
#######################################################
#                                                     #
#                        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   52 (  208),  selected   52 , name T0289TS125_3u-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS125_3u-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          3.310
LGA    M     225      M     225          3.205
LGA    E     226      E     226          2.722
LGA    K     227      K     227          1.307
LGA    V     228      V     228          0.697
LGA    N     245      D     229          1.166
LGA    L     246      Y     230          2.306
LGA    Q     247      P     231          3.807
LGA    D     248      R     232          3.339
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    Q     249      V     238          2.695
LGA    D     250      A     239          4.144
LGA    -       -      A     240           -
LGA    W     251      V     241          1.449
LGA    K     252      I     242          1.481
LGA    P     253      H     243          2.514
LGA    -       -      P     244           -
LGA    -       -      N     245           -
LGA    L     254      L     246          2.783
LGA    H     255      Q     247          3.797
LGA    P     256      D     248          2.435
LGA    G     257      -       -           -
LGA    D     258      Q     249          1.960
LGA    P     259      D     250          3.401
LGA    V     260      W     251          2.429
LGA    F     261      -       -           -
LGA    V     262      K     252          1.368
LGA    S     263      P     253          0.886
LGA    L     264      L     254          1.843
LGA    D     265      H     255          2.232
LGA    G     266      P     256          2.237
LGA    K     267      G     257          2.080
LGA    V     268      D     258          2.525
LGA    I     269      P     259          2.794
LGA    P     270      V     260          1.796
LGA    L     271      F     261          1.416
LGA    G     272      V     262           #
LGA    G     273      S     263          4.812
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    D     274      K     267          5.644
LGA    C     275      V     268           #
LGA    T     276      I     269          1.327
LGA    V     277      P     270          3.798
LGA    Y     278      L     271          3.396
LGA    P     279      G     272          4.039
LGA    -       -      G     273           -
LGA    -       -      D     274           -
LGA    -       -      C     275           -
LGA    -       -      T     276           -
LGA    -       -      V     277           -
LGA    -       -      Y     278           -
LGA    -       -      P     279           -
LGA    V     280      V     280          1.496
LGA    F     281      F     281          1.811
LGA    V     282      V     282          1.244
LGA    N     283      N     283          1.622
LGA    K     290      E     284          5.404
LGA    K     291      A     285          3.717
LGA    E     292      A     286          4.922
LGA    A     293      Y     287           #
LGA    F     294      Y     288          4.245
LGA    A     295      E     289          4.562
LGA    K     296      K     290          2.311
LGA    T     297      K     291          3.534
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)   52   74    5.0     47    2.99    25.53     38.299     1.521

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.585660 * X  +  -0.120918 * Y  +  -0.801487 * Z  +  40.285961
  Y_new =  -0.146021 * X  +  -0.956893 * Y  +   0.251064 * Z  +  64.355156
  Z_new =  -0.797296 * X  +   0.264073 * Y  +   0.542757 * Z  +  -3.392287 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.452821   -2.688772  [ DEG:    25.9447   -154.0553 ]
