
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0386AL380_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL380_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           -
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      E     228           #
LGA    F     229      F     229           -
LGA    M     230      -       -           -
LGA    H     231      M     230           #
LGA    T     232      H     231          1.973
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    M     233      K     234          0.744
LGA    K     234      N     235          3.317
LGA    N     235      T     236          4.610
LGA    -       -      G     237           -
LGA    T     236      R     238          4.626
LGA    G     237      N     239          2.538
LGA    -       -      V     240           -
LGA    R     238      N     241          4.305
LGA    N     239      D     242          3.334
LGA    V     240      R     243          2.342
LGA    N     241      P     244          4.821
LGA    D     242      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      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    -       -      N     269           -
LGA    R     243      V     270           #
LGA    M     246      K     271          2.318
LGA    V     247      G     272          2.566
LGA    A     248      A     273          1.993
LGA    K     249      -       -           -
LGA    E     250      -       -           -
LGA    G     251      Y     274          2.104
LGA    E     252      I     275          1.358
LGA    T     253      -       -           -
LGA    Y     254      -       -           -
LGA    T     255      I     276          1.986
LGA    G     256      G     277          0.587
LGA    T     257      -       -           -
LGA    Y     258      N     278          3.791
LGA    R     259      I     279          2.984
LGA    G     260      D     280          1.895
LGA    A     261      H     281          2.504
LGA    G     262      L     282          2.693
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)   33   81    5.0     22    2.94     9.09     18.130     0.724

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.178249 * X  +   0.048400 * Y  +   0.982794 * Z  + -14.084672
  Y_new =  -0.579356 * X  +   0.802149 * Y  +  -0.144581 * Z  +  -4.065675
  Z_new =  -0.795345 * X  +  -0.595159 * Y  +  -0.114941 * Z  + 121.129791 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.761574    1.380018  [ DEG:  -100.9308     79.0692 ]
  Theta =   0.919577    2.222015  [ DEG:    52.6879    127.3121 ]
  Phi   =  -1.869272    1.272321  [ DEG:  -107.1014     72.8986 ]
 
# 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: T0386AL380_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL380_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33   81   5.0   22   2.94    9.09  18.130
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL380_1-D2
REMARK Aligment from pdb entry: 2f6sB
ATOM    541  N   GLU   228       6.970  75.210  77.462  1.00  0.00              
ATOM    542  CA  GLU   228       7.654  74.000  77.010  1.00  0.00              
ATOM    543  C   GLU   228       8.536  74.250  75.791  1.00  0.00              
ATOM    544  O   GLU   228       9.641  73.701  75.718  1.00  0.00              
ATOM    545  N   PHE   229       8.083  75.108  74.870  1.00  0.00              
ATOM    546  CA  PHE   229       8.906  75.496  73.727  1.00  0.00              
ATOM    547  C   PHE   229      10.222  76.105  74.175  1.00  0.00              
ATOM    548  O   PHE   229      11.299  75.686  73.725  1.00  0.00              
ATOM    549  N   MET   230      10.133  77.080  75.068  1.00  0.00              
ATOM    550  CA  MET   230      11.307  77.821  75.500  1.00  0.00              
ATOM    551  C   MET   230      12.247  76.883  76.209  1.00  0.00              
ATOM    552  O   MET   230      13.447  76.958  76.039  1.00  0.00              
ATOM    553  N   HIS   231      11.689  75.974  76.990  1.00  0.00              
ATOM    554  CA  HIS   231      12.490  75.090  77.796  1.00  0.00              
ATOM    555  C   HIS   231      13.225  74.044  76.954  1.00  0.00              
ATOM    556  O   HIS   231      14.401  73.768  77.192  1.00  0.00              
ATOM    557  N   THR   232      12.549  73.473  75.966  1.00  0.00              
ATOM    558  CA  THR   232      13.221  72.561  75.050  1.00  0.00              
ATOM    559  C   THR   232      14.214  73.294  74.160  1.00  0.00              
ATOM    560  O   THR   232      15.336  72.827  73.961  1.00  0.00              
