
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS393_3-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    Y     230      -       -           -
LGA    P     231      -       -           -
LGA    R     232      -       -           -
LGA    N     233      -       -           -
LGA    E     234      -       -           -
LGA    S     235      -       -           -
LGA    G     236      -       -           -
LGA    D     237      -       -           -
LGA    V     238      -       -           -
LGA    A     239      V     228           #
LGA    A     240      D     229           #
LGA    V     241      Y     230           -
LGA    I     242      P     231          4.038
LGA    H     243      R     232          2.935
LGA    P     244      N     233          2.157
LGA    N     245      E     234          2.459
LGA    -       -      S     235           -
LGA    L     246      G     236          4.092
LGA    Q     247      D     237           -
LGA    D     248      V     238           -
LGA    Q     249      A     239           -
LGA    D     250      A     240           -
LGA    W     251      V     241           -
LGA    K     252      -       -           -
LGA    P     253      -       -           -
LGA    L     254      -       -           -
LGA    H     255      -       -           -
LGA    P     256      -       -           -
LGA    G     257      -       -           -
LGA    D     258      -       -           -
LGA    P     259      -       -           -
LGA    V     260      -       -           -
LGA    F     261      I     242           #
LGA    -       -      H     243           -
LGA    -       -      P     244           -
LGA    -       -      N     245           -
LGA    V     262      L     246          4.703
LGA    S     263      Q     247          4.005
LGA    L     264      D     248          4.804
LGA    D     265      Q     249          4.885
LGA    G     266      D     250          2.304
LGA    K     267      W     251          2.116
LGA    V     268      K     252          2.238
LGA    I     269      P     253          0.376
LGA    P     270      L     254          3.672
LGA    L     271      H     255           #
LGA    G     272      P     256           -
LGA    G     273      G     257           -
LGA    -       -      D     258           -
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    -       -      P     270           -
LGA    -       -      L     271           -
LGA    -       -      G     272           -
LGA    -       -      G     273           -
LGA    D     274      D     274           #
LGA    C     275      C     275          1.115
LGA    T     276      T     276          3.585
LGA    V     277      V     277          2.253
LGA    Y     278      Y     278          3.305
LGA    P     279      P     279          2.168
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      V     280          4.993
LGA    F     294      F     281          1.588
LGA    A     295      V     282          3.785
LGA    K     296      N     283           -
LGA    T     297      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     22    3.32    27.27     17.772     0.643

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.039693 * X  +  -0.539604 * Y  +  -0.840983 * Z  +  29.830658
  Y_new =  -0.282667 * X  +   0.813331 * Y  +  -0.508520 * Z  +  42.543877
  Z_new =   0.958396 * X  +   0.217534 * Y  +  -0.184812 * Z  +  36.035542 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.275046   -0.866546  [ DEG:   130.3505    -49.6495 ]
  Theta =  -1.281330   -1.860263  [ DEG:   -73.4148   -106.5852 ]
  Phi   =  -1.710308    1.431285  [ DEG:   -97.9934     82.0066 ]
 
# 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_3-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS393_3-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   22   3.32   27.27  17.772
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS393_3-D2
PFRMAT TS
TARGET T0289
MODEL 3
PARENT N/A
ATOM    224  CA  ILE   224      32.217  39.405  41.049  1.00 25.00           C
ATOM    225  CA  MET   225      33.130  35.871  42.030  1.00 25.00           C
ATOM    226  CA  GLU   226      34.612  32.486  42.574  1.00 25.00           C
ATOM    227  CA  LYS   227      35.860  29.792  40.245  1.00 25.00           C
ATOM    228  CA  VAL   228      33.691  28.832  37.270  1.00 25.00           C
ATOM    229  CA  ASP   229      29.977  28.036  36.813  1.00 25.00           C
ATOM    230  CA  TYR   230      30.342  24.439  38.121  1.00 25.00           C
ATOM    231  CA  PRO   231      28.348  21.665  39.791  1.00 25.00           C
ATOM    232  CA  ARG   232      25.668  19.787  37.849  1.00 25.00           C
ATOM    233  CA  ASN   233      24.444  16.647  36.096  1.00 25.00           C
ATOM    234  CA  GLU   234      24.400  17.770  32.441  1.00 25.00           C
ATOM    235  CA  SER   235      20.879  19.092  32.745  1.00 25.00           C
