
#######################################################
#                                                     #
#                        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 T0386TS393_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS393_2-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      -       -           -
LGA    P     220      -       -           -
LGA    E     221      -       -           -
LGA    K     222      N     219          0.498
LGA    I     223      P     220          1.834
LGA    R     224      E     221          2.378
LGA    L     225      K     222          1.082
LGA    L     226      I     223          1.072
LGA    K     227      R     224          1.817
LGA    E     228      L     225          1.727
LGA    F     229      L     226          0.799
LGA    M     230      K     227          0.703
LGA    H     231      E     228          1.422
LGA    T     232      F     229          1.659
LGA    M     233      M     230          1.626
LGA    K     234      H     231          1.538
LGA    N     235      T     232          3.330
LGA    T     236      M     233           -
LGA    G     237      K     234           -
LGA    R     238      N     235           -
LGA    N     239      T     236           -
LGA    V     240      G     237           -
LGA    N     241      R     238           -
LGA    D     242      N     239           -
LGA    R     243      V     240           -
LGA    P     244      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    V     245      V     247          3.220
LGA    M     246      A     248          1.564
LGA    V     247      K     249          2.348
LGA    A     248      E     250          3.185
LGA    K     249      G     251          4.189
LGA    E     250      E     252           #
LGA    G     251      -       -           -
LGA    E     252      T     253          4.146
LGA    T     253      Y     254          3.109
LGA    Y     254      T     255          5.144
LGA    T     255      G     256           #
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
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    G     256      N     269          3.871
LGA    T     257      V     270          3.262
LGA    Y     258      K     271           #
LGA    R     259      G     272          4.184
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      A     273          4.126
LGA    V     270      Y     274           -
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      -       -           -
LGA    P     283      -       -           -
LGA    P     284      -       -           -
LGA    E     285      -       -           -
LGA    Q     286      I     275           #
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    -       -      I     279           -
LGA    -       -      D     280           -
LGA    L     287      H     281          4.704
LGA    K     288      L     282          2.114
LGA    -       -      P     283           -
LGA    I     289      P     284           #
LGA    L     290      E     285           -
LGA    K     291      Q     286          4.498
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    P     292      K     295          4.395
LGA    G     293      I     296          3.551
LGA    D     294      T     297           -
LGA    K     295      F     298           -
LGA    I     296      T     299           -
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     31    3.00     6.45     26.724     1.002

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.252607 * X  +   0.952814 * Y  +   0.168331 * Z  +  16.284090
  Y_new =  -0.832938 * X  +   0.125616 * Y  +   0.538921 * Z  +  54.115181
  Z_new =   0.492346 * X  +  -0.276344 * Y  +   0.825366 * Z  +  63.560246 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.323083    2.818510  [ DEG:   -18.5113    161.4887 ]
  Theta =  -0.514783   -2.626809  [ DEG:   -29.4949   -150.5051 ]
  Phi   =  -1.276340    1.865252  [ DEG:   -73.1289    106.8711 ]
 
# 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: T0386TS393_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS393_2-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   31   3.00    6.45  26.724
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS393_2-D2
PFRMAT TS
TARGET T0386
MODEL 2
PARENT N/A
ATOM    219  CA  ASN   219      -3.256  52.485  76.193  1.00 25.00           C
ATOM    220  CA  PRO   220      -2.086  56.070  75.916  1.00 25.00           C
ATOM    221  CA  GLU   221       1.277  55.129  77.487  1.00 25.00           C
ATOM    222  CA  LYS   222       3.095  56.173  74.282  1.00 25.00           C
ATOM    223  CA  ILE   223       1.230  59.518  74.285  1.00 25.00           C
ATOM    224  CA  ARG   224       2.189  60.078  77.949  1.00 25.00           C
ATOM    225  CA  LEU   225       5.851  59.305  77.135  1.00 25.00           C
ATOM    226  CA  LEU   226       5.748  61.779  74.213  1.00 25.00           C
ATOM    227  CA  LYS   227       4.252  64.459  76.503  1.00 25.00           C
ATOM    228  CA  GLU   228       7.002  63.821  79.090  1.00 25.00           C
ATOM    229  CA  PHE   229       9.673  64.128  76.361  1.00 25.00           C
ATOM    230  CA  MET   230       8.124  67.427  75.183  1.00 25.00           C
ATOM    231  CA  HIS   231       8.120  68.739  78.780  1.00 25.00           C
