
#######################################################
#                                                     #
#                        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   14 (  113),  selected   14 , name T0356TS249_2_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS249_2_3-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    D     314      R     324          2.658
LGA    A     315      P     325          1.993
LGA    -       -      P     326           -
LGA    I     316      D     327          2.858
LGA    Y     317      E     328          1.489
LGA    H     318      P     329          2.783
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    S     319      L     332          1.002
LGA    T     320      G     333          2.827
LGA    -       -      V     334           -
LGA    -       -      A     335           -
LGA    Y     321      L     336          0.633
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    T     322      V     339          2.225
LGA    G     323      F     340          2.949
LGA    R     324      V     341          2.898
LGA    P     325      P     342          2.326
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    P     326      Q     345          1.159
LGA    D     327      K     346          1.905
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   14  124    5.0     14    2.25     7.14      8.467     0.595

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.566547 * X  +  -0.002830 * Y  +   0.824025 * Z  +  27.208654
  Y_new =  -0.718327 * X  +   0.488296 * Y  +   0.495553 * Z  + 103.563644
  Z_new =  -0.403770 * X  +  -0.872674 * Y  +   0.274610 * Z  + 113.149887 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.265930    1.875663  [ DEG:   -72.5324    107.4676 ]
  Theta =   0.415634    2.725958  [ DEG:    23.8141    156.1859 ]
  Phi   =  -0.902982    2.238611  [ DEG:   -51.7371    128.2629 ]
 
# 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: T0356TS249_2_3-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS249_2_3-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   14  124   5.0   14   2.25    7.14   8.467
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS249_2_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1geh_A
ATOM    417  N   ASP   314      50.349  61.834  80.307  1.00  9.99
ATOM    418  CA  ASP   314      51.182  60.703  80.064  1.00  9.99
ATOM    419  CB  ASP   314      51.076  60.195  78.618  1.00  9.99
ATOM    420  CG  ASP   314      51.535  61.308  77.687  1.00  9.99
ATOM    421  OD1 ASP   314      51.732  62.455  78.167  1.00  9.99
ATOM    422  OD2 ASP   314      51.684  61.023  76.469  1.00  9.99
ATOM    423  C   ASP   314      52.638  60.964  80.346  1.00  9.99
ATOM    424  O   ASP   314      53.435  60.033  80.225  1.00  9.99
ATOM    425  N   ALA   315      53.081  62.214  80.619  1.00  9.99
ATOM    426  CA  ALA   315      54.516  62.306  80.746  1.00  9.99
ATOM    427  CB  ALA   315      55.190  62.862  79.477  1.00  9.99
ATOM    428  C   ALA   315      55.021  63.136  81.900  1.00  9.99
ATOM    429  O   ALA   315      54.370  64.070  82.366  1.00  9.99
ATOM    430  N   ILE   316      56.213  62.735  82.417  1.00  9.99
ATOM    431  CA  ILE   316      56.908  63.371  83.510  1.00  9.99