ATOM    561  N   MET   233      13.833  74.464  73.656  1.00  0.00              
ATOM    562  CA  MET   233      14.727  75.193  72.761  1.00  0.00              
ATOM    563  C   MET   233      16.086  75.536  73.390  1.00  0.00              
ATOM    564  O   MET   233      17.105  75.509  72.708  1.00  0.00              
ATOM    565  N   LYS   234      16.092  75.831  74.686  1.00  0.00              
ATOM    566  CA  LYS   234      17.299  76.158  75.434  1.00  0.00              
ATOM    567  C   LYS   234      18.296  74.995  75.517  1.00  0.00              
ATOM    568  O   LYS   234      19.405  75.176  75.989  1.00  0.00              
ATOM    569  N   ASN   235      17.886  73.795  75.135  1.00  0.00              
ATOM    570  CA  ASN   235      18.654  72.608  75.470  1.00  0.00              
ATOM    571  C   ASN   235      18.709  71.584  74.347  1.00  0.00              
ATOM    572  O   ASN   235      18.610  70.383  74.585  1.00  0.00              
ATOM    573  N   THR   236      18.833  72.052  73.123  1.00  0.00              
ATOM    574  CA  THR   236      19.005  71.157  72.000  1.00  0.00              
ATOM    575  C   THR   236      20.483  70.838  71.855  1.00  0.00              
ATOM    576  O   THR   236      21.337  71.623  72.267  1.00  0.00              
ATOM    577  N   GLY   237      20.783  69.689  71.261  1.00  0.00              
ATOM    578  CA  GLY   237      22.164  69.300  70.971  1.00  0.00              
ATOM    579  C   GLY   237      22.232  68.675  69.590  1.00  0.00              
ATOM    580  O   GLY   237      21.263  68.061  69.140  1.00  0.00              
ATOM    581  N   ARG   238      23.380  68.835  68.936  1.00  0.00              
ATOM    582  CA  ARG   238      23.657  68.240  67.628  1.00  0.00              
ATOM    583  C   ARG   238      24.308  66.893  67.784  1.00  0.00              
ATOM    584  O   ARG   238      24.552  66.191  66.798  1.00  0.00              
ATOM    585  N   ASN   239      24.598  66.556  69.037  1.00  0.00              
ATOM    586  CA  ASN   239      25.286  65.326  69.386  1.00  0.00              
ATOM    587  C   ASN   239      24.280  64.186  69.440  1.00  0.00              
ATOM    588  O   ASN   239      23.967  63.610  70.472  1.00  0.00              
ATOM    589  N   VAL   240      23.817  63.859  68.258  1.00  0.00              
ATOM    590  CA  VAL   240      22.587  63.162  68.031  1.00  0.00              
ATOM    591  C   VAL   240      22.662  61.632  68.130  1.00  0.00              
ATOM    592  O   VAL   240      21.633  60.958  68.326  1.00  0.00              
ATOM    593  N   ASN   241      23.877  61.099  68.030  1.00  0.00              
ATOM    594  CA  ASN   241      24.107  59.662  67.946  1.00  0.00              
ATOM    595  C   ASN   241      24.950  59.127  69.073  1.00  0.00              
ATOM    596  O   ASN   241      25.160  57.918  69.159  1.00  0.00              
ATOM    597  N   ASP   242      25.460  60.019  69.914  1.00  0.00              
ATOM    598  CA  ASP   242      26.312  59.620  71.015  1.00  0.00              
ATOM    599  C   ASP   242      25.568  58.769  72.065  1.00  0.00              
ATOM    600  O   ASP   242      24.708  59.283  72.794  1.00  0.00              
ATOM    601  N   ARG   243      25.880  57.461  72.146  1.00  0.00              
ATOM    602  CA  ARG   243      25.139  56.574  73.066  1.00  0.00              
ATOM    603  C   ARG   243      25.044  57.078  74.520  1.00  0.00              
ATOM    604  O   ARG   243      23.944  57.056  75.100  1.00  0.00              
ATOM    605  N   MET   246      26.144  57.551  75.107  1.00  0.00              
ATOM    606  CA  MET   246      26.063  58.006  76.501  1.00  0.00              
ATOM    607  C   MET   246      25.251  59.305  76.702  1.00  0.00              
ATOM    608  O   MET   246      24.525  59.411  77.686  1.00  0.00              
ATOM    609  N   VAL   247      25.344  60.263  75.772  1.00  0.00              
ATOM    610  CA  VAL   247      24.465  61.434  75.788  1.00  0.00              
ATOM    611  C   VAL   247      22.987  60.993  75.793  1.00  0.00              
ATOM    612  O   VAL   247      22.186  61.431  76.636  1.00  0.00              
ATOM    613  N   ALA   248      22.645  60.094  74.873  1.00  0.00              
ATOM    614  CA  ALA   248      21.296  59.555  74.801  1.00  0.00              
ATOM    615  C   ALA   248      20.898  58.832  76.102  1.00  0.00              
ATOM    616  O   ALA   248      19.776  58.980  76.585  1.00  0.00              
