
#######################################################
#                                                     #
#                        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   17 (  145),  selected   17 , name T0386TS009_3_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected  206 , name T0386_D1.pdb
# PARAMETERS: T0386TS009_3_2-D1.T0386_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      I      13           -
LGA    -       -      I      14           -
LGA    -       -      S      15           -
LGA    -       -      P      16           -
LGA    -       -      H      17           -
LGA    -       -      H      18           -
LGA    -       -      Y      19           -
LGA    -       -      V      20           -
LGA    -       -      Y      21           -
LGA    -       -      P      22           -
LGA    -       -      N      23           -
LGA    -       -      T      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      N      29           -
LGA    -       -      K      30           -
LGA    -       -      Y      31           -
LGA    -       -      G      32           -
LGA    -       -      I      33           -
LGA    -       -      K      34           -
LGA    -       -      N      35           -
LGA    -       -      L      36           -
LGA    -       -      N      37           -
LGA    -       -      A      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      E      41           -
LGA    -       -      K      42           -
LGA    -       -      C      43           -
LGA    -       -      S      44           -
LGA    -       -      H      45           -
LGA    -       -      D      46           -
LGA    -       -      T      47           -
LGA    -       -      A      48           -
LGA    -       -      K      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      I      52           -
LGA    -       -      N      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      S      58           -
LGA    -       -      L      59           -
LGA    -       -      P      60           -
LGA    -       -      E      61           -
LGA    -       -      Y      62           -
LGA    -       -      F      63           -
LGA    -       -      D      64           -
LGA    -       -      T      65           -
LGA    -       -      A      66           -
LGA    -       -      Y      67           -
LGA    -       -      L      68           -
LGA    -       -      C      69           -
LGA    -       -      H      70           -
LGA    -       -      I      71           -
LGA    -       -      H      72           -
LGA    -       -      Q      73           -
LGA    -       -      Q      74           -
LGA    -       -      L      75           -
LGA    -       -      F      76           -
LGA    -       -      K      77           -
LGA    -       -      N      78           -
LGA    -       -      T      79           -
LGA    -       -      F      80           -
LGA    -       -      E      81           -
LGA    -       -      W      82           -
LGA    -       -      A      83           -
LGA    -       -      G      84           -
LGA    -       -      Y      85           -
LGA    -       -      L      86           -
LGA    -       -      R      87           -
LGA    -       -      H      88           -
LGA    F      80      I      89          3.744
LGA    E      81      P      90          2.069
LGA    W      82      F      91          2.732
LGA    -       -      T      92           -
LGA    -       -      F      93           -
LGA    -       -      A      94           -
LGA    -       -      D      95           -
LGA    -       -      G      96           -
LGA    -       -      T      97           -
LGA    -       -      T      98           -
LGA    A      83      A      99          2.814
LGA    G      84      A     100          1.836
LGA    Y      85      M     101          1.686
LGA    L      86      P     102          3.130
LGA    R      87      E     103          1.648
LGA    -       -      M     104           -
LGA    -       -      K     105           -
LGA    -       -      R     106           -
LGA    -       -      T     107           -
LGA    -       -      G     108           -
LGA    -       -      W     109           -
LGA    -       -      K     110           -
LGA    -       -      N     111           -