  Theta =   0.922801    2.218791  [ DEG:    52.8726    127.1274 ]
  Phi   =  -2.897246    0.244346  [ DEG:  -166.0000     14.0000 ]
 
# 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: T0289TS125_3u-D2                              
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS125_3u-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   52   74   5.0   47   2.99   25.53  38.299
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS125_3u-D2
PFRMAT   TS
TARGET   T0289
MODEL    3  UNREFINED
PARENT   2bcoa   
ATOM     1   N   ILE   224      25.583  26.597  21.757    1.00  0.50
ATOM     1   CA  ILE   224      25.246  27.722  22.616    1.00  0.50
ATOM     1   C   ILE   224      25.182  27.339  24.100    1.00  0.50
ATOM     1   O   ILE   224      24.266  26.641  24.530    1.00  0.50
ATOM     1   N   MET   225      26.168  27.786  24.874    1.00  0.50
ATOM     1   CA  MET   225      26.197  27.503  26.306    1.00  0.50
ATOM     1   C   MET   225      24.946  28.111  26.904    1.00  0.50
ATOM     1   O   MET   225      24.167  27.429  27.562    1.00  0.50
ATOM     1   N   GLU   226      24.764  29.408  26.675    1.00  0.50
ATOM     1   CA  GLU   226      23.585  30.110  27.154    1.00  0.50
ATOM     1   C   GLU   226      23.361  31.403  26.389    1.00  0.50
ATOM     1   O   GLU   226      24.275  31.941  25.758    1.00  0.50
ATOM     1   N   LYS   227      22.124  31.881  26.434    1.00  0.50
ATOM     1   CA  LYS   227      21.742  33.101  25.744    1.00  0.50
ATOM     1   C   LYS   227      21.499  34.213  26.767    1.00  0.50
ATOM     1   O   LYS   227      20.775  34.018  27.740    1.00  0.50
ATOM     1   N   VAL   228      22.122  35.369  26.550    1.00  0.50
ATOM     1   CA  VAL   228      21.991  36.512  27.450    1.00  0.50
ATOM     1   C   VAL   228      20.849  37.438  27.022    1.00  0.50
ATOM     1   O   VAL   228      20.813  37.905  25.884    1.00  0.50
ATOM     1   N   ASN   245      19.928  37.712  27.939    1.00  0.50
ATOM     1   CA  ASN   245      18.794  38.584  27.645    1.00  0.50
ATOM     1   C   ASN   245      18.771  39.817  28.554    1.00  0.50
ATOM     1   O   ASN   245      18.863  39.693  29.775    1.00  0.50
ATOM     1   N   LEU   246      18.643  40.999  27.954    1.00  0.50
ATOM     1   CA  LEU   246      18.601  42.253  28.712    1.00  0.50
ATOM     1   C   LEU   246      17.293  42.389  29.493    1.00  0.50
ATOM     1   O   LEU   246      16.208  42.460  28.911    1.00  0.50
ATOM     1   N   GLN   247      17.414  42.428  30.818    1.00  0.50
ATOM     1   CA  GLN   247      16.264  42.541  31.705    1.00  0.50
ATOM     1   C   GLN   247      15.967  43.963  32.172    1.00  0.50
ATOM     1   O   GLN   247      14.804  44.337  32.318    1.00  0.50
ATOM     1   N   ASP   248      17.010  44.754  32.408    1.00  0.50
ATOM     1   CA  ASP   248      16.823  46.122  32.879    1.00  0.50
ATOM     1   C   ASP   248      17.430  47.172  31.958    1.00  0.50
ATOM     1   O   ASP   248      18.170  46.854  31.028    1.00  0.50
ATOM     1   N   GLN   249      17.111  48.431  32.238    1.00  0.50
ATOM     1   CA  GLN   249      17.603  49.557  31.453    1.00  0.50
ATOM     1   C   GLN   249      19.096  49.772  31.708    1.00  0.50
ATOM     1   O   GLN   249      19.846  50.150  30.805    1.00  0.50
ATOM     1   N   ASP   250      19.516  49.528  32.947    1.00  0.50
ATOM     1   CA  ASP   250      20.912  49.674  33.350    1.00  0.50
ATOM     1   C   ASP   250      21.643  48.368  33.063    1.00  0.50
ATOM     1   O   ASP   250      21.814  47.522  33.940    1.00  0.50
ATOM     1   N   TRP   251      22.072  48.222  31.818    1.00  0.50
ATOM     1   CA  TRP   251      22.760  47.027  31.348    1.00  0.50