ATOM    617  N   LYS   249      21.818  58.065  76.677  1.00  0.00              
ATOM    618  CA  LYS   249      21.501  57.304  77.884  1.00  0.00              
ATOM    619  C   LYS   249      21.316  58.215  79.092  1.00  0.00              
ATOM    620  O   LYS   249      20.406  57.995  79.879  1.00  0.00              
ATOM    621  N   GLU   250      22.137  59.257  79.209  1.00  0.00              
ATOM    622  CA  GLU   250      21.940  60.262  80.250  1.00  0.00              
ATOM    623  C   GLU   250      20.571  60.925  80.162  1.00  0.00              
ATOM    624  O   GLU   250      19.943  61.157  81.194  1.00  0.00              
ATOM    625  N   GLY   251      20.117  61.227  78.941  1.00  0.00              
ATOM    626  CA  GLY   251      18.785  61.787  78.717  1.00  0.00              
ATOM    627  C   GLY   251      17.650  60.831  79.107  1.00  0.00              
ATOM    628  O   GLY   251      16.639  61.245  79.697  1.00  0.00              
ATOM    629  N   GLU   252      17.810  59.548  78.799  1.00  0.00              
ATOM    630  CA  GLU   252      16.784  58.585  79.139  1.00  0.00              
ATOM    631  C   GLU   252      16.728  58.347  80.642  1.00  0.00              
ATOM    632  O   GLU   252      15.656  58.197  81.211  1.00  0.00              
ATOM    633  N   THR   253      17.886  58.338  81.279  1.00  0.00              
ATOM    634  CA  THR   253      17.940  58.241  82.726  1.00  0.00              
ATOM    635  C   THR   253      17.141  59.392  83.351  1.00  0.00              
ATOM    636  O   THR   253      16.311  59.167  84.241  1.00  0.00              
ATOM    637  N   TYR   254      17.355  60.609  82.856  1.00  0.00              
ATOM    638  CA  TYR   254      16.633  61.758  83.373  1.00  0.00              
ATOM    639  C   TYR   254      15.136  61.647  83.069  1.00  0.00              
ATOM    640  O   TYR   254      14.290  62.026  83.893  1.00  0.00              
ATOM    641  N   THR   255      14.820  61.131  81.881  1.00  0.00              
ATOM    642  CA  THR   255      13.441  60.947  81.468  1.00  0.00              
ATOM    643  C   THR   255      12.703  60.032  82.461  1.00  0.00              
ATOM    644  O   THR   255      11.540  60.264  82.779  1.00  0.00              
ATOM    645  N   GLY   256      13.391  59.007  82.954  1.00  0.00              
ATOM    646  CA  GLY   256      12.804  58.127  83.944  1.00  0.00              
ATOM    647  C   GLY   256      12.782  58.770  85.323  1.00  0.00              
ATOM    648  O   GLY   256      11.871  58.549  86.099  1.00  0.00              
ATOM    649  N   THR   257      13.779  59.577  85.625  1.00  0.00              
ATOM    650  CA  THR   257      13.759  60.339  86.863  1.00  0.00              
ATOM    651  C   THR   257      12.496  61.234  86.951  1.00  0.00              
ATOM    652  O   THR   257      11.949  61.425  88.039  1.00  0.00              
ATOM    653  N   TYR   258      12.028  61.756  85.811  1.00  0.00              
ATOM    654  CA  TYR   258      10.847  62.625  85.794  1.00  0.00              
ATOM    655  C   TYR   258       9.626  61.884  86.328  1.00  0.00              
ATOM    656  O   TYR   258       8.709  62.493  86.862  1.00  0.00              
ATOM    657  N   ARG   259       9.619  60.568  86.160  1.00  0.00              
ATOM    658  CA  ARG   259       8.521  59.732  86.597  1.00  0.00              
ATOM    659  C   ARG   259       8.647  59.314  88.076  1.00  0.00              
ATOM    660  O   ARG   259       7.742  58.688  88.616  1.00  0.00              
ATOM    661  N   GLY   260       9.761  59.646  88.721  1.00  0.00              
ATOM    662  CA  GLY   260       9.956  59.299  90.136  1.00  0.00              
ATOM    663  C   GLY   260      11.056  58.280  90.426  1.00  0.00              
ATOM    664  O   GLY   260      11.317  57.953  91.592  1.00  0.00              
ATOM    665  N   ALA   261      11.709  57.772  89.382  1.00  0.00              
ATOM    666  CA  ALA   261      12.783  56.793  89.572  1.00  0.00              
ATOM    667  C   ALA   261      14.160  57.451  89.820  1.00  0.00              
ATOM    668  O   ALA   261      14.771  57.998  88.888  1.00  0.00              
ATOM    669  N   GLY   262      14.647  57.378  91.065  1.00  0.00              
ATOM    670  CA  GLY   262      15.853  58.101  91.486  1.00  0.00              
ATOM    671  C   GLY   262      17.062  57.212  91.672  1.00  0.00              
ATOM    672  O   GLY   262      17.349  56.369  90.822  1.00  0.00              
END
