
#######################################################
#                                                     #
#                        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 T0289TS168_1-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS168_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      I     224           -
LGA    M     225      M     225           -
LGA    E     226      E     226           -
LGA    K     227      K     227           -
LGA    -       -      V     228           -
LGA    -       -      D     229           -
LGA    V     228      Y     230           #
LGA    D     229      P     231          4.571
LGA    Y     230      R     232          3.239
LGA    P     231      N     233          2.137
LGA    R     232      E     234          2.603
LGA    N     233      S     235          2.097
LGA    E     234      G     236          3.085
LGA    S     235      D     237          2.027
LGA    G     236      V     238          2.426
LGA    -       -      A     239           -
LGA    D     237      A     240           #
LGA    V     238      V     241          2.621
LGA    A     239      I     242          2.360
LGA    -       -      H     243           -
LGA    -       -      P     244           -
LGA    -       -      N     245           -
LGA    A     240      L     246          3.594
LGA    V     241      Q     247           #
LGA    I     242      D     248          4.485
LGA    H     243      Q     249          4.568
LGA    P     244      D     250           #
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      W     251          3.428
LGA    V     260      K     252          3.222
LGA    F     261      P     253          4.344
LGA    V     262      L     254          3.859
LGA    -       -      H     255           -
LGA    -       -      P     256           -
LGA    -       -      G     257           -
LGA    -       -      D     258           -
LGA    S     263      P     259           #
LGA    L     264      V     260          3.552
LGA    D     265      F     261          4.220
LGA    G     266      V     262           -
LGA    K     267      S     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    -       -      K     267           -
LGA    V     268      V     268          4.708
LGA    I     269      I     269          3.915
LGA    P     270      -       -           -
LGA    L     271      -       -           -
LGA    G     272      -       -           -
LGA    G     273      -       -           -
LGA    D     274      -       -           -
LGA    C     275      P     270           #
LGA    T     276      L     271           #
LGA    V     277      G     272          1.430
LGA    Y     278      G     273           #
LGA    -       -      D     274           -
LGA    -       -      C     275           -
LGA    P     279      T     276          4.682
LGA    V     280      V     277          2.973
LGA    F     281      Y     278          3.052
LGA    V     282      P     279          3.859
LGA    N     283      V     280          1.795
LGA    E     284      F     281          2.418
LGA    A     285      V     282          4.820
LGA    A     286      -       -           -
LGA    Y     287      N     283          4.254
LGA    Y     288      E     284          3.432
LGA    E     289      A     285          2.951
LGA    K     290      A     286          3.547
LGA    K     291      Y     287          3.319
LGA    -       -      Y     288           -
LGA    -       -      E     289           -
LGA    -       -      K     290           -
LGA    -       -      K     291           -
LGA    E     292      E     292          4.798
LGA    A     293      A     293          3.280
LGA    F     294      F     294          3.464
LGA    A     295      A     295          4.720
LGA    K     296      K     296          2.815
LGA    T     297      T     297          1.264

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   74   74    5.0     40    3.49    25.00     28.841     1.116

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.032427 * X  +   0.472562 * Y  +  -0.880701 * Z  +  34.184925
  Y_new =   0.885320 * X  +   0.395363 * Y  +   0.244739 * Z  +  46.257782
  Z_new =   0.463851 * X  +  -0.787638 * Y  +  -0.405548 * Z  +  32.063671 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.046286    1.095306  [ DEG:  -117.2436     62.7564 ]
  Theta =  -0.482337   -2.659256  [ DEG:   -27.6359   -152.3641 ]
  Phi   =   1.534185   -1.607407  [ DEG:    87.9024    -92.0976 ]
 