ATOM    432  CB  ILE   316      58.058  62.566  84.030  1.00  9.99
ATOM    433  CG2 ILE   316      58.814  63.462  85.026  1.00  9.99
ATOM    434  CG1 ILE   316      57.600  61.236  84.629  1.00  9.99
ATOM    435  CD1 ILE   316      56.722  61.401  85.868  1.00  9.99
ATOM    436  C   ILE   316      57.559  64.683  83.166  1.00  9.99
ATOM    437  O   ILE   316      57.240  65.728  83.730  1.00  9.99
ATOM    438  N   TYR   317      58.487  64.650  82.193  1.00  9.99
ATOM    439  CA  TYR   317      59.303  65.779  81.851  1.00  9.99
ATOM    440  CB  TYR   317      60.791  65.457  82.071  1.00  9.99
ATOM    441  CG  TYR   317      61.650  66.614  81.705  1.00  9.99
ATOM    442  CD1 TYR   317      61.841  67.656  82.584  1.00  9.99
ATOM    443  CD2 TYR   317      62.286  66.638  80.487  1.00  9.99
ATOM    444  CE1 TYR   317      62.644  68.716  82.240  1.00  9.99
ATOM    445  CE2 TYR   317      63.090  67.696  80.137  1.00  9.99
ATOM    446  CZ  TYR   317      63.272  68.736  81.017  1.00  9.99
ATOM    447  OH  TYR   317      64.098  69.824  80.663  1.00  9.99
ATOM    448  C   TYR   317      59.076  65.986  80.397  1.00  9.99
ATOM    449  O   TYR   317      59.161  65.045  79.609  1.00  9.99
ATOM    450  N   HIS   318      58.760  67.221  79.979  1.00  9.99
ATOM    451  CA  HIS   318      58.506  67.300  78.579  1.00  9.99
ATOM    452  ND1 HIS   318      57.074  68.484  75.824  1.00  9.99
ATOM    453  CG  HIS   318      56.725  67.567  76.792  1.00  9.99
ATOM    454  CB  HIS   318      57.064  67.715  78.245  1.00  9.99
ATOM    455  NE2 HIS   318      55.987  66.847  74.787  1.00  9.99
ATOM    456  CD2 HIS   318      56.058  66.574  76.141  1.00  9.99
ATOM    457  CE1 HIS   318      56.609  68.003  74.645  1.00  9.99
ATOM    458  C   HIS   318      59.431  68.285  77.961  1.00  9.99
ATOM    459  O   HIS   318      59.374  69.468  78.264  1.00  9.99
ATOM    460  N   SER   319      60.315  67.811  77.069  1.00  9.99
ATOM    461  CA  SER   319      61.202  68.657  76.343  1.00  9.99
ATOM    462  CB  SER   319      62.584  68.027  76.123  1.00  9.99
ATOM    463  OG  SER   319      63.398  68.902  75.361  1.00  9.99
ATOM    464  C   SER   319      60.587  68.830  75.000  1.00  9.99
ATOM    465  O   SER   319      60.001  67.908  74.430  1.00  9.99
ATOM    466  N   THR   320      60.692  70.052  74.463  1.00  9.99
ATOM    467  CA  THR   320      60.151  70.306  73.176  1.00  9.99
ATOM    468  CB  THR   320      59.566  71.679  73.031  1.00  9.99
ATOM    469  OG1 THR   320      60.577  72.664  73.193  1.00  9.99
ATOM    470  CG2 THR   320      58.483  71.854  74.108  1.00  9.99
ATOM    471  C   THR   320      61.290  70.185  72.234  1.00  9.99
ATOM    472  O   THR   320      62.447  70.029  72.622  1.00  9.99
ATOM    473  N   TYR   321      60.954  70.285  70.950  1.00  9.99
ATOM    474  CA  TYR   321      61.844  70.054  69.866  1.00  9.99
ATOM    475  CB  TYR   321      61.187  69.129  68.845  1.00  9.99
ATOM    476  CG  TYR   321      59.896  69.797  68.445  1.00  9.99
ATOM    477  CD1 TYR   321      58.771  69.779  69.247  1.00  9.99
ATOM    478  CD2 TYR   321      59.801  70.496  67.270  1.00  9.99
ATOM    479  CE1 TYR   321      57.600  70.388  68.875  1.00  9.99
ATOM    480  CE2 TYR   321      58.641  71.115  66.876  1.00  9.99
