
#######################################################
#                                                     #
#                        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_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL380_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           -
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          1.824
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    M     233      K     234          0.802
LGA    K     234      N     235          3.348
LGA    N     235      T     236          4.839
LGA    -       -      G     237           -
LGA    T     236      R     238          4.789
LGA    G     237      N     239          2.647
LGA    -       -      V     240           -
LGA    R     238      N     241          4.049
LGA    N     239      D     242          2.994
LGA    V     240      R     243          2.059
LGA    N     241      P     244          4.567
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          1.910
LGA    V     247      G     272          2.611
LGA    A     248      A     273          1.724
LGA    K     249      -       -           -
LGA    E     250      -       -           -
LGA    G     251      Y     274          2.006
LGA    E     252      I     275          1.206
LGA    T     253      -       -           -
LGA    Y     254      -       -           -
LGA    T     255      I     276          2.154
LGA    G     256      G     277          0.948
LGA    T     257      -       -           -
LGA    Y     258      N     278          4.192
LGA    R     259      I     279          2.233
LGA    G     260      D     280          2.596
LGA    -       -      H     281           -
LGA    A     261      L     282          1.847
LGA    G     262      P     283          4.770
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    3.01     9.09     17.935     0.708

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.237276 * X  +   0.141082 * Y  +  -0.961143 * Z  +   6.186409
  Y_new =  -0.926838 * X  +  -0.329241 * Y  +   0.180479 * Z  +  62.372955
  Z_new =  -0.290985 * X  +   0.933647 * Y  +   0.208881 * Z  +  22.587069 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.350695   -1.790898  [ DEG:    77.3891   -102.6109 ]
  Theta =   0.295256    2.846336  [ DEG:    16.9169    163.0831 ]
  Phi   =  -1.821420    1.320173  [ DEG:  -104.3597     75.6403 ]
 
# 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_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL380_2-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   3.01    9.09  17.935
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL380_2-D2
REMARK Aligment from pdb entry: 2f6sA
ATOM    541  N   GLU   228       7.020  75.188  77.853  1.00  0.00              
ATOM    542  CA  GLU   228       7.661  73.992  77.357  1.00  0.00              
ATOM    543  C   GLU   228       8.474  74.295  76.102  1.00  0.00              
ATOM    544  O   GLU   228       9.592  73.808  75.976  1.00  0.00              
ATOM    545  N   PHE   229       7.940  75.116  75.195  1.00  0.00              
ATOM    546  CA  PHE   229       8.683  75.470  73.978  1.00  0.00              
ATOM    547  C   PHE   229      10.002  76.135  74.337  1.00  0.00              
ATOM    548  O   PHE   229      11.037  75.783  73.789  1.00  0.00              
ATOM    549  N   MET   230       9.969  77.082  75.271  1.00  0.00              
ATOM    550  CA  MET   230      11.162  77.830  75.670  1.00  0.00              
ATOM    551  C   MET   230      12.162  76.921  76.367  1.00  0.00              
ATOM    552  O   MET   230      13.367  76.999  76.114  1.00  0.00              
ATOM    553  N   HIS   231      11.659  76.059  77.244  1.00  0.00              
ATOM    554  CA  HIS   231      12.500  75.194  78.047  1.00  0.00              
ATOM    555  C   HIS   231      13.260  74.222  77.159  1.00  0.00              
ATOM    556  O   HIS   231      14.480  74.072  77.291  1.00  0.00              
ATOM    557  N   THR   232      12.535  73.568  76.251  1.00  0.00              
ATOM    558  CA  THR   232      13.148  72.636  75.305  1.00  0.00              
ATOM    559  C   THR   232      14.117  73.300  74.342  1.00  0.00              
ATOM    560  O   THR   232      15.189  72.757  74.092  1.00  0.00              
ATOM    561  N   MET   233      13.763  74.474  73.816  1.00  0.00              
ATOM    562  CA  MET   233      14.602  75.121  72.798  1.00  0.00              