LGA    -       -      A     112           -
LGA    -       -      F     113           -
LGA    -       -      A     114           -
LGA    H      88      I     115          4.282
LGA    -       -      G     116           -
LGA    -       -      D     117           -
LGA    -       -      E     118           -
LGA    -       -      I     119           -
LGA    -       -      Q     120           -
LGA    -       -      E     121           -
LGA    -       -      G     122           -
LGA    -       -      L     123           -
LGA    -       -      Q     124           -
LGA    -       -      R     125           -
LGA    -       -      L     126           -
LGA    -       -      D     127           -
LGA    -       -      Q     128           -
LGA    -       -      T     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      E     132           -
LGA    -       -      K     133           -
LGA    -       -      N     134           -
LGA    -       -      N     135           -
LGA    -       -      L     136           -
LGA    -       -      Q     137           -
LGA    -       -      G     138           -
LGA    -       -      L     139           -
LGA    -       -      T     140           -
LGA    -       -      R     141           -
LGA    -       -      E     142           -
LGA    -       -      E     143           -
LGA    -       -      F     144           -
LGA    -       -      N     145           -
LGA    -       -      S     146           -
LGA    -       -      E     147           -
LGA    -       -      A     148           -
LGA    -       -      I     149           -
LGA    -       -      E     150           -
LGA    -       -      L     151           -
LGA    -       -      F     152           -
LGA    -       -      N     153           -
LGA    -       -      S     154           -
LGA    -       -      L     155           -
LGA    -       -      N     156           -
LGA    -       -      Q     157           -
LGA    -       -      L     158           -
LGA    I      89      H     159           #
LGA    P      90      P     160          3.514
LGA    F      91      F     161          2.608
LGA    T      92      R     162          2.596
LGA    F      93      E     163          2.656
LGA    -       -      G     164           -
LGA    A      94      N     165          0.855
LGA    D      95      G     166          3.137
LGA    G      96      R     167          3.259
LGA    -       -      T     168           -
LGA    -       -      Q     169           -
LGA    -       -      R     170           -
LGA    -       -      L     171           -
LGA    -       -      F     172           -
LGA    -       -      F     173           -
LGA    -       -      E     174           -
LGA    -       -      N     175           -
LGA    -       -      L     176           -
LGA    -       -      A     177           -
LGA    -       -      K     178           -
LGA    -       -      A     179           -
LGA    -       -      A     180           -
LGA    -       -      G     181           -
LGA    -       -      H     182           -
LGA    -       -      Q     183           -
LGA    -       -      L     184           -
LGA    -       -      N     185           -
LGA    -       -      F     186           -
LGA    -       -      S     187           -
LGA    -       -      L     188           -
LGA    -       -      I     189           -
LGA    -       -      T     190           -
LGA    -       -      K     191           -
LGA    -       -      E     192           -
LGA    -       -      R     193           -
LGA    -       -      M     194           -
LGA    -       -      M     195           -
LGA    -       -      V     196           -
LGA    -       -      A     197           -
LGA    -       -      S     198           -
LGA    -       -      V     199           -
LGA    -       -      A     200           -
LGA    -       -      V     201           -
LGA    -       -      A     202           -
LGA    -       -      E     203           -
LGA    -       -      N     204           -
LGA    -       -      G     205           -
LGA    -       -      D     206           -
LGA    -       -      L     207           -
LGA    -       -      E     208           -
LGA    -       -      P     209           -
LGA    -       -      M     210           -
LGA    -       -      Q     211           -
