
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0386AL333_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL333_3-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           -
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    N     219      M     233          2.752
LGA    P     220      K     234          4.437
LGA    E     221      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    K     222      P     244           #
LGA    I     223      -       -           -
LGA    R     224      -       -           -
LGA    L     225      V     245          3.437
LGA    L     226      M     246          2.748
LGA    K     227      V     247          2.184
LGA    E     228      -       -           -
LGA    F     229      -       -           -
LGA    M     230      A     248          1.390
LGA    H     231      K     249          2.080
LGA    T     232      -       -           -
LGA    M     233      E     250           #
LGA    K     234      G     251          4.371
LGA    N     235      E     252          3.034
LGA    T     236      T     253          3.406
LGA    G     237      Y     254          3.102
LGA    R     238      T     255          3.917
LGA    N     239      G     256           #
LGA    V     240      T     257          3.898
LGA    N     241      Y     258          1.343
LGA    D     242      R     259           -
LGA    R     243      G     260           #
LGA    P     244      A     261          2.567
LGA    V     245      G     262          2.569
LGA    M     246      L     263          3.423
LGA    -       -      E     264           -
LGA    V     247      G     265          1.721
LGA    A     248      F     266          3.248
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    K     249      I     279          1.290
LGA    E     250      D     280          4.232
LGA    G     251      H     281          4.538
LGA    E     252      L     282          2.634
LGA    T     253      P     283          2.825
LGA    E     285      P     284          3.720
LGA    -       -      E     285           -
LGA    Q     286      Q     286          2.101
LGA    L     287      L     287           #
LGA    -       -      K     288           -
LGA    K     288      I     289          1.778
LGA    I     289      L     290          3.872
LGA    L     290      K     291          4.323
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)   41   81    5.0     29    3.15     6.90     20.893     0.892

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.799576 * X  +  -0.404408 * Y  +  -0.443995 * Z  +  83.806915
  Y_new =   0.283904 * X  +   0.396948 * Y  +  -0.872829 * Z  +  91.003731
  Z_new =   0.529223 * X  +  -0.823945 * Y  +  -0.202577 * Z  + 110.105850 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.811877    1.329715  [ DEG:  -103.8129     76.1871 ]
  Theta =  -0.557684   -2.583908  [ DEG:   -31.9530   -148.0470 ]
  Phi   =   2.800410   -0.341183  [ DEG:   160.4517    -19.5483 ]
 
# 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: T0386AL333_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL333_3-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   81   5.0   29   3.15    6.90  20.893
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL333_3-D2
REMARK Aligment from pdb entry: 1qde_A
ATOM    545  N   ASN   219      15.508  70.858  77.000  1.00  0.00              
ATOM    546  CA  ASN   219      15.070  72.117  76.407  1.00  0.00              
ATOM    547  C   ASN   219      15.317  72.141  74.905  1.00  0.00              
ATOM    548  O   ASN   219      14.759  72.976  74.199  1.00  0.00              
ATOM    549  N   PRO   220      16.149  71.227  74.417  1.00  0.00              
ATOM    550  CA  PRO   220      16.458  71.162  72.994  1.00  0.00              
ATOM    551  C   PRO   220      15.608  70.127  72.283  1.00  0.00              
ATOM    552  O   PRO   220      15.975  69.641  71.216  1.00  0.00              
ATOM    553  N   GLU   221      14.487  69.768  72.894  1.00  0.00              
ATOM    554  CA  GLU   221      13.589  68.813  72.274  1.00  0.00              
ATOM    555  C   GLU   221      13.972  67.347  72.320  1.00  0.00              