ATOM    563  C   MET   233      16.002  75.429  73.314  1.00  0.00              
ATOM    564  O   MET   233      16.946  75.477  72.545  1.00  0.00              
ATOM    565  N   LYS   234      16.126  75.598  74.624  1.00  0.00              
ATOM    566  CA  LYS   234      17.392  75.970  75.258  1.00  0.00              
ATOM    567  C   LYS   234      18.330  74.805  75.561  1.00  0.00              
ATOM    568  O   LYS   234      19.447  75.029  75.992  1.00  0.00              
ATOM    569  N   ASN   235      17.874  73.571  75.365  1.00  0.00              
ATOM    570  CA  ASN   235      18.653  72.403  75.735  1.00  0.00              
ATOM    571  C   ASN   235      18.614  71.371  74.635  1.00  0.00              
ATOM    572  O   ASN   235      18.390  70.188  74.876  1.00  0.00              
ATOM    573  N   THR   236      18.835  71.835  73.414  1.00  0.00              
ATOM    574  CA  THR   236      18.959  70.957  72.263  1.00  0.00              
ATOM    575  C   THR   236      20.428  70.680  71.953  1.00  0.00              
ATOM    576  O   THR   236      21.291  71.511  72.233  1.00  0.00              
ATOM    577  N   GLY   237      20.706  69.509  71.383  1.00  0.00              
ATOM    578  CA  GLY   237      22.063  69.143  70.981  1.00  0.00              
ATOM    579  C   GLY   237      22.069  68.547  69.583  1.00  0.00              
ATOM    580  O   GLY   237      21.116  67.852  69.196  1.00  0.00              
ATOM    581  N   ARG   238      23.146  68.819  68.840  1.00  0.00              
ATOM    582  CA  ARG   238      23.397  68.195  67.533  1.00  0.00              
ATOM    583  C   ARG   238      24.013  66.799  67.655  1.00  0.00              
ATOM    584  O   ARG   238      24.069  66.049  66.687  1.00  0.00              
ATOM    585  N   ASN   239      24.448  66.459  68.858  1.00  0.00              
ATOM    586  CA  ASN   239      25.114  65.203  69.117  1.00  0.00              
ATOM    587  C   ASN   239      24.122  64.055  69.306  1.00  0.00              
ATOM    588  O   ASN   239      24.057  63.427  70.371  1.00  0.00              
ATOM    589  N   VAL   240      23.373  63.762  68.254  1.00  0.00              
ATOM    590  CA  VAL   240      22.177  62.927  68.375  1.00  0.00              
ATOM    591  C   VAL   240      22.465  61.440  68.540  1.00  0.00              
ATOM    592  O   VAL   240      21.542  60.642  68.743  1.00  0.00              
ATOM    593  N   ASN   241      23.738  61.071  68.438  1.00  0.00              
ATOM    594  CA  ASN   241      24.110  59.670  68.336  1.00  0.00              
ATOM    595  C   ASN   241      25.026  59.185  69.450  1.00  0.00              
ATOM    596  O   ASN   241      25.235  57.980  69.585  1.00  0.00              
ATOM    597  N   ASP   242      25.578  60.112  70.233  1.00  0.00              
ATOM    598  CA  ASP   242      26.412  59.741  71.366  1.00  0.00              
ATOM    599  C   ASP   242      25.625  58.911  72.404  1.00  0.00              
ATOM    600  O   ASP   242      24.676  59.428  73.031  1.00  0.00              
ATOM    601  N   ARG   243      25.998  57.619  72.596  1.00  0.00              
ATOM    602  CA  ARG   243      25.115  56.862  73.501  1.00  0.00              
ATOM    603  C   ARG   243      25.279  57.270  74.983  1.00  0.00              
ATOM    604  O   ARG   243      24.327  57.095  75.755  1.00  0.00              
ATOM    605  N   MET   246      26.429  57.841  75.367  1.00  0.00              
ATOM    606  CA  MET   246      26.569  58.399  76.728  1.00  0.00              
ATOM    607  C   MET   246      25.534  59.518  76.963  1.00  0.00              
ATOM    608  O   MET   246      24.785  59.498  77.953  1.00  0.00              
ATOM    609  N   VAL   247      25.490  60.472  76.033  1.00  0.00              
ATOM    610  CA  VAL   247      24.522  61.565  76.047  1.00  0.00              
ATOM    611  C   VAL   247      23.081  61.038  76.108  1.00  0.00              
ATOM    612  O   VAL   247      22.256  61.550  76.859  1.00  0.00              
ATOM    613  N   ALA   248      22.807  60.001  75.325  1.00  0.00              
ATOM    614  CA  ALA   248      21.480  59.427  75.238  1.00  0.00              
ATOM    615  C   ALA   248      21.082  58.735  76.542  1.00  0.00              
ATOM    616  O   ALA   248      19.954  58.887  77.009  1.00  0.00              
ATOM    617  N   LYS   249      22.016  58.004  77.139  1.00  0.00              
