
#######################################################
#                                                     #
#                        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   81 (   81),  selected   81 , name T0386TS168_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS168_1-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219           -
LGA    P     220      P     220           -
LGA    E     221      E     221           -
LGA    K     222      K     222           -
LGA    I     223      I     223           -
LGA    R     224      R     224           -
LGA    L     225      -       -           -
LGA    L     226      -       -           -
LGA    K     227      -       -           -
LGA    E     228      L     225           #
LGA    F     229      L     226           #
LGA    M     230      K     227          5.100
LGA    H     231      E     228          3.132
LGA    T     232      F     229          0.958
LGA    M     233      -       -           -
LGA    K     234      M     230          2.652
LGA    N     235      H     231           #
LGA    T     236      T     232          3.272
LGA    G     237      M     233          2.795
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    R     238      V     240          3.579
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    N     239      R     243          5.398
LGA    V     240      P     244          5.337
LGA    N     241      V     245          3.240
LGA    D     242      -       -           -
LGA    R     243      M     246          2.011
LGA    P     244      V     247          3.695
LGA    V     245      A     248          1.275
LGA    M     246      K     249           #
LGA    V     247      E     250           -
LGA    A     248      G     251           -
LGA    K     249      -       -           -
LGA    E     250      -       -           -
LGA    G     251      -       -           -
LGA    E     252      -       -           -
LGA    T     253      -       -           -
LGA    Y     254      E     252          5.536
LGA    T     255      T     253          2.979
LGA    G     256      Y     254           -
LGA    T     257      T     255           -
LGA    Y     258      G     256           -
LGA    R     259      -       -           -
LGA    G     260      -       -           -
LGA    A     261      -       -           -
LGA    G     262      -       -           -
LGA    L     263      -       -           -
LGA    E     264      -       -           -
LGA    G     265      -       -           -
LGA    F     266      -       -           -
LGA    A     267      -       -           -
LGA    L     268      -       -           -
LGA    N     269      -       -           -
LGA    V     270      -       -           -
LGA    K     271      -       -           -
LGA    G     272      -       -           -
LGA    A     273      -       -           -
LGA    Y     274      -       -           -
LGA    I     275      -       -           -
LGA    I     276      -       -           -
LGA    G     277      -       -           -
LGA    N     278      -       -           -
LGA    I     279      -       -           -
LGA    D     280      -       -           -
LGA    H     281      -       -           -
LGA    L     282      T     257          1.258
LGA    P     283      Y     258          2.187
LGA    P     284      R     259          3.912
LGA    E     285      G     260           #
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    Q     286      F     266          3.153
LGA    L     287      A     267          2.668
LGA    K     288      L     268          2.277
LGA    I     289      N     269          3.061
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    L     290      G     272          4.475
LGA    K     291      A     273          3.859
LGA    P     292      Y     274           -