ATOM    556  O   GLU   221      13.354  66.519  71.639  1.00  0.00              
ATOM    557  N   LYS   222      14.973  67.005  73.117  1.00  0.00              
ATOM    558  CA  LYS   222      15.380  65.612  73.205  1.00  0.00              
ATOM    559  C   LYS   222      14.541  64.824  74.205  1.00  0.00              
ATOM    560  O   LYS   222      14.675  63.606  74.303  1.00  0.00              
ATOM    561  N   ILE   223      13.664  65.507  74.932  1.00  0.00              
ATOM    562  CA  ILE   223      12.860  64.835  75.937  1.00  0.00              
ATOM    563  C   ILE   223      12.290  63.496  75.525  1.00  0.00              
ATOM    564  O   ILE   223      12.413  62.521  76.260  1.00  0.00              
ATOM    565  N   ARG   224      11.654  63.448  74.357  1.00  0.00              
ATOM    566  CA  ARG   224      11.045  62.206  73.885  1.00  0.00              
ATOM    567  C   ARG   224      12.056  61.109  73.589  1.00  0.00              
ATOM    568  O   ARG   224      11.832  59.954  73.937  1.00  0.00              
ATOM    569  N   LEU   225      13.166  61.462  72.950  1.00  0.00              
ATOM    570  CA  LEU   225      14.196  60.471  72.647  1.00  0.00              
ATOM    571  C   LEU   225      14.712  59.867  73.949  1.00  0.00              
ATOM    572  O   LEU   225      14.892  58.658  74.059  1.00  0.00              
ATOM    573  N   LEU   226      14.934  60.720  74.943  1.00  0.00              
ATOM    574  CA  LEU   226      15.438  60.266  76.227  1.00  0.00              
ATOM    575  C   LEU   226      14.465  59.323  76.919  1.00  0.00              
ATOM    576  O   LEU   226      14.883  58.304  77.454  1.00  0.00              
ATOM    577  N   LYS   227      13.176  59.658  76.903  1.00  0.00              
ATOM    578  CA  LYS   227      12.162  58.814  77.529  1.00  0.00              
ATOM    579  C   LYS   227      12.173  57.450  76.883  1.00  0.00              
ATOM    580  O   LYS   227      11.986  56.436  77.552  1.00  0.00              
ATOM    581  N   GLU   228      12.376  57.431  75.572  1.00  0.00              
ATOM    582  CA  GLU   228      12.396  56.186  74.819  1.00  0.00              
ATOM    583  C   GLU   228      13.640  55.365  75.100  1.00  0.00              
ATOM    584  O   GLU   228      13.589  54.140  75.189  1.00  0.00              
ATOM    585  N   PHE   229      14.773  56.037  75.215  1.00  0.00              
ATOM    586  CA  PHE   229      15.997  55.322  75.510  1.00  0.00              
ATOM    587  C   PHE   229      15.801  54.652  76.877  1.00  0.00              
ATOM    588  O   PHE   229      16.074  53.464  77.030  1.00  0.00              
ATOM    589  N   MET   230      15.292  55.408  77.849  1.00  0.00              
ATOM    590  CA  MET   230      15.042  54.878  79.190  1.00  0.00              
ATOM    591  C   MET   230      14.327  53.537  79.134  1.00  0.00              
ATOM    592  O   MET   230      14.778  52.559  79.728  1.00  0.00              
ATOM    593  N   HIS   231      13.203  53.497  78.424  1.00  0.00              
ATOM    594  CA  HIS   231      12.409  52.277  78.309  1.00  0.00              
ATOM    595  C   HIS   231      13.177  51.113  77.659  1.00  0.00              
ATOM    596  O   HIS   231      12.937  49.946  77.976  1.00  0.00              
ATOM    597  N   THR   232      14.118  51.432  76.774  1.00  0.00              
ATOM    598  CA  THR   232      14.909  50.415  76.085  1.00  0.00              
ATOM    599  C   THR   232      16.064  49.856  76.918  1.00  0.00              
ATOM    600  O   THR   232      16.717  48.882  76.516  1.00  0.00              
ATOM    601  N   MET   233      16.328  50.474  78.067  1.00  0.00              
ATOM    602  CA  MET   233      17.423  50.025  78.922  1.00  0.00              
ATOM    603  C   MET   233      16.922  49.083  79.999  1.00  0.00              
ATOM    604  O   MET   233      15.740  49.100  80.353  1.00  0.00              
ATOM    605  N   LYS   234      17.818  48.249  80.542  1.00  0.00              
ATOM    606  CA  LYS   234      17.424  47.310  81.594  1.00  0.00              
