######################################################
#                                                     #
#                        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_2-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS393_2-D2.T0289_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      I     224           -
LGA    -       -      M     225           -
LGA    -       -      E     226           -
LGA    -       -      K     227           -
LGA    -       -      V     228           -
LGA    -       -      D     229           -
LGA    I     224      Y     230           #
LGA    -       -      P     231           -
LGA    M     225      R     232          3.180
LGA    E     226      N     233          4.801
LGA    K     227      -       -           -
LGA    V     228      -       -           -
LGA    D     229      -       -           -
LGA    Y     230      -       -           -
LGA    P     231      -       -           -
LGA    R     232      E     234           #
LGA    N     233      -       -           -
LGA    E     234      -       -           -
LGA    S     235      S     235           #
LGA    G     236      G     236          4.612
LGA    D     237      D     237          1.022
LGA    V     238      V     238          2.126
LGA    A     239      A     239          2.695
LGA    A     240      A     240          0.932
LGA    -       -      V     241           -
LGA    V     241      I     242          4.241
LGA    I     242      H     243          2.072
LGA    H     243      P     244          1.558
LGA    -       -      N     245           -
LGA    -       -      L     246           -
LGA    P     244      Q     247          4.274
LGA    N     245      D     248           #
LGA    L     246      Q     249           #
LGA    Q     247      D     250           -
LGA    D     248      W     251           -
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      K     252           #
LGA    V     260      P     253           #
LGA    F     261      L     254          3.756
LGA    -       -      H     255           -
LGA    -       -      P     256           -
LGA    -       -      G     257           -
LGA    V     262      D     258          4.578
LGA    S     263      P     259          4.548
LGA    L     264      V     260          4.591
LGA    D     265      -       -           -
LGA    G     266      -       -           -
LGA    K     267      -       -           -
LGA    V     268      -       -           -
LGA    I     269      F     261          4.707
LGA    P     270      V     262          4.894
LGA    L     271      S     263          1.361
LGA    G     272      L     264          1.678
LGA    G     273      D     265          4.029
LGA    D     274      G     266          3.424
LGA    C     275      -       -           -
LGA    T     276      K     267          2.451
LGA    V     277      V     268          1.775
LGA    Y     278      I     269          4.575
LGA    P     279      P     270          2.976
LGA    V     280      -       -           -
LGA    F     281      L     271          2.507
LGA    V     282      G     272          4.205
LGA    N     283      G     273          2.486
LGA    E     284      D     274          3.040
LGA    A     285      C     275           -
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    F     294      T     276           #
LGA    A     295      V     277          3.269
LGA    K     296      Y     278           #
LGA    T     297      P     279           -
LGA    -       -      V     280           -
LGA    -       -      F     281           -
LGA    -       -      V     282           -
LGA    -       -      N     283           -
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    -       -      F     294           -
LGA    -       -      A     295           -
LGA    -       -      K     296           -
LGA    -       -      T     297           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   74   74    5.0     30    3.44    23.33     22.512     0.847

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.552888 * X  +   0.833160 * Y  +  -0.012635 * Z  +  27.981630
  Y_new =   0.595757 * X  +  -0.405857 * Y  +  -0.693076 * Z  +  39.628078
  Z_new =  -0.582571 * X  +   0.375666 * Y  +  -0.720754 * Z  +  35.984180 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.661120   -0.480473  [ DEG:   152.4709    -27.5291 ]
  Theta =   0.621888    2.519704  [ DEG:    35.6316    144.3684 ]
  Phi   =   0.822703   -2.318890  [ DEG:    47.1374   -132.8626 ]
 
# 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_2-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS393_2-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   30   3.44   23.33  22.512
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS393_2-D2
PFRMAT TS
TARGET T0289
MODEL 2
PARENT N/A
ATOM    224  CA  ILE   224      19.274  38.939  35.862  1.00 25.00           C
ATOM    225  CA  MET   225      17.131  40.868  33.382  1.00 25.00           C
ATOM    226  CA  GLU   226      13.733  40.916  35.093  1.00 25.00           C
ATOM    227  CA  LYS   227      14.115  37.407  36.500  1.00 25.00           C
ATOM    228  CA  VAL   228      16.123  34.243  35.738  1.00 25.00           C
ATOM    229  CA  ASP   229      13.943  33.842  32.684  1.00 25.00           C
