
#######################################################
#                                                     #
#                        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 T0289TS599_2-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS599_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    Y     230      -       -           -
LGA    P     231      -       -           -
LGA    R     232      -       -           -
LGA    N     233      -       -           -
LGA    E     234      -       -           -
LGA    S     235      -       -           -
LGA    G     236      -       -           -
LGA    D     237      I     224          3.879
LGA    V     238      M     225          4.258
LGA    A     239      E     226          4.753
LGA    A     240      K     227          1.687
LGA    V     241      V     228          1.964
LGA    I     242      D     229          1.485
LGA    H     243      Y     230          1.516
LGA    P     244      P     231          1.644
LGA    N     245      R     232          1.663
LGA    L     246      N     233           -
LGA    Q     247      E     234           #
LGA    D     248      S     235          3.084
LGA    Q     249      G     236          1.699
LGA    D     250      D     237          1.692
LGA    W     251      V     238          1.453
LGA    K     252      A     239          2.403
LGA    P     253      -       -           -
LGA    L     254      A     240          4.091
LGA    H     255      V     241           -
LGA    P     256      I     242           -
LGA    G     257      -       -           -
LGA    D     258      -       -           -
LGA    P     259      -       -           -
LGA    V     260      H     243           #
LGA    F     261      P     244           -
LGA    -       -      N     245           -
LGA    V     262      L     246          4.778
LGA    S     263      Q     247           -
LGA    -       -      D     248           -
LGA    -       -      Q     249           -
LGA    L     264      D     250          2.455
LGA    D     265      W     251          1.948
LGA    G     266      K     252          4.969
LGA    K     267      P     253          1.153
LGA    V     268      L     254          0.977
LGA    -       -      H     255           -
LGA    -       -      P     256           -
LGA    -       -      G     257           -
LGA    I     269      D     258           #
LGA    P     270      P     259          2.897
LGA    L     271      V     260          3.400
LGA    G     272      F     261          3.802
LGA    G     273      V     262          2.154
LGA    D     274      S     263          1.016
LGA    C     275      L     264          4.946
LGA    T     276      D     265           -
LGA    -       -      G     266           -
LGA    -       -      K     267           -
LGA    -       -      V     268           -
LGA    -       -      I     269           -
LGA    -       -      P     270           -
LGA    -       -      L     271           -
LGA    -       -      G     272           -
LGA    -       -      G     273           -
LGA    -       -      D     274           -
LGA    -       -      C     275           -
LGA    -       -      T     276           -
LGA    -       -      V     277           -
LGA    -       -      Y     278           -
LGA    -       -      P     279           -
LGA    -       -      V     280           -
LGA    -       -      F     281           -
LGA    -       -      V     282           -
LGA    V     277      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    Y     278      A     293          4.516
LGA    P     279      F     294          3.352
LGA    V     280      A     295           #
LGA    F     281      K     296          1.328
LGA    V     282      T     297          4.257
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     31    3.05    12.90     26.439     0.985

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.151881 * X  +   0.481363 * Y  +   0.863262 * Z  +  24.966595
  Y_new =   0.505641 * X  +  -0.788294 * Y  +   0.350599 * Z  +  41.967918
  Z_new =   0.849270 * X  +   0.383251 * Y  +  -0.363124 * Z  +  47.317261 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.329234   -0.812358  [ DEG:   133.4553    -46.5447 ]
  Theta =  -1.014601   -2.126992  [ DEG:   -58.1323   -121.8677 ]
  Phi   =   1.278997   -1.862596  [ DEG:    73.2811   -106.7189 ]
 
# 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: T0289TS599_2-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS599_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   31   3.05   12.90  26.439
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS599_2-D2
PFRMAT TS                                                                       
TARGET T0289                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM    224  CA  ILE   224      20.780  14.656  29.907  1.00  0.00              
ATOM    225  CA  MET   225      23.968  14.370  30.345  1.00  0.00              
ATOM    226  CA  GLU   226      24.661  12.410  27.231  1.00  0.00              
ATOM    227  CA  LYS   227      23.127  15.197  25.515  1.00  0.00              
ATOM    228  CA  VAL   228      24.818  18.517  26.121  1.00  0.00              
ATOM    229  CA  ASP   229      24.503  20.604  22.884  1.00  0.00              
ATOM    230  CA  TYR   230      24.283  24.341  23.046  1.00  0.00              
ATOM    231  CA  PRO   231      22.569  25.483  19.824  1.00  0.00              
