
#######################################################
#                                                     #
#                        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_5-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS393_5-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           -
LGA    -       -      E     226           -
LGA    -       -      K     227           -
LGA    M     225      V     228          4.683
LGA    E     226      D     229           #
LGA    K     227      Y     230           #
LGA    V     228      P     231          2.137
LGA    D     229      R     232          3.136
LGA    Y     230      N     233          2.119
LGA    P     231      E     234          1.605
LGA    R     232      S     235          1.265
LGA    N     233      -       -           -
LGA    E     234      -       -           -
LGA    S     235      -       -           -
LGA    G     236      G     236           #
LGA    D     237      D     237          5.634
LGA    V     238      V     238          5.601
LGA    A     239      A     239           -
LGA    A     240      A     240           -
LGA    V     241      V     241           -
LGA    I     242      I     242           -
LGA    H     243      H     243           -
LGA    P     244      P     244           -
LGA    N     245      N     245           -
LGA    L     246      L     246           -
LGA    Q     247      Q     247           -
LGA    D     248      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           #
LGA    V     260      D     250          4.442
LGA    F     261      W     251          3.815
LGA    V     262      K     252          4.904
LGA    S     263      P     253           #
LGA    L     264      L     254          3.126
LGA    D     265      H     255          2.686
LGA    G     266      P     256          3.127
LGA    K     267      G     257          1.968
LGA    V     268      D     258          1.208
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    I     269      P     270          3.095
LGA    P     270      L     271          1.831
LGA    L     271      G     272          1.714
LGA    G     272      G     273          3.106
LGA    -       -      D     274           -
LGA    G     273      C     275          2.991
LGA    -       -      T     276           -
LGA    D     274      V     277          2.770
LGA    C     275      Y     278          4.590
LGA    T     276      P     279          3.154
LGA    V     277      V     280          2.156
LGA    Y     278      F     281          0.845
LGA    P     279      V     282          3.050
LGA    V     280      N     283          2.800
LGA    -       -      E     284           -
LGA    F     281      A     285          3.710
LGA    V     282      A     286           -
LGA    -       -      Y     287           -
LGA    N     283      Y     288          3.856
LGA    E     284      E     289           -
LGA    -       -      K     290           -
LGA    A     285      K     291           #
LGA    A     286      E     292          1.364
LGA    Y     287      A     293          2.423
LGA    Y     288      F     294          1.062
LGA    E     289      A     295          2.671
LGA    K     290      K     296           -
LGA    K     291      T     297           -
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     34    3.16    14.71     27.249     1.044

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.538446 * X  +   0.828269 * Y  +  -0.155071 * Z  +  28.514986
  Y_new =  -0.388933 * X  +   0.407529 * Y  +   0.826227 * Z  +  38.813393
  Z_new =   0.747534 * X  +  -0.384566 * Y  +   0.541573 * Z  +  28.786207 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.617466    2.524127  [ DEG:   -35.3782    144.6218 ]
  Theta =  -0.844342   -2.297251  [ DEG:   -48.3772   -131.6228 ]
  Phi   =  -0.625553    2.516040  [ DEG:   -35.8415    144.1585 ]
 
# 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_5-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS393_5-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   34   3.16   14.71  27.249
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS393_5-D2
PFRMAT TS
TARGET T0289
MODEL 5
PARENT N/A
ATOM    224  CA  ILE   224      24.552  37.342  34.325  1.00 25.00           C
ATOM    225  CA  MET   225      21.274  37.137  32.414  1.00 25.00           C
ATOM    226  CA  GLU   226      17.667  36.576  33.397  1.00 25.00           C
ATOM    227  CA  LYS   227      17.413  39.497  35.709  1.00 25.00           C
ATOM    228  CA  VAL   228      20.592  41.530  35.649  1.00 25.00           C
ATOM    229  CA  ASP   229      18.404  44.545  34.875  1.00 25.00           C
ATOM    230  CA  TYR   230      14.968  43.957  36.450  1.00 25.00           C
ATOM    231  CA  PRO   231      11.222  44.610  37.021  1.00 25.00           C
ATOM    232  CA  ARG   232       7.741  45.765  36.016  1.00 25.00           C
ATOM    233  CA  ASN   233       4.553  47.828  35.752  1.00 25.00           C