LGA    G     293      -       -           -
LGA    D     294      I     275          3.335
LGA    K     295      I     276          2.962
LGA    I     296      G     277          3.491
LGA    T     297      N     278          2.940
LGA    F     298      I     279          2.928
LGA    T     299      D     280          3.073
LGA    -       -      H     281           -
LGA    -       -      L     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   81   81    5.0     30    3.41     6.67     21.610     0.855

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.161928 * X  +   0.770321 * Y  +   0.616753 * Z  +   3.603196
  Y_new =   0.740273 * X  +  -0.318451 * Y  +   0.592102 * Z  +  53.973732
  Z_new =   0.652514 * X  +   0.552444 * Y  +  -0.518682 * Z  +  95.182983 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.324684   -0.816908  [ DEG:   133.1946    -46.8054 ]
  Theta =  -0.710898   -2.430695  [ DEG:   -40.7314   -139.2686 ]
  Phi   =   1.786146   -1.355447  [ DEG:   102.3386    -77.6614 ]
 
# 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: T0386TS168_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS168_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   81   81   5.0   30   3.41    6.67  21.610
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS168_1-D2
PFRMAT TS
TARGET T0386
MODEL 1
PARENT N/A
ATOM    219  CA  ASN   219       9.357  77.258  96.776  1.00 25.00           C
ATOM    220  CA  PRO   220       7.919  75.322  93.839  1.00 25.00           C
ATOM    221  CA  GLU   221      10.806  72.810  93.670  1.00 25.00           C
ATOM    222  CA  LYS   222       8.392  70.078  92.497  1.00 25.00           C
ATOM    223  CA  ILE   223       7.010  72.422  89.802  1.00 25.00           C
ATOM    224  CA  ARG   224      10.570  73.224  88.639  1.00 25.00           C
ATOM    225  CA  LEU   225      11.381  69.485  88.465  1.00 25.00           C
ATOM    226  CA  LEU   226       8.206  68.864  86.417  1.00 25.00           C
ATOM    227  CA  LYS   227       9.162  71.702  84.029  1.00 25.00           C
ATOM    228  CA  GLU   228      12.672  70.220  83.635  1.00 25.00           C
ATOM    229  CA  PHE   229      11.163  66.781  82.888  1.00 25.00           C
ATOM    230  CA  MET   230       8.843  68.340  80.269  1.00 25.00           C
ATOM    231  CA  HIS   231      11.824  70.122  78.654  1.00 25.00           C
ATOM    232  CA  THR   232      13.774  66.827  78.561  1.00 25.00           C
ATOM    233  CA  MET   233      10.782  65.073  76.936  1.00 25.00           C
ATOM    234  CA  LYS   234      10.537  67.861  74.321  1.00 25.00           C
ATOM    235  CA  ASN   235      14.280  67.529  73.582  1.00 25.00           C
ATOM    236  CA  THR   236      15.437  70.795  75.081  1.00 25.00           C
ATOM    237  CA  GLY   237      19.211  70.624  74.713  1.00 25.00           C
ATOM    238  CA  ARG   238      19.763  66.986  73.752  1.00 25.00           C
ATOM    239  CA  ASN   239      17.848  64.663  71.448  1.00 25.00           C
ATOM    240  CA  VAL   240      16.098  61.842  73.285  1.00 25.00           C
ATOM    241  CA  ASN   241      17.378  59.786  70.296  1.00 25.00           C
ATOM    242  CA  ASP   242      19.046  56.570  71.448  1.00 25.00           C
ATOM    243  CA  ARG   243      16.065  56.306  73.814  1.00 25.00           C
ATOM    244  CA  PRO   244      14.795  53.880  76.428  1.00 25.00           C
ATOM    245  CA  VAL   245      13.280  54.716  79.846  1.00 25.00           C
ATOM    246  CA  MET   246      14.470  55.732  83.313  1.00 25.00           C
ATOM    247  CA  VAL   247      16.240  54.907  86.566  1.00 25.00           C
ATOM    248  CA  ALA   248      19.650  55.003  88.101  1.00 25.00           C
ATOM    249  CA  LYS   249      23.423  54.933  88.458  1.00 25.00           C
ATOM    250  CA  GLU   250      26.788  54.382  90.057  1.00 25.00           C