ATOM    607  C   LYS   234      16.674  48.058  82.691  1.00  0.00              
ATOM    608  O   LYS   234      17.027  49.177  83.042  1.00  0.00              
ATOM    609  N   ASN   235      15.637  47.439  83.259  1.00  0.00              
ATOM    610  CA  ASN   235      14.857  48.087  84.312  1.00  0.00              
ATOM    611  C   ASN   235      15.676  48.374  85.557  1.00  0.00              
ATOM    612  O   ASN   235      15.256  49.139  86.425  1.00  0.00              
ATOM    613  N   THR   236      16.850  47.761  85.633  1.00  0.00              
ATOM    614  CA  THR   236      17.733  47.927  86.778  1.00  0.00              
ATOM    615  C   THR   236      18.886  48.926  86.575  1.00  0.00              
ATOM    616  O   THR   236      19.835  48.957  87.359  1.00  0.00              
ATOM    617  N   GLY   237      18.811  49.747  85.537  1.00  0.00              
ATOM    618  CA  GLY   237      19.875  50.701  85.270  1.00  0.00              
ATOM    619  C   GLY   237      19.933  51.844  86.266  1.00  0.00              
ATOM    620  O   GLY   237      18.913  52.434  86.618  1.00  0.00              
ATOM    621  N   ARG   238      21.142  52.152  86.718  1.00  0.00              
ATOM    622  CA  ARG   238      21.339  53.251  87.649  1.00  0.00              
ATOM    623  C   ARG   238      21.272  54.535  86.819  1.00  0.00              
ATOM    624  O   ARG   238      21.830  54.606  85.717  1.00  0.00              
ATOM    625  N   ASN   239      20.581  55.545  87.333  1.00  0.00              
ATOM    626  CA  ASN   239      20.454  56.797  86.606  1.00  0.00              
ATOM    627  C   ASN   239      21.166  57.937  87.321  1.00  0.00              
ATOM    628  O   ASN   239      20.949  58.173  88.515  1.00  0.00              
ATOM    629  N   VAL   240      22.020  58.635  86.581  1.00  0.00              
ATOM    630  CA  VAL   240      22.751  59.770  87.112  1.00  0.00              
ATOM    631  C   VAL   240      22.432  60.979  86.243  1.00  0.00              
ATOM    632  O   VAL   240      22.737  61.012  85.050  1.00  0.00              
ATOM    633  N   ASN   241      21.821  61.978  86.859  1.00  0.00              
ATOM    634  CA  ASN   241      21.443  63.169  86.140  1.00  0.00              
ATOM    635  C   ASN   241      22.146  64.402  86.717  1.00  0.00              
ATOM    636  O   ASN   241      22.072  64.663  87.916  1.00  0.00              
ATOM    637  N   ASP   242      11.217  72.621  85.936  1.00  0.00              
ATOM    638  CA  ASP   242      10.187  71.662  86.338  1.00  0.00              
ATOM    639  C   ASP   242      10.323  70.376  85.527  1.00  0.00              
ATOM    640  O   ASP   242       9.961  69.286  85.981  1.00  0.00              
ATOM    641  N   ARG   243      10.847  70.521  84.318  1.00  0.00              
ATOM    642  CA  ARG   243      11.030  69.395  83.422  1.00  0.00              
ATOM    643  C   ARG   243      12.074  68.429  83.950  1.00  0.00              
ATOM    644  O   ARG   243      11.923  67.213  83.825  1.00  0.00              
ATOM    645  N   PRO   244      13.136  68.971  84.537  1.00  0.00              
ATOM    646  CA  PRO   244      14.192  68.142  85.088  1.00  0.00              
ATOM    647  C   PRO   244      13.641  67.353  86.265  1.00  0.00              
ATOM    648  O   PRO   244      13.879  66.154  86.366  1.00  0.00              
ATOM    649  N   VAL   245      12.894  68.016  87.145  1.00  0.00              
ATOM    650  CA  VAL   245      12.323  67.331  88.308  1.00  0.00              
ATOM    651  C   VAL   245      11.413  66.201  87.863  1.00  0.00              
ATOM    652  O   VAL   245      11.302  65.164  88.521  1.00  0.00              
ATOM    653  N   MET   246      10.762  66.418  86.731  1.00  0.00              
ATOM    654  CA  MET   246       9.855  65.444  86.172  1.00  0.00              
ATOM    655  C   MET   246      10.567  64.153  85.781  1.00  0.00              
ATOM    656  O   MET   246      10.143  63.067  86.166  1.00  0.00              
ATOM    657  N   VAL   247      11.642  64.259  85.013  1.00  0.00              