LGA    -       -      H     212           -
LGA    -       -      L     213           -
LGA    -       -      F     214           -
LGA    -       -      E     215           -
LGA    -       -      D     216           -
LGA    -       -      I     217           -
LGA    -       -      S     218           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   17  206    5.0     16    2.79    18.75      5.126     0.553

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.492283 * X  +  -0.409772 * Y  +   0.767948 * Z  + -61.786938
  Y_new =  -0.824210 * X  +   0.064242 * Y  +   0.562629 * Z  +  54.362862
  Z_new =  -0.279884 * X  +  -0.909923 * Y  +  -0.306113 * Z  +  71.417953 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.895319    1.246274  [ DEG:  -108.5938     71.4062 ]
  Theta =   0.283673    2.857920  [ DEG:    16.2533    163.7467 ]
  Phi   =  -1.032380    2.109213  [ DEG:   -59.1510    120.8490 ]
 
# 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: T0386TS009_3_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS009_3_2-D1.T0386_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17  206   5.0   16   2.79   18.75   5.126
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS009_3_2-D1
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0386                                                                    
PARENT N/A                                                                      
ATOM    647  N   PHE    80      11.232  57.892  32.511  1.00  0.00             
ATOM    648  CA  PHE    80      10.921  58.352  33.858  1.00  0.00             
ATOM    649  C   PHE    80      12.060  58.045  34.824  1.00  0.00             
ATOM    650  O   PHE    80      12.303  58.793  35.771  1.00  0.00             
ATOM    651  CB  PHE    80      10.623  59.854  33.855  1.00  0.00             
ATOM    652  CG  PHE    80       9.323  60.213  33.197  1.00  0.00             
ATOM    653  CD1 PHE    80       8.653  59.295  32.407  1.00  0.00             
ATOM    654  CD2 PHE    80       8.768  61.469  33.366  1.00  0.00             
ATOM    655  CE1 PHE    80       7.456  59.625  31.801  1.00  0.00             
ATOM    656  CE2 PHE    80       7.571  61.800  32.761  1.00  0.00             
ATOM    657  CZ  PHE    80       6.915  60.884  31.980  1.00  0.00             
ATOM    658  N   GLU    81      12.756  56.940  34.577  1.00  0.00             
ATOM    659  CA  GLU    81      13.871  56.532  35.423  1.00  0.00             
ATOM    660  C   GLU    81      14.644  57.741  35.939  1.00  0.00             
ATOM    661  O   GLU    81      15.863  57.688  36.103  1.00  0.00             
ATOM    662  CB  GLU    81      13.372  55.687  36.597  1.00  0.00             
ATOM    663  CG  GLU    81      11.892  55.342  36.528  1.00  0.00             
ATOM    664  CD  GLU    81      11.645  53.928  36.041  1.00  0.00             
ATOM    665  OE1 GLU    81      12.257  53.534  35.026  1.00  0.00             
ATOM    666  OE2 GLU    81      10.840  53.214  36.674  1.00  0.00             
ATOM    667  N   TRP    82      13.925  58.831  36.194  1.00  0.00             
ATOM    668  CA  TRP    82      14.542  60.055  36.692  1.00  0.00             
ATOM    669  C   TRP    82      15.718  59.746  37.614  1.00  0.00             
ATOM    670  O   TRP    82      15.533  59.451  38.794  1.00  0.00             
ATOM    671  CB  TRP    82      15.002  60.935  35.528  1.00  0.00             
ATOM    672  CG  TRP    82      13.896  61.322  34.595  1.00  0.00             
ATOM    673  CD1 TRP    82      13.486  62.587  34.290  1.00  0.00             
ATOM    674  CD2 TRP    82      13.058  60.435  33.844  1.00  0.00             
ATOM    675  NE1 TRP    82      12.444  62.546  33.396  1.00  0.00             
ATOM    676  CE2 TRP    82      12.162  61.235  33.106  1.00  0.00             
ATOM    677  CE3 TRP    82      12.978  59.044  33.725  1.00  0.00             
ATOM    678  CZ2 TRP    82      11.198  60.689  32.260  1.00  0.00             
ATOM    679  CZ3 TRP    82      12.021  58.506  32.885  1.00  0.00             
ATOM    680  CH2 TRP    82      11.142  59.326  32.162  1.00  0.00             
ATOM    681  N   ALA    83      16.926  59.814  37.065  1.00  0.00             
ATOM    682  CA  ALA    83      18.134  59.541  37.834  1.00  0.00             