ATOM    230  CA  TYR   230      11.694  36.664  31.514  1.00 25.00           C
ATOM    231  CA  PRO   231       8.685  38.547  30.135  1.00 25.00           C
ATOM    232  CA  ARG   232       5.748  40.589  28.736  1.00 25.00           C
ATOM    233  CA  ASN   233       3.346  43.478  28.997  1.00 25.00           C
ATOM    234  CA  GLU   234       5.019  46.457  27.338  1.00 25.00           C
ATOM    235  CA  SER   235       7.127  48.769  29.566  1.00 25.00           C
ATOM    236  CA  GLY   236      10.651  49.035  30.973  1.00 25.00           C
ATOM    237  CA  ASP   237      13.859  47.452  32.335  1.00 25.00           C
ATOM    238  CA  VAL   238      17.283  46.543  33.722  1.00 25.00           C
ATOM    239  CA  ALA   239      20.228  45.338  35.828  1.00 25.00           C
ATOM    240  CA  ALA   240      22.410  47.612  33.775  1.00 25.00           C
ATOM    241  CA  VAL   241      25.858  46.060  33.644  1.00 25.00           C
ATOM    242  CA  ILE   242      29.205  47.701  32.750  1.00 25.00           C
ATOM    243  CA  HIS   243      31.929  47.086  30.262  1.00 25.00           C
ATOM    244  CA  PRO   244      34.910  48.004  28.097  1.00 25.00           C
ATOM    245  CA  ASN   245      38.323  48.622  26.567  1.00 25.00           C
ATOM    246  CA  LEU   246      41.514  48.650  24.477  1.00 25.00           C
ATOM    247  CA  GLN   247      44.406  50.707  23.141  1.00 25.00           C
ATOM    248  CA  ASP   248      47.414  51.369  20.917  1.00 25.00           C
ATOM    249  CA  GLN   249      50.455  50.807  18.748  1.00 25.00           C
ATOM    250  CA  ASP   250      52.288  48.084  20.617  1.00 25.00           C
ATOM    251  CA  TRP   251      53.497  50.822  22.914  1.00 25.00           C
ATOM    252  CA  LYS   252      57.031  49.822  23.967  1.00 25.00           C
ATOM    253  CA  PRO   253      57.517  47.969  27.267  1.00 25.00           C
ATOM    254  CA  LEU   254      57.754  44.157  27.275  1.00 25.00           C
ATOM    255  CA  HIS   255      55.300  41.697  28.877  1.00 25.00           C
ATOM    256  CA  PRO   256      51.974  41.279  30.699  1.00 25.00           C
ATOM    257  CA  GLY   257      48.427  40.581  31.960  1.00 25.00           C
ATOM    258  CA  ASP   258      44.738  40.356  33.012  1.00 25.00           C
ATOM    259  CA  PRO   259      41.422  38.529  32.598  1.00 25.00           C
ATOM    260  CA  VAL   260      37.834  37.621  33.443  1.00 25.00           C
ATOM    261  CA  PHE   261      34.343  37.727  31.879  1.00 25.00           C
ATOM    262  CA  VAL   262      30.669  38.169  32.638  1.00 25.00           C
ATOM    263  CA  SER   263      29.888  41.550  31.088  1.00 25.00           C
ATOM    264  CA  LEU   264      27.090  41.656  28.506  1.00 25.00           C
ATOM    265  CA  ASP   265      24.302  43.008  26.276  1.00 25.00           C
ATOM    266  CA  GLY   266      21.715  40.493  27.397  1.00 25.00           C
ATOM    267  CA  LYS   267      22.665  41.316  30.938  1.00 25.00           C
ATOM    268  CA  VAL   268      25.310  39.671  33.060  1.00 25.00           C
ATOM    269  CA  ILE   269      23.788  41.382  36.069  1.00 25.00           C
ATOM    270  CA  PRO   270      24.360  44.158  38.575  1.00 25.00           C
ATOM    271  CA  LEU   271      24.501  47.985  38.434  1.00 25.00           C
ATOM    272  CA  GLY   272      24.206  51.338  36.749  1.00 25.00           C
ATOM    273  CA  GLY   273      27.129  53.283  38.104  1.00 25.00           C
ATOM    274  CA  ASP   274      30.691  52.373  38.918  1.00 25.00           C
ATOM    275  CA  CYS   275      31.249  49.746  41.620  1.00 25.00           C
ATOM    276  CA  THR   276      29.421  46.452  42.169  1.00 25.00           C
ATOM    277  CA  VAL   277      29.064  46.042  38.440  1.00 25.00           C
ATOM    278  CA  TYR   278      30.449  43.811  35.770  1.00 25.00           C
ATOM    279  CA  PRO   279      28.337  40.918  36.956  1.00 25.00           C
ATOM    280  CA  VAL   280      28.111  37.108  36.846  1.00 25.00           C
ATOM    281  CA  PHE   281      30.221  34.176  35.836  1.00 25.00           C
ATOM    282  CA  VAL   282      31.843  30.973  34.558  1.00 25.00           C
ATOM    283  CA  ASN   283      29.306  28.537  33.200  1.00 25.00           C
ATOM    284  CA  GLU   284      28.896  27.393  36.757  1.00 25.00           C
ATOM    285  CA  ALA   285      26.671  27.539  39.872  1.00 25.00           C
ATOM    286  CA  ALA   286      24.448  30.166  38.191  1.00 25.00           C
ATOM    287  CA  TYR   287      24.167  27.966  35.069  1.00 25.00           C
ATOM    288  CA  TYR   288      23.211  24.961  37.243  1.00 25.00           C
ATOM    289  CA  GLU   289      20.547  27.063  39.019  1.00 25.00           C
ATOM    290  CA  LYS   290      19.150  28.195  35.637  1.00 25.00           C
ATOM    291  CA  LYS   291      19.776  30.261  32.523  1.00 25.00           C
ATOM    292  CA  GLU   292      23.014  31.866  31.281  1.00 25.00           C
ATOM    293  CA  ALA   293      26.196  33.620  32.550  1.00 25.00           C
ATOM    294  CA  PHE   294      29.521  33.726  30.764  1.00 25.00           C
ATOM    295  CA  ALA   295      32.386  31.347  30.147  1.00 25.00           C
ATOM    296  CA  LYS   296      35.413  29.276  29.106  1.00 25.00           C
ATOM    297  CA  THR   297      38.074  28.698  26.473  1.00 25.00           C
TER
END