ATOM    618  CA  LYS   249      21.770  57.322  78.406  1.00  0.00              
ATOM    619  C   LYS   249      21.550  58.329  79.545  1.00  0.00              
ATOM    620  O   LYS   249      20.615  58.172  80.329  1.00  0.00              
ATOM    621  N   GLU   250      22.392  59.359  79.620  1.00  0.00              
ATOM    622  CA  GLU   250      22.176  60.457  80.561  1.00  0.00              
ATOM    623  C   GLU   250      20.788  61.070  80.405  1.00  0.00              
ATOM    624  O   GLU   250      20.111  61.356  81.395  1.00  0.00              
ATOM    625  N   GLY   251      20.367  61.245  79.156  1.00  0.00              
ATOM    626  CA  GLY   251      19.054  61.746  78.839  1.00  0.00              
ATOM    627  C   GLY   251      17.941  60.860  79.362  1.00  0.00              
ATOM    628  O   GLY   251      16.995  61.345  80.008  1.00  0.00              
ATOM    629  N   GLU   252      18.040  59.561  79.097  1.00  0.00              
ATOM    630  CA  GLU   252      16.976  58.644  79.482  1.00  0.00              
ATOM    631  C   GLU   252      16.938  58.449  80.988  1.00  0.00              
ATOM    632  O   GLU   252      15.870  58.307  81.555  1.00  0.00              
ATOM    633  N   THR   253      18.101  58.465  81.639  1.00  0.00              
ATOM    634  CA  THR   253      18.168  58.393  83.089  1.00  0.00              
ATOM    635  C   THR   253      17.395  59.573  83.691  1.00  0.00              
ATOM    636  O   THR   253      16.683  59.415  84.673  1.00  0.00              
ATOM    637  N   TYR   254      17.520  60.753  83.097  1.00  0.00              
ATOM    638  CA  TYR   254      16.834  61.924  83.609  1.00  0.00              
ATOM    639  C   TYR   254      15.333  61.801  83.367  1.00  0.00              
ATOM    640  O   TYR   254      14.527  62.145  84.240  1.00  0.00              
ATOM    641  N   THR   255      14.966  61.287  82.191  1.00  0.00              
ATOM    642  CA  THR   255      13.574  61.053  81.870  1.00  0.00              
ATOM    643  C   THR   255      12.922  60.186  82.958  1.00  0.00              
ATOM    644  O   THR   255      11.823  60.490  83.424  1.00  0.00              
ATOM    645  N   GLY   256      13.604  59.112  83.359  1.00  0.00              
ATOM    646  CA  GLY   256      13.105  58.224  84.417  1.00  0.00              
ATOM    647  C   GLY   256      13.119  58.898  85.784  1.00  0.00              
ATOM    648  O   GLY   256      12.265  58.626  86.637  1.00  0.00              
ATOM    649  N   THR   257      14.081  59.797  85.973  1.00  0.00              
ATOM    650  CA  THR   257      14.141  60.584  87.177  1.00  0.00              
ATOM    651  C   THR   257      12.927  61.497  87.330  1.00  0.00              
ATOM    652  O   THR   257      12.506  61.771  88.458  1.00  0.00              
ATOM    653  N   TYR   258      12.373  61.962  86.198  1.00  0.00              
ATOM    654  CA  TYR   258      11.217  62.853  86.195  1.00  0.00              
ATOM    655  C   TYR   258      10.014  62.143  86.821  1.00  0.00              
ATOM    656  O   TYR   258       9.127  62.787  87.363  1.00  0.00              
ATOM    657  N   ARG   259       9.996  60.813  86.703  1.00  0.00              
ATOM    658  CA  ARG   259       8.930  59.980  87.216  1.00  0.00              
ATOM    659  C   ARG   259       9.198  59.511  88.653  1.00  0.00              
ATOM    660  O   ARG   259       8.428  58.712  89.192  1.00  0.00              
ATOM    661  N   GLY   260      10.286  59.993  89.267  1.00  0.00              
ATOM    662  CA  GLY   260      10.620  59.655  90.654  1.00  0.00              
ATOM    663  C   GLY   260      11.620  58.523  90.878  1.00  0.00              
ATOM    664  O   GLY   260      11.774  58.042  92.005  1.00  0.00              
ATOM    665  N   ALA   261      12.301  58.084  89.823  1.00  0.00              
ATOM    666  CA  ALA   261      13.348  57.069  89.967  1.00  0.00              
ATOM    667  C   ALA   261      14.684  57.730  90.307  1.00  0.00              
ATOM    668  O   ALA   261      15.213  58.509  89.511  1.00  0.00              
ATOM    669  N   GLY   262      15.227  57.413  91.487  1.00  0.00              
ATOM    670  CA  GLY   262      16.404  58.108  92.022  1.00  0.00              
ATOM    671  C   GLY   262      17.628  57.216  92.119  1.00  0.00              
ATOM    672  O   GLY   262      18.256  56.891  91.105  1.00  0.00              
END