ATOM    232  CA  THR   232      11.800  67.752  79.170  1.00 25.00           C
ATOM    233  CA  MET   233      12.654  69.549  75.897  1.00 25.00           C
ATOM    234  CA  LYS   234      10.807  72.678  77.105  1.00 25.00           C
ATOM    235  CA  ASN   235      12.724  72.562  80.418  1.00 25.00           C
ATOM    236  CA  THR   236      12.681  71.708  84.157  1.00 25.00           C
ATOM    237  CA  GLY   237      15.095  73.300  86.611  1.00 25.00           C
ATOM    238  CA  ARG   238      17.592  70.763  85.269  1.00 25.00           C
ATOM    239  CA  ASN   239      19.205  67.575  86.404  1.00 25.00           C
ATOM    240  CA  VAL   240      16.378  65.462  85.119  1.00 25.00           C
ATOM    241  CA  ASN   241      14.575  65.940  88.432  1.00 25.00           C
ATOM    242  CA  ASP   242      11.302  64.072  88.925  1.00 25.00           C
ATOM    243  CA  ARG   243      12.432  62.106  85.859  1.00 25.00           C
ATOM    244  CA  PRO   244      11.655  59.279  83.525  1.00 25.00           C
ATOM    245  CA  VAL   245      13.805  57.680  80.838  1.00 25.00           C
ATOM    246  CA  MET   246      13.263  53.890  81.143  1.00 25.00           C
ATOM    247  CA  VAL   247      13.548  50.055  81.272  1.00 25.00           C
ATOM    248  CA  ALA   248      12.787  46.959  83.344  1.00 25.00           C
ATOM    249  CA  LYS   249      12.341  46.854  87.117  1.00 25.00           C
ATOM    250  CA  GLU   250      15.570  45.176  88.116  1.00 25.00           C
ATOM    251  CA  GLY   251      19.266  45.938  88.518  1.00 25.00           C
ATOM    252  CA  GLU   252      21.359  49.051  87.898  1.00 25.00           C
ATOM    253  CA  THR   253      22.888  50.218  84.632  1.00 25.00           C
ATOM    254  CA  TYR   254      20.828  51.993  81.986  1.00 25.00           C
ATOM    255  CA  THR   255      21.153  55.529  80.503  1.00 25.00           C
ATOM    256  CA  GLY   256      24.290  57.361  79.379  1.00 25.00           C
ATOM    257  CA  THR   257      26.633  60.023  77.973  1.00 25.00           C
ATOM    258  CA  TYR   258      26.849  63.145  75.846  1.00 25.00           C
ATOM    259  CA  ARG   259      30.579  62.554  75.203  1.00 25.00           C
ATOM    260  CA  GLY   260      31.438  66.256  75.354  1.00 25.00           C
ATOM    261  CA  ALA   261      32.128  66.900  71.679  1.00 25.00           C
ATOM    262  CA  GLY   262      31.331  68.805  68.560  1.00 25.00           C
ATOM    263  CA  LEU   263      27.632  68.150  68.062  1.00 25.00           C
ATOM    264  CA  GLU   264      27.100  70.399  71.037  1.00 25.00           C
ATOM    265  CA  GLY   265      25.239  67.337  72.490  1.00 25.00           C
ATOM    266  CA  PHE   266      24.427  63.954  71.029  1.00 25.00           C
ATOM    267  CA  ALA   267      21.798  62.782  73.429  1.00 25.00           C
ATOM    268  CA  LEU   268      23.074  59.280  74.389  1.00 25.00           C
ATOM    269  CA  ASN   269      25.315  56.197  74.616  1.00 25.00           C
ATOM    270  CA  VAL   270      27.306  58.117  71.943  1.00 25.00           C
ATOM    271  CA  LYS   271      30.094  56.138  73.510  1.00 25.00           C
ATOM    272  CA  GLY   272      29.252  53.427  75.972  1.00 25.00           C
ATOM    273  CA  ALA   273      29.130  50.278  73.771  1.00 25.00           C
ATOM    274  CA  TYR   274      26.829  50.384  70.733  1.00 25.00           C
ATOM    275  CA  ILE   275      23.632  50.906  72.728  1.00 25.00           C
ATOM    276  CA  ILE   276      20.807  49.296  74.670  1.00 25.00           C
ATOM    277  CA  GLY   277      17.759  48.399  76.773  1.00 25.00           C
ATOM    278  CA  ASN   278      20.333  47.649  79.411  1.00 25.00           C
ATOM    279  CA  ILE   279      22.368  45.420  81.634  1.00 25.00           C
ATOM    280  CA  ASP   280      21.505  42.794  84.236  1.00 25.00           C
ATOM    281  CA  HIS   281      17.667  42.582  84.081  1.00 25.00           C
ATOM    282  CA  LEU   282      17.743  46.337  83.595  1.00 25.00           C
ATOM    283  CA  PRO   283      16.640  49.589  85.253  1.00 25.00           C
ATOM    284  CA  PRO   284      16.872  51.621  88.456  1.00 25.00           C
ATOM    285  CA  GLU   285      18.144  55.075  89.518  1.00 25.00           C
ATOM    286  CA  GLN   286      17.234  56.495  86.079  1.00 25.00           C
ATOM    287  CA  LEU   287      13.730  54.974  86.350  1.00 25.00           C
ATOM    288  CA  LYS   288      13.307  56.507  89.835  1.00 25.00           C
ATOM    289  CA  ILE   289      14.171  60.077  90.831  1.00 25.00           C
ATOM    290  CA  LEU   290      17.637  60.289  89.418  1.00 25.00           C
ATOM    291  CA  LYS   291      19.399  59.210  92.618  1.00 25.00           C
ATOM    292  CA  PRO   292      22.515  58.283  90.556  1.00 25.00           C
ATOM    293  CA  GLY   293      22.869  60.655  87.660  1.00 25.00           C
ATOM    294  CA  ASP   294      20.439  62.151  85.172  1.00 25.00           C
ATOM    295  CA  LYS   295      18.790  62.045  81.751  1.00 25.00           C
ATOM    296  CA  ILE   296      17.563  61.682  78.194  1.00 25.00           C
ATOM    297  CA  THR   297      15.303  61.828  75.223  1.00 25.00           C
ATOM    298  CA  PHE   298      14.711  58.538  73.473  1.00 25.00           C
ATOM    299  CA  THR   299      15.328  59.945  69.982  1.00 25.00           C
TER
END