ATOM    234  CA  GLU   234       2.854  49.562  32.830  1.00 25.00           C
ATOM    235  CA  SER   235       3.871  49.064  29.177  1.00 25.00           C
ATOM    236  CA  GLY   236       6.964  46.971  28.640  1.00 25.00           C
ATOM    237  CA  ASP   237      10.221  45.523  27.341  1.00 25.00           C
ATOM    238  CA  VAL   238      13.811  44.332  27.786  1.00 25.00           C
ATOM    239  CA  ALA   239      15.597  43.193  24.583  1.00 25.00           C
ATOM    240  CA  ALA   240      18.010  44.190  21.868  1.00 25.00           C
ATOM    241  CA  VAL   241      19.117  41.321  19.638  1.00 25.00           C
ATOM    242  CA  ILE   242      18.888  39.471  16.280  1.00 25.00           C
ATOM    243  CA  HIS   243      20.717  39.429  12.945  1.00 25.00           C
ATOM    244  CA  PRO   244      20.486  42.817  11.177  1.00 25.00           C
ATOM    245  CA  ASN   245      19.351  44.999   8.274  1.00 25.00           C
ATOM    246  CA  LEU   246      21.633  47.897   7.298  1.00 25.00           C
ATOM    247  CA  GLN   247      22.538  47.159   3.721  1.00 25.00           C
ATOM    248  CA  ASP   248      25.323  49.445   2.569  1.00 25.00           C
ATOM    249  CA  GLN   249      27.348  47.572  -0.094  1.00 25.00           C
ATOM    250  CA  ASP   250      29.953  45.207  -1.356  1.00 25.00           C
ATOM    251  CA  TRP   251      33.412  45.467  -2.899  1.00 25.00           C
ATOM    252  CA  LYS   252      35.986  45.641  -0.121  1.00 25.00           C
ATOM    253  CA  PRO   253      39.766  46.082   0.156  1.00 25.00           C
ATOM    254  CA  LEU   254      41.542  43.523   2.317  1.00 25.00           C
ATOM    255  CA  HIS   255      42.893  44.225   5.798  1.00 25.00           C
ATOM    256  CA  PRO   256      43.841  44.104   9.453  1.00 25.00           C
ATOM    257  CA  GLY   257      43.425  42.919  13.015  1.00 25.00           C
ATOM    258  CA  ASP   258      42.121  42.251  16.491  1.00 25.00           C
ATOM    259  CA  PRO   259      40.485  41.130  19.757  1.00 25.00           C
ATOM    260  CA  VAL   260      37.480  38.999  20.748  1.00 25.00           C
ATOM    261  CA  PHE   261      36.171  37.689  24.088  1.00 25.00           C
ATOM    262  CA  VAL   262      33.416  36.068  26.190  1.00 25.00           C
ATOM    263  CA  SER   263      32.628  36.304  29.917  1.00 25.00           C
ATOM    264  CA  LEU   264      34.800  33.952  32.015  1.00 25.00           C
ATOM    265  CA  ASP   265      37.937  32.296  33.492  1.00 25.00           C
ATOM    266  CA  GLY   266      35.828  32.273  36.664  1.00 25.00           C
ATOM    267  CA  LYS   267      35.970  36.066  36.549  1.00 25.00           C
ATOM    268  CA  VAL   268      34.205  39.162  35.160  1.00 25.00           C
ATOM    269  CA  ILE   269      31.307  36.834  34.482  1.00 25.00           C
ATOM    270  CA  PRO   270      28.221  35.417  32.776  1.00 25.00           C
ATOM    271  CA  LEU   271      28.997  32.322  34.857  1.00 25.00           C
ATOM    272  CA  GLY   272      31.476  29.453  34.421  1.00 25.00           C
ATOM    273  CA  GLY   273      31.520  29.649  30.648  1.00 25.00           C
ATOM    274  CA  ASP   274      30.078  31.698  27.848  1.00 25.00           C
ATOM    275  CA  CYS   275      28.810  33.923  25.084  1.00 25.00           C
ATOM    276  CA  THR   276      28.681  35.122  21.500  1.00 25.00           C
ATOM    277  CA  VAL   277      29.873  37.045  18.468  1.00 25.00           C
ATOM    278  CA  TYR   278      27.430  39.874  19.315  1.00 25.00           C
ATOM    279  CA  PRO   279      25.894  43.133  20.402  1.00 25.00           C
ATOM    280  CA  VAL   280      23.217  45.686  21.094  1.00 25.00           C
ATOM    281  CA  PHE   281      22.063  49.063  22.298  1.00 25.00           C
ATOM    282  CA  VAL   282      19.604  49.128  25.205  1.00 25.00           C
ATOM    283  CA  ASN   283      19.777  45.443  26.145  1.00 25.00           C
ATOM    284  CA  GLU   284      22.422  43.861  28.314  1.00 25.00           C
ATOM    285  CA  ALA   285      21.531  40.138  28.456  1.00 25.00           C
ATOM    286  CA  ALA   286      19.849  40.385  25.024  1.00 25.00           C
ATOM    287  CA  TYR   287      22.954  42.118  23.600  1.00 25.00           C
ATOM    288  CA  TYR   288      25.186  39.366  25.053  1.00 25.00           C
ATOM    289  CA  GLU   289      22.935  36.685  23.499  1.00 25.00           C
ATOM    290  CA  LYS   290      23.114  38.464  20.112  1.00 25.00           C
ATOM    291  CA  LYS   291      23.568  38.009  16.423  1.00 25.00           C
ATOM    292  CA  GLU   292      23.363  41.777  16.501  1.00 25.00           C
ATOM    293  CA  ALA   293      26.746  43.342  15.672  1.00 25.00           C
ATOM    294  CA  PHE   294      30.402  42.515  15.540  1.00 25.00           C
ATOM    295  CA  ALA   295      34.077  43.397  16.033  1.00 25.00           C
ATOM    296  CA  LYS   296      37.306  43.755  14.120  1.00 25.00           C
ATOM    297  CA  THR   297      38.254  40.118  14.081  1.00 25.00           C
TER
END