ATOM    236  CA  GLY   236      21.925  22.740  32.750  1.00 25.00           C
ATOM    237  CA  ASP   237      23.186  26.291  33.304  1.00 25.00           C
ATOM    238  CA  VAL   238      25.226  29.525  33.645  1.00 25.00           C
ATOM    239  CA  ALA   239      21.925  31.297  34.024  1.00 25.00           C
ATOM    240  CA  ALA   240      19.288  33.978  33.492  1.00 25.00           C
ATOM    241  CA  VAL   241      19.262  35.797  36.875  1.00 25.00           C
ATOM    242  CA  ILE   242      18.192  39.410  37.394  1.00 25.00           C
ATOM    243  CA  HIS   243      15.383  41.964  36.901  1.00 25.00           C
ATOM    244  CA  PRO   244      12.143  43.806  36.141  1.00 25.00           C
ATOM    245  CA  ASN   245       8.451  42.904  36.498  1.00 25.00           C
ATOM    246  CA  LEU   246       7.285  45.830  34.441  1.00 25.00           C
ATOM    247  CA  GLN   247       4.124  45.747  32.367  1.00 25.00           C
ATOM    248  CA  ASP   248       1.823  44.974  29.400  1.00 25.00           C
ATOM    249  CA  GLN   249       2.682  46.808  26.258  1.00 25.00           C
ATOM    250  CA  ASP   250       1.078  50.223  25.824  1.00 25.00           C
ATOM    251  CA  TRP   251       3.089  52.576  23.634  1.00 25.00           C
ATOM    252  CA  LYS   252       0.793  52.318  20.597  1.00 25.00           C
ATOM    253  CA  PRO   253       3.992  53.045  18.699  1.00 25.00           C
ATOM    254  CA  LEU   254       7.141  52.834  16.583  1.00 25.00           C
ATOM    255  CA  HIS   255       9.382  50.006  15.460  1.00 25.00           C
ATOM    256  CA  PRO   256      13.157  49.914  15.559  1.00 25.00           C
ATOM    257  CA  GLY   257      15.796  49.848  18.253  1.00 25.00           C
ATOM    258  CA  ASP   258      19.129  48.278  19.261  1.00 25.00           C
ATOM    259  CA  PRO   259      22.142  46.875  21.136  1.00 25.00           C
ATOM    260  CA  VAL   260      25.492  45.580  22.435  1.00 25.00           C
ATOM    261  CA  PHE   261      29.236  46.368  22.402  1.00 25.00           C
ATOM    262  CA  VAL   262      31.901  46.758  25.105  1.00 25.00           C
ATOM    263  CA  SER   263      34.172  44.442  23.072  1.00 25.00           C
ATOM    264  CA  LEU   264      38.009  44.416  22.872  1.00 25.00           C
ATOM    265  CA  ASP   265      38.480  42.166  19.835  1.00 25.00           C
ATOM    266  CA  GLY   266      35.456  40.021  20.656  1.00 25.00           C
ATOM    267  CA  LYS   267      37.023  36.585  20.051  1.00 25.00           C
ATOM    268  CA  VAL   268      35.372  36.251  23.433  1.00 25.00           C
ATOM    269  CA  ILE   269      37.332  34.179  25.945  1.00 25.00           C
ATOM    270  CA  PRO   270      37.161  32.170  29.177  1.00 25.00           C
ATOM    271  CA  LEU   271      40.439  30.629  27.970  1.00 25.00           C
ATOM    272  CA  GLY   272      42.134  27.528  26.636  1.00 25.00           C
ATOM    273  CA  GLY   273      40.329  25.725  29.396  1.00 25.00           C
ATOM    274  CA  ASP   274      37.352  27.519  30.853  1.00 25.00           C
ATOM    275  CA  CYS   275      33.710  28.227  31.585  1.00 25.00           C
ATOM    276  CA  THR   276      32.444  31.759  31.112  1.00 25.00           C
ATOM    277  CA  VAL   277      31.151  32.701  27.629  1.00 25.00           C
ATOM    278  CA  TYR   278      30.249  34.722  24.584  1.00 25.00           C
ATOM    279  CA  PRO   279      31.069  38.319  23.847  1.00 25.00           C
ATOM    280  CA  VAL   280      30.295  41.897  24.736  1.00 25.00           C
ATOM    281  CA  PHE   281      27.844  43.992  26.762  1.00 25.00           C
ATOM    282  CA  VAL   282      26.115  47.332  27.360  1.00 25.00           C
ATOM    283  CA  ASN   283      24.207  48.537  30.378  1.00 25.00           C
ATOM    284  CA  GLU   284      22.827  45.067  30.103  1.00 25.00           C
ATOM    285  CA  ALA   285      21.292  46.178  26.775  1.00 25.00           C
ATOM    286  CA  ALA   286      22.705  43.061  25.054  1.00 25.00           C
ATOM    287  CA  TYR   287      21.246  40.846  27.817  1.00 25.00           C
ATOM    288  CA  TYR   288      17.838  42.545  27.414  1.00 25.00           C
ATOM    289  CA  GLU   289      17.977  41.984  23.629  1.00 25.00           C
ATOM    290  CA  LYS   290      18.835  38.292  24.183  1.00 25.00           C
ATOM    291  CA  LYS   291      21.162  35.799  25.798  1.00 25.00           C
ATOM    292  CA  GLU   292      24.576  35.058  24.256  1.00 25.00           C
ATOM    293  CA  ALA   293      25.477  38.643  23.627  1.00 25.00           C
ATOM    294  CA  PHE   294      27.104  40.830  20.963  1.00 25.00           C
ATOM    295  CA  ALA   295      30.204  42.701  19.911  1.00 25.00           C
ATOM    296  CA  LYS   296      29.337  45.257  17.295  1.00 25.00           C
ATOM    297  CA  THR   297      32.256  44.763  14.930  1.00 25.00           C
TER
END