ATOM     1   C   TRP   251      24.030  47.452  30.612    1.00  0.50
ATOM     1   O   TRP   251      24.030  48.464  29.913    1.00  0.50
ATOM     1   N   LYS   252      25.112  46.697  30.766    1.00  0.50
ATOM     1   CA  LYS   252      26.348  47.029  30.062    1.00  0.50
ATOM     1   C   LYS   252      27.400  45.937  30.225    1.00  0.50
ATOM     1   O   LYS   252      27.232  45.006  31.011    1.00  0.50
ATOM     1   N   PRO   253      28.484  46.061  29.470    1.00  0.50
ATOM     1   CA  PRO   253      29.579  45.103  29.520    1.00  0.50
ATOM     1   C   PRO   253      30.822  45.843  29.988    1.00  0.50
ATOM     1   O   PRO   253      30.884  47.061  29.889    1.00  0.50
ATOM     1   N   LEU   254      33.969  45.084  28.807    1.00  0.50
ATOM     1   CA  LEU   254      34.863  45.185  27.657    1.00  0.50
ATOM     1   C   LEU   254      34.438  46.327  26.740    1.00  0.50
ATOM     1   O   LEU   254      33.304  46.800  26.809    1.00  0.50
ATOM     1   N   HIS   255      35.356  46.764  25.884    1.00  0.50
ATOM     1   CA  HIS   255      35.096  47.854  24.950    1.00  0.50
ATOM     1   C   HIS   255      34.212  47.420  23.795    1.00  0.50
ATOM     1   O   HIS   255      34.015  46.227  23.562    1.00  0.50
ATOM     1   N   PRO   256      33.692  48.401  23.065    1.00  0.50
ATOM     1   CA  PRO   256      32.824  48.123  21.928    1.00  0.50
ATOM     1   C   PRO   256      33.525  47.364  20.802    1.00  0.50
ATOM     1   O   PRO   256      32.863  46.702  20.007    1.00  0.50
ATOM     1   N   GLY   257      34.850  47.460  20.725    1.00  0.50
ATOM     1   CA  GLY   257      35.591  46.742  19.693    1.00  0.50
ATOM     1   C   GLY   257      35.918  45.323  20.169    1.00  0.50
ATOM     1   O   GLY   257      36.846  44.677  19.672    1.00  0.50
ATOM     1   N   ASP   258      35.149  44.852  21.144    1.00  0.50
ATOM     1   CA  ASP   258      35.322  43.513  21.695    1.00  0.50
ATOM     1   C   ASP   258      35.212  42.479  20.566    1.00  0.50
ATOM     1   O   ASP   258      34.299  42.539  19.748    1.00  0.50
ATOM     1   N   PRO   259      36.139  41.531  20.528    1.00  0.50
ATOM     1   CA  PRO   259      36.147  40.509  19.485    1.00  0.50
ATOM     1   C   PRO   259      35.121  39.401  19.699    1.00  0.50
ATOM     1   O   PRO   259      34.748  39.095  20.835    1.00  0.50
ATOM     1   N   VAL   260      34.648  38.817  18.599    1.00  0.50
ATOM     1   CA  VAL   260      33.719  37.703  18.686    1.00  0.50
ATOM     1   C   VAL   260      34.553  36.536  19.199    1.00  0.50
ATOM     1   O   VAL   260      35.754  36.448  18.921    1.00  0.50
ATOM     1   N   PHE   261      33.917  35.647  19.946    1.00  0.50
ATOM     1   CA  PHE   261      34.592  34.492  20.533    1.00  0.50
ATOM     1   C   PHE   261      35.669  34.884  21.528    1.00  0.50
ATOM     1   O   PHE   261      36.714  34.242  21.599    1.00  0.50
ATOM     1   N   VAL   262      35.424  35.951  22.281    1.00  0.50
ATOM     1   CA  VAL   262      36.363  36.371  23.311    1.00  0.50
ATOM     1   C   VAL   262      36.001  35.478  24.497    1.00  0.50
ATOM     1   O   VAL   262      34.864  35.495  24.972    1.00  0.50
ATOM     1   N   SER   263      36.966  34.695  24.966    1.00  0.50
ATOM     1   CA  SER   263      36.724  33.769  26.068    1.00  0.50
ATOM     1   C   SER   263      36.861  34.373  27.453    1.00  0.50
ATOM     1   O   SER   263      37.403  35.463  27.625    1.00  0.50
ATOM     1   N   LEU   264      36.361  33.645  28.443    1.00  0.50
ATOM     1   CA  LEU   264      36.423  34.081  29.829    1.00  0.50
ATOM     1   C   LEU   264      36.778  32.884  30.692    1.00  0.50
ATOM     1   O   LEU   264      36.722  31.746  30.236    1.00  0.50