ATOM    683  C   ALA    83      18.377  58.042  37.966  1.00  0.00             
ATOM    684  O   ALA    83      19.057  57.592  38.889  1.00  0.00             
ATOM    685  CB  ALA    83      19.337  60.214  37.191  1.00  0.00             
ATOM    686  N   GLY    84      17.820  57.273  37.036  1.00  0.00             
ATOM    687  CA  GLY    84      17.990  55.833  37.069  1.00  0.00             
ATOM    688  C   GLY    84      18.288  55.315  38.463  1.00  0.00             
ATOM    689  O   GLY    84      18.991  54.318  38.628  1.00  0.00             
ATOM    690  N   TYR    85      17.752  55.993  39.472  1.00  0.00             
ATOM    691  CA  TYR    85      17.963  55.597  40.859  1.00  0.00             
ATOM    692  C   TYR    85      19.162  54.664  40.990  1.00  0.00             
ATOM    693  O   TYR    85      19.404  54.094  42.054  1.00  0.00             
ATOM    694  CB  TYR    85      18.159  56.831  41.744  1.00  0.00             
ATOM    695  CG  TYR    85      18.904  57.959  41.068  1.00  0.00             
ATOM    696  CD1 TYR    85      18.649  59.282  41.404  1.00  0.00             
ATOM    697  CD2 TYR    85      19.860  57.697  40.096  1.00  0.00             
ATOM    698  CE1 TYR    85      19.325  60.320  40.790  1.00  0.00             
ATOM    699  CE2 TYR    85      20.547  58.721  39.473  1.00  0.00             
ATOM    700  CZ  TYR    85      20.271  60.041  39.828  1.00  0.00             
ATOM    701  OH  TYR    85      20.948  61.069  39.215  1.00  0.00             
ATOM    702  N   LEU    86      19.908  54.511  39.901  1.00  0.00             
ATOM    703  CA  LEU    86      21.082  53.647  39.892  1.00  0.00             
ATOM    704  C   LEU    86      21.035  52.640  41.037  1.00  0.00             
ATOM    705  O   LEU    86      21.679  52.830  42.069  1.00  0.00             
ATOM    706  CB  LEU    86      21.198  52.915  38.553  1.00  0.00             
ATOM    707  CG  LEU    86      22.175  51.738  38.505  1.00  0.00             
ATOM    708  CD1 LEU    86      22.769  51.589  37.113  1.00  0.00             
ATOM    709  CD2 LEU    86      21.491  50.453  38.944  1.00  0.00             
ATOM    710  N   ARG    87      20.269  51.572  40.848  1.00  0.00             
ATOM    711  CA  ARG    87      20.135  50.535  41.864  1.00  0.00             
ATOM    712  C   ARG    87      19.087  50.912  42.904  1.00  0.00             
ATOM    713  O   ARG    87      19.261  50.660  44.096  1.00  0.00             
ATOM    714  CB  ARG    87      19.778  49.194  41.218  1.00  0.00             
ATOM    715  CG  ARG    87      18.558  48.519  41.824  1.00  0.00             
ATOM    716  CD  ARG    87      18.227  49.100  43.189  1.00  0.00             
ATOM    717  NE  ARG    87      19.392  49.711  43.820  1.00  0.00             
ATOM    718  CZ  ARG    87      19.416  50.154  45.073  1.00  0.00             
ATOM    719  NH1 ARG    87      18.334  50.056  45.833  1.00  0.00             
ATOM    720  NH2 ARG    87      20.522  50.696  45.564  1.00  0.00             
ATOM    721  N   HIS    88      17.996  51.518  42.444  1.00  0.00             
ATOM    722  CA  HIS    88      16.917  51.932  43.333  1.00  0.00             
ATOM    723  C   HIS    88      17.114  53.367  43.810  1.00  0.00             
ATOM    724  O   HIS    88      16.337  53.875  44.617  1.00  0.00             
ATOM    725  CB  HIS    88      15.563  51.790  42.635  1.00  0.00             
ATOM    726  CG  HIS    88      14.480  51.256  43.519  1.00  0.00             
ATOM    727  ND1 HIS    88      14.729  50.744  44.775  1.00  0.00             
ATOM    728  CD2 HIS    88      13.143  51.154  43.330  1.00  0.00             
ATOM    729  CE1 HIS    88      13.591  50.350  45.319  1.00  0.00             
ATOM    730  NE2 HIS    88      12.615  50.588  44.465  1.00  0.00             
ATOM    731  N   ILE    89      18.158  54.015  43.303  1.00  0.00             
ATOM    732  CA  ILE    89      18.466  55.424  43.684  1.00  0.00             
ATOM    733  C   ILE    89      17.198  56.182  44.061  1.00  0.00             
ATOM    734  O   ILE    89      17.118  57.402  43.910  1.00  0.00             
ATOM    735  CB  ILE    89      19.460  55.487  44.858  1.00  0.00             
ATOM    736  CG2 ILE    89      20.379  54.275  44.844  1.00  0.00             
ATOM    737  CG1 ILE    89      18.709  55.581  46.188  1.00  0.00             