ATOM    251  CA  GLY   251      28.143  53.452  86.557  1.00 25.00           C
ATOM    252  CA  GLU   252      25.922  51.121  84.591  1.00 25.00           C
ATOM    253  CA  THR   253      23.243  48.500  84.567  1.00 25.00           C
ATOM    254  CA  TYR   254      20.089  50.484  85.531  1.00 25.00           C
ATOM    255  CA  THR   255      16.827  50.543  83.547  1.00 25.00           C
ATOM    256  CA  GLY   256      13.002  50.877  83.352  1.00 25.00           C
ATOM    257  CA  THR   257       9.661  52.181  82.218  1.00 25.00           C
ATOM    258  CA  TYR   258       6.939  54.172  80.559  1.00 25.00           C
ATOM    259  CA  ARG   259       5.427  52.980  77.231  1.00 25.00           C
ATOM    260  CA  GLY   260       6.874  50.378  74.850  1.00 25.00           C
ATOM    261  CA  ALA   261       3.884  49.052  72.907  1.00 25.00           C
ATOM    262  CA  GLY   262       0.317  49.927  71.977  1.00 25.00           C
ATOM    263  CA  LEU   263       0.044  53.028  74.172  1.00 25.00           C
ATOM    264  CA  GLU   264      -2.116  51.308  76.725  1.00 25.00           C
ATOM    265  CA  GLY   265       0.270  52.781  79.212  1.00 25.00           C
ATOM    266  CA  PHE   266       2.150  49.546  79.861  1.00 25.00           C
ATOM    267  CA  ALA   267       5.887  49.185  80.696  1.00 25.00           C
ATOM    268  CA  LEU   268       9.226  47.588  79.890  1.00 25.00           C
ATOM    269  CA  ASN   269      11.157  46.172  82.857  1.00 25.00           C
ATOM    270  CA  VAL   270      13.764  43.431  82.470  1.00 25.00           C
ATOM    271  CA  LYS   271      16.513  43.163  85.086  1.00 25.00           C
ATOM    272  CA  GLY   272      17.749  45.049  88.082  1.00 25.00           C
ATOM    273  CA  ALA   273      15.660  45.751  91.190  1.00 25.00           C
ATOM    274  CA  TYR   274      12.565  47.769  90.108  1.00 25.00           C
ATOM    275  CA  ILE   275      13.965  50.516  92.262  1.00 25.00           C
ATOM    276  CA  ILE   276      15.553  53.883  92.940  1.00 25.00           C
ATOM    277  CA  GLY   277      16.632  57.036  94.768  1.00 25.00           C
ATOM    278  CA  ASN   278      19.918  57.351  92.924  1.00 25.00           C
ATOM    279  CA  ILE   279      22.593  59.454  91.389  1.00 25.00           C
ATOM    280  CA  ASP   280      24.845  62.335  92.320  1.00 25.00           C
ATOM    281  CA  HIS   281      27.335  60.977  89.785  1.00 25.00           C
ATOM    282  CA  LEU   282      25.406  60.917  86.481  1.00 25.00           C
ATOM    283  CA  PRO   283      24.060  64.287  87.752  1.00 25.00           C
ATOM    284  CA  PRO   284      20.278  64.271  88.144  1.00 25.00           C
ATOM    285  CA  GLU   285      20.013  60.781  86.590  1.00 25.00           C
ATOM    286  CA  GLN   286      17.139  61.968  84.355  1.00 25.00           C
ATOM    287  CA  LEU   287      19.210  64.998  83.259  1.00 25.00           C
ATOM    288  CA  LYS   288      22.173  62.710  82.448  1.00 25.00           C
ATOM    289  CA  ILE   289      22.632  63.058  78.686  1.00 25.00           C
ATOM    290  CA  LEU   290      22.550  60.032  76.392  1.00 25.00           C
ATOM    291  CA  LYS   291      25.264  58.202  78.370  1.00 25.00           C
ATOM    292  CA  PRO   292      25.029  54.573  77.360  1.00 25.00           C
ATOM    293  CA  GLY   293      21.747  53.566  75.749  1.00 25.00           C
ATOM    294  CA  ASP   294      19.384  55.913  77.595  1.00 25.00           C
ATOM    295  CA  LYS   295      17.013  58.051  79.730  1.00 25.00           C
ATOM    296  CA  ILE   296      14.122  60.251  80.724  1.00 25.00           C
ATOM    297  CA  THR   297      11.094  60.349  83.015  1.00 25.00           C
ATOM    298  CA  PHE   298       9.682  59.101  86.363  1.00 25.00           C
ATOM    299  CA  THR   299       6.323  59.125  88.172  1.00 25.00           C
TER
END