ATOM    481  CZ  TYR   321      57.534  71.061  67.682  1.00  9.99
ATOM    482  OH  TYR   321      56.336  71.692  67.287  1.00  9.99
ATOM    483  C   TYR   321      62.029  71.332  69.123  1.00  9.99
ATOM    484  O   TYR   321      61.375  72.338  69.398  1.00  9.99
ATOM    485  N   THR   322      63.013  71.322  68.203  1.00  9.99
ATOM    486  CA  THR   322      63.174  72.406  67.289  1.00  9.99
ATOM    487  CB  THR   322      64.542  72.489  66.683  1.00  9.99
ATOM    488  OG1 THR   322      65.525  72.618  67.695  1.00  9.99
ATOM    489  CG2 THR   322      64.578  73.718  65.762  1.00  9.99
ATOM    490  C   THR   322      62.242  72.034  66.179  1.00  9.99
ATOM    491  O   THR   322      62.098  70.849  65.880  1.00  9.99
ATOM    492  N   GLY   323      61.586  73.018  65.534  1.00  9.99
ATOM    493  CA  GLY   323      60.637  72.669  64.518  1.00  9.99
ATOM    494  C   GLY   323      61.255  72.856  63.171  1.00  9.99
ATOM    495  O   GLY   323      61.842  73.897  62.876  1.00  9.99
ATOM    496  N   ARG   324      61.121  71.830  62.304  1.00  9.99
ATOM    497  CA  ARG   324      61.647  71.947  60.981  1.00  9.99
ATOM    498  CB  ARG   324      62.676  70.862  60.613  1.00  9.99
ATOM    499  CG  ARG   324      63.985  70.986  61.395  1.00  9.99
ATOM    500  CD  ARG   324      63.894  70.498  62.844  1.00  9.99
ATOM    501  NE  ARG   324      64.670  69.229  62.946  1.00  9.99
ATOM    502  CZ  ARG   324      66.002  69.282  63.241  1.00  9.99
ATOM    503  NH1 ARG   324      66.605  70.492  63.441  1.00  9.99
ATOM    504  NH2 ARG   324      66.730  68.133  63.347  1.00  9.99
ATOM    505  C   ARG   324      60.502  71.840  60.026  1.00  9.99
ATOM    506  O   ARG   324      59.785  70.841  59.978  1.00  9.99
ATOM    507  N   PRO   325      60.320  72.903  59.292  1.00  9.99
ATOM    508  CA  PRO   325      59.293  72.968  58.287  1.00  9.99
ATOM    509  CD  PRO   325      60.627  74.218  59.834  1.00  9.99
ATOM    510  CB  PRO   325      58.920  74.445  58.140  1.00  9.99
ATOM    511  CG  PRO   325      60.096  75.202  58.781  1.00  9.99
ATOM    512  C   PRO   325      59.751  72.359  57.004  1.00  9.99
ATOM    513  O   PRO   325      60.953  72.213  56.789  1.00  9.99
ATOM    514  N   PRO   326      58.807  72.025  56.169  1.00  9.99
ATOM    515  CA  PRO   326      59.110  71.466  54.881  1.00  9.99
ATOM    516  CD  PRO   326      57.516  71.578  56.667  1.00  9.99
ATOM    517  CB  PRO   326      57.799  70.884  54.359  1.00  9.99
ATOM    518  CG  PRO   326      57.007  70.553  55.638  1.00  9.99
ATOM    519  C   PRO   326      59.646  72.561  54.028  1.00  9.99
ATOM    520  O   PRO   326      59.538  73.719  54.427  1.00  9.99
ATOM    521  N   ASP   327      60.246  72.217  52.871  1.00  9.99
ATOM    522  CA  ASP   327      60.797  73.203  51.985  1.00  9.99
ATOM    523  CB  ASP   327      61.146  72.641  50.596  1.00  9.99
ATOM    524  CG  ASP   327      62.333  71.699  50.728  1.00  9.99
ATOM    525  OD1 ASP   327      63.419  72.165  51.164  1.00  9.99
ATOM    526  OD2 ASP   327      62.166  70.497  50.387  1.00  9.99
ATOM    527  C   ASP   327      59.775  74.319  51.763  1.00  9.99
ATOM    528  O   ASP   327      58.564  74.096  52.032  1.00  9.99
ATOM    529  OXT ASP   327      60.201  75.413  51.302  1.00  9.99
TER
END