ATOM    738  CD1 ILE    89      19.604  55.485  47.403  1.00  0.00             
ATOM    739  N   PRO    90      16.185  55.460  44.561  1.00  0.00             
ATOM    740  CA  PRO    90      14.910  56.061  44.965  1.00  0.00             
ATOM    741  C   PRO    90      15.081  57.513  45.397  1.00  0.00             
ATOM    742  O   PRO    90      15.064  57.823  46.588  1.00  0.00             
ATOM    743  CB  PRO    90      14.074  55.986  43.685  1.00  0.00             
ATOM    744  CG  PRO    90      14.988  55.375  42.677  1.00  0.00             
ATOM    745  CD  PRO    90      16.209  54.001  44.769  1.00  0.00             
ATOM    746  N   PHE    91      15.245  58.400  44.421  1.00  0.00             
ATOM    747  CA  PHE    91      15.417  59.821  44.699  1.00  0.00             
ATOM    748  C   PHE    91      16.090  60.041  46.049  1.00  0.00             
ATOM    749  O   PHE    91      15.826  61.031  46.731  1.00  0.00             
ATOM    750  CB  PHE    91      16.234  60.488  43.589  1.00  0.00             
ATOM    751  CG  PHE    91      15.505  60.593  42.280  1.00  0.00             
ATOM    752  CD1 PHE    91      15.764  59.702  41.253  1.00  0.00             
ATOM    753  CD2 PHE    91      14.561  61.584  42.076  1.00  0.00             
ATOM    754  CE1 PHE    91      15.093  59.800  40.048  1.00  0.00             
ATOM    755  CE2 PHE    91      13.890  61.681  40.871  1.00  0.00             
ATOM    756  CZ  PHE    91      14.153  60.795  39.861  1.00  0.00             
ATOM    757  N   THR    92      16.961  59.112  46.430  1.00  0.00             
ATOM    758  CA  THR    92      17.689  59.204  47.727  1.00  0.00             
ATOM    759  C   THR    92      16.937  60.087  48.719  1.00  0.00             
ATOM    760  O   THR    92      17.430  60.366  49.813  1.00  0.00             
ATOM    761  CB  THR    92      17.906  57.814  48.353  1.00  0.00             
ATOM    762  OG1 THR    92      17.228  56.824  47.571  1.00  0.00             
ATOM    763  CG2 THR    92      19.390  57.481  48.410  1.00  0.00             
ATOM    764  N   PHE    93      15.743  60.521  48.330  1.00  0.00             
ATOM    765  CA  PHE    93      14.922  61.371  49.184  1.00  0.00             
ATOM    766  C   PHE    93      14.277  60.566  50.307  1.00  0.00             
ATOM    767  O   PHE    93      14.487  59.358  50.418  1.00  0.00             
ATOM    768  CB  PHE    93      15.759  62.511  49.768  1.00  0.00             
ATOM    769  CG  PHE    93      15.080  63.248  50.887  1.00  0.00             
ATOM    770  CD1 PHE    93      15.213  62.824  52.198  1.00  0.00             
ATOM    771  CD2 PHE    93      14.309  64.369  50.629  1.00  0.00             
ATOM    772  CE1 PHE    93      14.589  63.503  53.227  1.00  0.00             
ATOM    773  CE2 PHE    93      13.685  65.048  51.658  1.00  0.00             
ATOM    774  CZ  PHE    93      13.822  64.619  52.952  1.00  0.00             
ATOM    775  N   ALA    94      13.489  61.243  51.136  1.00  0.00             
ATOM    776  CA  ALA    94      12.811  60.592  52.251  1.00  0.00             
ATOM    777  C   ALA    94      12.653  61.545  53.432  1.00  0.00             
ATOM    778  O   ALA    94      11.848  61.305  54.332  1.00  0.00             
ATOM    779  CB  ALA    94      11.452  60.069  51.814  1.00  0.00             
ATOM    780  N   ASP    95      13.425  62.626  53.422  1.00  0.00             
ATOM    781  CA  ASP    95      13.372  63.616  54.491  1.00  0.00             
ATOM    782  C   ASP    95      13.389  62.948  55.861  1.00  0.00             
ATOM    783  O   ASP    95      13.815  63.548  56.849  1.00  0.00             
ATOM    784  CB  ASP    95      14.539  64.598  54.369  1.00  0.00             
ATOM    785  CG  ASP    95      15.239  64.508  53.027  1.00  0.00             
ATOM    786  OD1 ASP    95      14.644  63.948  52.083  1.00  0.00             
ATOM    787  OD2 ASP    95      16.383  64.999  52.920  1.00  0.00             
ATOM    788  N   GLY    96      12.923  61.705  55.914  1.00  0.00             
ATOM    789  CA  GLY    96      12.895  60.980  57.170  1.00  0.00             
ATOM    790  C   GLY    96      12.760  61.899  58.368  1.00  0.00             
ATOM    791  O   GLY    96      12.877  63.119  58.244  1.00  0.00             
TER
END