ATOM    232  CA  ARG   232      23.795  28.976  19.180  1.00  0.00              
ATOM    233  CA  ASN   233      21.473  31.601  17.524  1.00  0.00              
ATOM    234  CA  GLU   234      21.263  32.113  14.035  1.00  0.00              
ATOM    235  CA  SER   235      24.459  33.641  13.208  1.00  0.00              
ATOM    236  CA  GLY   236      26.476  31.178  14.798  1.00  0.00              
ATOM    237  CA  ASP   237      27.423  32.456  17.930  1.00  0.00              
ATOM    238  CA  VAL   238      26.256  31.613  21.438  1.00  0.00              
ATOM    239  CA  ALA   239      24.679  34.175  22.856  1.00  0.00              
ATOM    240  CA  ALA   240      22.616  34.012  26.015  1.00  0.00              
ATOM    241  CA  VAL   241      21.076  37.537  27.075  1.00  0.00              
ATOM    242  CA  ILE   242      20.140  38.624  29.921  1.00  0.00              
ATOM    243  CA  HIS   243      18.450  41.797  30.681  1.00  0.00              
ATOM    244  CA  PRO   244      17.356  41.745  34.429  1.00  0.00              
ATOM    245  CA  ASN   245      13.906  43.049  34.499  1.00  0.00              
ATOM    246  CA  LEU   246      12.462  40.354  31.985  1.00  0.00              
ATOM    247  CA  GLN   247       9.213  40.027  33.001  1.00  0.00              
ATOM    248  CA  ASP   248       8.430  43.467  34.059  1.00  0.00              
ATOM    249  CA  GLN   249       9.913  45.399  31.210  1.00  0.00              
ATOM    250  CA  ASP   250      12.729  47.325  33.379  1.00  0.00              
ATOM    251  CA  TRP   251      15.510  46.806  31.069  1.00  0.00              
ATOM    252  CA  LYS   252      18.815  47.554  32.968  1.00  0.00              
ATOM    253  CA  PRO   253      18.077  46.646  36.422  1.00  0.00              
ATOM    254  CA  LEU   254      21.278  45.483  38.063  1.00  0.00              
ATOM    255  CA  HIS   255      21.831  44.089  41.654  1.00  0.00              
ATOM    256  CA  PRO   256      25.231  43.843  43.214  1.00  0.00              
ATOM    257  CA  GLY   257      27.023  40.790  42.517  1.00  0.00              
ATOM    258  CA  ASP   258      25.120  39.920  39.565  1.00  0.00              
ATOM    259  CA  PRO   259      27.206  38.439  36.726  1.00  0.00              
ATOM    260  CA  VAL   260      27.517  39.850  33.353  1.00  0.00              
ATOM    261  CA  PHE   261      29.220  37.993  31.335  1.00  0.00              
ATOM    262  CA  VAL   262      30.345  39.280  27.480  1.00  0.00              
ATOM    263  CA  SER   263      31.337  36.885  24.967  1.00  0.00              
ATOM    264  CA  LEU   264      33.431  37.857  21.951  1.00  0.00              
ATOM    265  CA  ASP   265      34.473  35.028  20.028  1.00  0.00              
ATOM    266  CA  GLY   266      35.535  32.697  22.995  1.00  0.00              
ATOM    267  CA  LYS   267      37.054  35.346  25.377  1.00  0.00              
ATOM    268  CA  VAL   268      35.447  35.935  28.578  1.00  0.00              
ATOM    269  CA  ILE   269      34.853  39.862  29.550  1.00  0.00              
ATOM    270  CA  PRO   270      33.459  40.654  32.259  1.00  0.00              
ATOM    271  CA  LEU   271      31.339  44.007  32.435  1.00  0.00              
ATOM    272  CA  GLY   272      29.609  45.631  35.707  1.00  0.00              
ATOM    273  CA  GLY   273      28.494  48.597  35.243  1.00  0.00              
ATOM    274  CA  ASP   274      24.854  48.667  36.488  1.00  0.00              
ATOM    275  CA  CYS   275      22.671  50.224  33.733  1.00  0.00              
ATOM    276  CA  THR   276      22.372  47.559  30.465  1.00  0.00              
ATOM    277  CA  VAL   277      22.428  44.643  28.905  1.00  0.00              
ATOM    278  CA  TYR   278      24.487  41.327  29.944  1.00  0.00              
ATOM    279  CA  PRO   279      25.467  39.018  27.435  1.00  0.00              
ATOM    280  CA  VAL   280      26.169  35.510  28.277  1.00  0.00              
ATOM    281  CA  PHE   281      28.164  33.167  25.775  1.00  0.00              
ATOM    282  CA  VAL   282      26.946  29.878  25.697  1.00  0.00              
ATOM    283  CA  ASN   283      29.331  27.041  24.587  1.00  0.00              
ATOM    284  CA  GLU   284      28.595  23.825  24.393  1.00  0.00              
ATOM    285  CA  ALA   285      31.065  22.391  27.051  1.00  0.00              
ATOM    286  CA  ALA   286      30.095  24.658  29.767  1.00  0.00              
ATOM    287  CA  TYR   287      26.830  24.206  30.439  1.00  0.00              
ATOM    288  CA  TYR   288      26.683  20.566  30.229  1.00  0.00              
ATOM    289  CA  GLU   289      29.653  19.542  32.192  1.00  0.00              
ATOM    290  CA  LYS   290      28.818  21.823  35.164  1.00  0.00              
ATOM    291  CA  LYS   291      25.346  20.556  34.865  1.00  0.00              
ATOM    292  CA  GLU   292      25.592  17.403  34.763  1.00  0.00              
ATOM    293  CA  ALA   293      23.212  14.781  36.938  1.00  0.00              
ATOM    294  CA  PHE   294      24.387  11.255  35.951  1.00  0.00              
ATOM    295  CA  ALA   295      21.973   8.490  37.292  1.00  0.00              
ATOM    296  CA  LYS   296      22.925   5.146  37.260  1.00  0.00              
ATOM    297  CA  THR   297      20.183   2.441  37.298  1.00  0.00              
TER                                                                             
END