ATOM    658  CA  VAL   247      12.377  63.064  84.617  1.00  0.00              
ATOM    659  C   VAL   247      12.875  62.357  85.864  1.00  0.00              
ATOM    660  O   VAL   247      12.934  61.131  85.921  1.00  0.00              
ATOM    661  N   ALA   248      13.230  63.152  86.865  1.00  0.00              
ATOM    662  CA  ALA   248      13.736  62.632  88.122  1.00  0.00              
ATOM    663  C   ALA   248      12.720  61.791  88.868  1.00  0.00              
ATOM    664  O   ALA   248      13.053  60.740  89.415  1.00  0.00              
ATOM    665  N   LYS   249      11.481  62.259  88.915  1.00  0.00              
ATOM    666  CA  LYS   249      10.456  61.514  89.626  1.00  0.00              
ATOM    667  C   LYS   249      10.018  60.301  88.833  1.00  0.00              
ATOM    668  O   LYS   249       9.582  59.318  89.413  1.00  0.00              
ATOM    669  N   GLU   250      10.158  60.361  87.510  1.00  0.00              
ATOM    670  CA  GLU   250       9.751  59.253  86.656  1.00  0.00              
ATOM    671  C   GLU   250      10.762  58.119  86.465  1.00  0.00              
ATOM    672  O   GLU   250      10.366  56.965  86.258  1.00  0.00              
ATOM    673  N   GLY   251      12.055  58.421  86.544  1.00  0.00              
ATOM    674  CA  GLY   251      13.065  57.381  86.333  1.00  0.00              
ATOM    675  C   GLY   251      14.026  57.065  87.482  1.00  0.00              
ATOM    676  O   GLY   251      14.802  56.115  87.411  1.00  0.00              
ATOM    677  N   GLU   252      13.966  57.851  88.544  1.00  0.00              
ATOM    678  CA  GLU   252      14.827  57.604  89.675  1.00  0.00              
ATOM    679  C   GLU   252      14.049  57.033  90.846  1.00  0.00              
ATOM    680  O   GLU   252      12.863  57.303  91.022  1.00  0.00              
ATOM    681  N   THR   253      14.738  56.224  91.635  1.00  0.00              
ATOM    682  CA  THR   253      14.154  55.572  92.789  1.00  0.00              
ATOM    683  C   THR   253      14.913  56.003  94.035  1.00  0.00              
ATOM    684  O   THR   253      16.086  55.657  94.207  1.00  0.00              
ATOM    685  N   GLU   285      14.238  56.773  94.887  1.00  0.00              
ATOM    686  CA  GLU   285      14.814  57.270  96.133  1.00  0.00              
ATOM    687  C   GLU   285      16.221  57.758  95.856  1.00  0.00              
ATOM    688  O   GLU   285      17.184  57.308  96.475  1.00  0.00              
ATOM    689  N   GLN   286      16.354  58.713  94.930  1.00  0.00              
ATOM    690  CA  GLN   286      17.658  59.258  94.556  1.00  0.00              
ATOM    691  C   GLN   286      18.406  60.033  95.624  1.00  0.00              
ATOM    692  O   GLN   286      17.815  60.571  96.555  1.00  0.00              
ATOM    693  N   LEU   287      19.726  60.057  95.481  1.00  0.00              
ATOM    694  CA  LEU   287      20.577  60.838  96.354  1.00  0.00              
ATOM    695  C   LEU   287      20.470  62.209  95.695  1.00  0.00              
ATOM    696  O   LEU   287      20.540  62.310  94.465  1.00  0.00              
ATOM    697  N   LYS   288      20.262  63.248  96.493  1.00  0.00              
ATOM    698  CA  LYS   288      20.130  64.603  95.964  1.00  0.00              
ATOM    699  C   LYS   288      21.272  65.466  96.479  1.00  0.00              
ATOM    700  O   LYS   288      21.524  65.515  97.675  1.00  0.00              
ATOM    701  N   ILE   289      21.970  66.134  95.572  1.00  0.00              
ATOM    702  CA  ILE   289      23.077  66.999  95.963  1.00  0.00              
ATOM    703  C   ILE   289      22.861  68.320  95.245  1.00  0.00              
ATOM    704  O   ILE   289      23.082  68.418  94.041  1.00  0.00              
ATOM    705  N   LEU   290      22.413  69.328  95.986  1.00  0.00              
ATOM    706  CA  LEU   290      22.144  70.639  95.414  1.00  0.00              
ATOM    707  C   LEU   290      22.973  71.719  96.097  1.00  0.00              
ATOM    708  O   LEU   290      23.936  72.167  95.435  1.00  0.00              
END