ATOM     1   N   ASP   265      37.154  33.147  31.936    1.00  0.50
ATOM     1   CA  ASP   265      37.490  32.082  32.867    1.00  0.50
ATOM     1   C   ASP   265      36.272  31.928  33.758    1.00  0.50
ATOM     1   O   ASP   265      35.492  32.865  33.889    1.00  0.50
ATOM     1   N   GLY   266      33.601  32.148  36.432    1.00  0.50
ATOM     1   CA  GLY   266      33.342  33.152  37.448    1.00  0.50
ATOM     1   C   GLY   266      33.817  34.552  37.122    1.00  0.50
ATOM     1   O   GLY   266      33.694  35.454  37.952    1.00  0.50
ATOM     1   N   LYS   267      34.370  34.750  35.930    1.00  0.50
ATOM     1   CA  LYS   267      34.835  36.080  35.555    1.00  0.50
ATOM     1   C   LYS   267      33.638  36.966  35.213    1.00  0.50
ATOM     1   O   LYS   267      32.741  36.550  34.475    1.00  0.50
ATOM     1   N   VAL   268      33.617  38.176  35.762    1.00  0.50
ATOM     1   CA  VAL   268      32.526  39.102  35.486    1.00  0.50
ATOM     1   C   VAL   268      32.899  39.900  34.248    1.00  0.50
ATOM     1   O   VAL   268      34.039  40.336  34.107    1.00  0.50
ATOM     1   N   ILE   269      31.947  40.079  33.340    1.00  0.50
ATOM     1   CA  ILE   269      32.227  40.822  32.118    1.00  0.50
ATOM     1   C   ILE   269      31.139  41.840  31.815    1.00  0.50
ATOM     1   O   ILE   269      31.160  42.498  30.776    1.00  0.50
ATOM     1   N   PRO   270      30.183  41.963  32.726    1.00  0.50
ATOM     1   CA  PRO   270      29.110  42.916  32.532    1.00  0.50
ATOM     1   C   PRO   270      28.143  42.872  33.693    1.00  0.50
ATOM     1   O   PRO   270      28.438  42.286  34.736    1.00  0.50
ATOM     1   N   LEU   271      26.983  43.487  33.514    1.00  0.50
ATOM     1   CA  LEU   271      25.984  43.502  34.563    1.00  0.50
ATOM     1   C   LEU   271      24.619  43.870  33.989    1.00  0.50
ATOM     1   O   LEU   271      24.515  44.626  33.018    1.00  0.50
ATOM     1   N   GLY   272      23.577  43.309  34.585    1.00  0.50
ATOM     1   CA  GLY   272      22.209  43.565  34.162    1.00  0.50
ATOM     1   C   GLY   272      21.484  44.016  35.424    1.00  0.50
ATOM     1   O   GLY   272      21.126  43.194  36.278    1.00  0.50
ATOM     1   N   GLY   273      21.276  45.324  35.547    1.00  0.50
ATOM     1   CA  GLY   273      20.628  45.844  36.733    1.00  0.50
ATOM     1   C   GLY   273      21.601  45.698  37.887    1.00  0.50
ATOM     1   O   GLY   273      22.637  46.363  37.915    1.00  0.50
ATOM     1   N   ASP   274      21.285  44.815  38.829    1.00  0.50
ATOM     1   CA  ASP   274      22.154  44.588  39.981    1.00  0.50
ATOM     1   C   ASP   274      22.941  43.297  39.795    1.00  0.50
ATOM     1   O   ASP   274      24.122  43.220  40.134    1.00  0.50
ATOM     1   N   CYS   275      22.265  42.286  39.259    1.00  0.50
ATOM     1   CA  CYS   275      22.862  40.973  39.025    1.00  0.50
ATOM     1   C   CYS   275      23.914  41.057  37.919    1.00  0.50
ATOM     1   O   CYS   275      23.593  41.349  36.768    1.00  0.50
ATOM     1   N   THR   276      25.186  40.794  38.258    1.00  0.50
ATOM     1   CA  THR   276      26.278  40.847  37.282    1.00  0.50
ATOM     1   C   THR   276      26.312  39.672  36.303    1.00  0.50
ATOM     1   O   THR   276      25.670  38.646  36.520    1.00  0.50
ATOM     1   N   VAL   277      27.066  39.844  35.222    1.00  0.50
ATOM     1   CA  VAL   277      27.210  38.811  34.201    1.00  0.50
ATOM     1   C   VAL   277      28.578  38.156  34.365    1.00  0.50
ATOM     1   O   VAL   277      29.600  38.844  34.354    1.00  0.50
ATOM     1   N   TYR   278      30.938  34.296  33.515    1.00  0.50
ATOM     1   CA  TYR   278      31.003  33.006  32.840    1.00  0.50