# 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: T0289TS168_1-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS168_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   40   3.49   25.00  28.841
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS168_1-D2
PFRMAT TS
TARGET T0289
MODEL 1
PARENT N/A
ATOM    224  CA  ILE   224      32.434  49.949  37.239  1.00 25.00           C
ATOM    225  CA  MET   225      30.286  50.457  40.308  1.00 25.00           C
ATOM    226  CA  GLU   226      27.624  47.841  40.408  1.00 25.00           C
ATOM    227  CA  LYS   227      24.240  46.510  39.395  1.00 25.00           C
ATOM    228  CA  VAL   228      23.537  44.758  36.092  1.00 25.00           C
ATOM    229  CA  ASP   229      19.857  45.710  36.538  1.00 25.00           C
ATOM    230  CA  TYR   230      16.320  44.430  37.336  1.00 25.00           C
ATOM    231  CA  PRO   231      12.637  43.705  37.947  1.00 25.00           C
ATOM    232  CA  ARG   232      10.258  46.472  36.864  1.00 25.00           C
ATOM    233  CA  ASN   233       7.421  44.556  35.219  1.00 25.00           C
ATOM    234  CA  GLU   234       8.246  46.462  32.008  1.00 25.00           C
ATOM    235  CA  SER   235      11.700  46.735  30.511  1.00 25.00           C
ATOM    236  CA  GLY   236      15.407  46.287  29.848  1.00 25.00           C
ATOM    237  CA  ASP   237      19.205  46.583  29.891  1.00 25.00           C
ATOM    238  CA  VAL   238      22.981  46.181  29.320  1.00 25.00           C
ATOM    239  CA  ALA   239      25.940  43.974  28.569  1.00 25.00           C
ATOM    240  CA  ALA   240      29.404  42.431  28.341  1.00 25.00           C
ATOM    241  CA  VAL   241      30.459  41.043  24.919  1.00 25.00           C
ATOM    242  CA  ILE   242      32.961  41.349  22.070  1.00 25.00           C
ATOM    243  CA  HIS   243      35.580  40.145  19.551  1.00 25.00           C
ATOM    244  CA  PRO   244      37.710  39.546  16.457  1.00 25.00           C
ATOM    245  CA  ASN   245      39.787  40.590  13.429  1.00 25.00           C
ATOM    246  CA  LEU   246      37.946  42.842  11.044  1.00 25.00           C
ATOM    247  CA  GLN   247      37.940  41.376   7.557  1.00 25.00           C
ATOM    248  CA  ASP   248      38.271  40.498   3.840  1.00 25.00           C
ATOM    249  CA  GLN   249      41.513  38.639   3.958  1.00 25.00           C
ATOM    250  CA  ASP   250      41.132  36.947   0.581  1.00 25.00           C
ATOM    251  CA  TRP   251      38.735  34.032   0.225  1.00 25.00           C
ATOM    252  CA  LYS   252      39.271  30.835   2.236  1.00 25.00           C
ATOM    253  CA  PRO   253      36.023  31.624   4.025  1.00 25.00           C
ATOM    254  CA  LEU   254      34.480  30.040   7.115  1.00 25.00           C
ATOM    255  CA  HIS   255      36.739  27.292   8.384  1.00 25.00           C
ATOM    256  CA  PRO   256      37.591  29.193  11.535  1.00 25.00           C
ATOM    257  CA  GLY   257      38.113  31.610  14.385  1.00 25.00           C
ATOM    258  CA  ASP   258      37.958  34.210  17.179  1.00 25.00           C
ATOM    259  CA  PRO   259      38.355  36.224  20.397  1.00 25.00           C
ATOM    260  CA  VAL   260      36.002  34.451  22.827  1.00 25.00           C
ATOM    261  CA  PHE   261      35.563  38.000  24.189  1.00 25.00           C
ATOM    262  CA  VAL   262      33.507  38.239  27.395  1.00 25.00           C
ATOM    263  CA  SER   263      30.629  37.968  29.905  1.00 25.00           C
ATOM    264  CA  LEU   264      27.127  38.743  31.282  1.00 25.00           C
ATOM    265  CA  ASP   265      24.238  40.737  32.761  1.00 25.00           C
ATOM    266  CA  GLY   266      24.652  38.527  35.821  1.00 25.00           C
ATOM    267  CA  LYS   267      24.182  40.820  38.846  1.00 25.00           C
ATOM    268  CA  VAL   268      27.829  39.835  38.924  1.00 25.00           C
ATOM    269  CA  ILE   269      29.210  42.694  41.012  1.00 25.00           C
ATOM    270  CA  PRO   270      31.567  45.141  42.735  1.00 25.00           C
ATOM    271  CA  LEU   271      28.444  46.136  44.692  1.00 25.00           C
ATOM    272  CA  GLY   272      26.952  44.071  47.481  1.00 25.00           C
ATOM    273  CA  GLY   273      28.347  40.582  47.421  1.00 25.00           C
ATOM    274  CA  ASP   274      27.233  38.657  44.379  1.00 25.00           C
ATOM    275  CA  CYS   275      29.590  37.063  41.889  1.00 25.00           C
ATOM    276  CA  THR   276      29.821  34.326  39.287  1.00 25.00           C
ATOM    277  CA  VAL   277      29.897  32.755  35.793  1.00 25.00           C
ATOM    278  CA  TYR   278      29.660  34.139  32.300  1.00 25.00           C
ATOM    279  CA  PRO   279      32.940  33.834  30.481  1.00 25.00           C
ATOM    280  CA  VAL   280      32.384  34.123  26.767  1.00 25.00           C
ATOM    281  CA  PHE   281      31.136  35.652  23.510  1.00 25.00           C
ATOM    282  CA  VAL   282      31.154  37.377  20.116  1.00 25.00           C
ATOM    283  CA  ASN   283      27.440  37.977  20.348  1.00 25.00           C
ATOM    284  CA  GLU   284      28.826  41.278  19.248  1.00 25.00           C
ATOM    285  CA  ALA   285      28.626  45.095  19.006  1.00 25.00           C
ATOM    286  CA  ALA   286      25.296  44.826  17.132  1.00 25.00           C
ATOM    287  CA  TYR   287      23.946  42.458  19.823  1.00 25.00           C
ATOM    288  CA  TYR   288      25.037  44.906  22.559  1.00 25.00           C
ATOM    289  CA  GLU   289      23.301  47.779  20.715  1.00 25.00           C
ATOM    290  CA  LYS   290      20.106  45.690  20.416  1.00 25.00           C
ATOM    291  CA  LYS   291      19.864  43.200  23.241  1.00 25.00           C
ATOM    292  CA  GLU   292      22.668  42.770  25.798  1.00 25.00           C
ATOM    293  CA  ALA   293      25.464  40.616  24.529  1.00 25.00           C
ATOM    294  CA  PHE   294      27.421  37.904  26.358  1.00 25.00           C
ATOM    295  CA  ALA   295      27.446  34.218  27.151  1.00 25.00           C
ATOM    296  CA  LYS   296      28.228  30.604  26.475  1.00 25.00           C
ATOM    297  CA  THR   297      30.198  30.116  23.276  1.00 25.00           C
TER
END