ATOM     1   C   TYR   278      30.594  31.889  33.796    1.00  0.50
ATOM     1   O   TYR   278      30.909  31.934  34.984    1.00  0.50
ATOM     1   N   PRO   279      29.889  30.893  33.266    1.00  0.50
ATOM     1   CA  PRO   279      29.427  29.759  34.057    1.00  0.50
ATOM     1   C   PRO   279      30.482  28.657  34.029    1.00  0.50
ATOM     1   O   PRO   279      31.023  28.273  35.066    1.00  0.50
ATOM     1   N   VAL   280      29.777  35.731  21.863    1.00  0.50
ATOM     1   CA  VAL   280      29.604  35.948  20.423    1.00  0.50
ATOM     1   C   VAL   280      28.437  36.906  20.143    1.00  0.50
ATOM     1   O   VAL   280      27.388  36.813  20.779    1.00  0.50
ATOM     1   N   PHE   281      28.615  37.820  19.190    1.00  0.50
ATOM     1   CA  PHE   281      27.554  38.778  18.839    1.00  0.50
ATOM     1   C   PHE   281      27.103  39.627  20.029    1.00  0.50
ATOM     1   O   PHE   281      25.935  39.602  20.409    1.00  0.50
ATOM     1   N   VAL   282      28.019  40.383  20.645    1.00  0.50
ATOM     1   CA  VAL   282      27.600  41.209  21.785    1.00  0.50
ATOM     1   C   VAL   282      26.946  42.492  21.277    1.00  0.50
ATOM     1   O   VAL   282      27.389  43.060  20.285    1.00  0.50
ATOM     1   N   ASN   283      25.899  42.947  21.954    1.00  0.50
ATOM     1   CA  ASN   283      25.216  44.178  21.553    1.00  0.50
ATOM     1   C   ASN   283      24.503  44.787  22.758    1.00  0.50
ATOM     1   O   ASN   283      23.449  44.304  23.171    1.00  0.50
ATOM     1   N   LYS   290      25.086  45.847  23.310    1.00  0.50
ATOM     1   CA  LYS   290      24.532  46.522  24.483    1.00  0.50
ATOM     1   C   LYS   290      23.370  47.466  24.162    1.00  0.50
ATOM     1   O   LYS   290      22.662  47.913  25.066    1.00  0.50
ATOM     1   N   LYS   291      23.172  47.766  22.882    1.00  0.50
ATOM     1   CA  LYS   291      22.097  48.660  22.473    1.00  0.50
ATOM     1   C   LYS   291      20.781  47.916  22.290    1.00  0.50
ATOM     1   O   LYS   291      19.719  48.528  22.174    1.00  0.50
ATOM     1   N   GLU   292      20.868  46.591  22.267    1.00  0.50
ATOM     1   CA  GLU   292      19.705  45.734  22.108    1.00  0.50
ATOM     1   C   GLU   292      18.569  46.170  23.028    1.00  0.50
ATOM     1   O   GLU   292      18.759  46.334  24.231    1.00  0.50
ATOM     1   N   ALA   293      17.387  46.358  22.452    1.00  0.50
ATOM     1   CA  ALA   293      16.227  46.781  23.224    1.00  0.50
ATOM     1   C   ALA   293      15.936  45.818  24.369    1.00  0.50
ATOM     1   O   ALA   293      16.386  44.673  24.367    1.00  0.50
ATOM     1   N   PHE   294      15.172  46.297  25.344    1.00  0.50
ATOM     1   CA  PHE   294      14.799  45.505  26.509    1.00  0.50
ATOM     1   C   PHE   294      14.086  44.209  26.110    1.00  0.50
ATOM     1   O   PHE   294      13.261  44.200  25.202    1.00  0.50
ATOM     1   N   ALA   295      14.416  43.113  26.788    1.00  0.50
ATOM     1   CA  ALA   295      13.773  41.844  26.496    1.00  0.50
ATOM     1   C   ALA   295      14.355  41.025  25.358    1.00  0.50
ATOM     1   O   ALA   295      14.017  39.853  25.216    1.00  0.50
ATOM     1   N   LYS   296      15.207  41.632  24.535    1.00  0.50
ATOM     1   CA  LYS   296      15.836  40.924  23.418    1.00  0.50
ATOM     1   C   LYS   296      17.183  40.361  23.882    1.00  0.50
ATOM     1   O   LYS   296      17.636  40.666  24.985    1.00  0.50
ATOM     1   N   THR   297      17.829  39.545  23.054    1.00  0.50
ATOM     1   CA  THR   297      19.108  38.976  23.462    1.00  0.50
ATOM     1   C   THR   297      20.252  39.939  23.204    1.00  0.50
ATOM     1   O   THR   297      20.320  40.577  22.151    1.00  0.50
TER
END
