
#######################################################
#                                                     #
#                        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 T0289AL243_1-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289AL243_1-D2.T0289_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I     224      I     224          1.283
LGA    M     225      M     225          1.403
LGA    E     226      E     226          1.418
LGA    K     227      K     227          0.839
LGA    V     228      V     228          1.202
LGA    D     229      D     229          1.152
LGA    R     232      Y     230          1.979
LGA    -       -      P     231           -
LGA    N     233      R     232          2.143
LGA    E     234      N     233          3.154
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    -       -      V     238           -
LGA    -       -      A     239           -
LGA    W     251      A     240          1.689
LGA    K     252      V     241          3.437
LGA    L     254      I     242          2.134
LGA    H     255      H     243          2.610
LGA    -       -      P     244           -
LGA    -       -      N     245           -
LGA    -       -      L     246           -
LGA    -       -      Q     247           -
LGA    -       -      D     248           -
LGA    P     256      Q     249          2.717
LGA    G     257      D     250          1.750
LGA    F     261      W     251          0.592
LGA    V     262      K     252          1.240
LGA    S     263      P     253          0.492
LGA    L     264      L     254          0.426
LGA    D     265      H     255          1.895
LGA    G     266      P     256          2.699
LGA    K     267      G     257          2.259
LGA    -       -      D     258           -
LGA    -       -      P     259           -
LGA    -       -      V     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      S     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      G     266           -
LGA    -       -      K     267           -
LGA    -       -      V     268           -
LGA    -       -      I     269           -
LGA    -       -      P     270           -
LGA    V     268      L     271          1.057
LGA    I     269      G     272          4.723
LGA    P     270      G     273           -
LGA    -       -      D     274           -
LGA    -       -      C     275           -
LGA    T     276      T     276          2.846
LGA    V     277      V     277          0.685
LGA    Y     278      Y     278          0.931
LGA    P     279      P     279          0.933
LGA    V     280      V     280          0.563
LGA    F     281      F     281          0.877
LGA    V     282      V     282          0.649
LGA    N     283      N     283          0.845
LGA    -       -      E     284           -
LGA    -       -      A     285           -
LGA    -       -      A     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      E     289           -
LGA    -       -      K     290           -
LGA    -       -      K     291           -
LGA    -       -      E     292           -
LGA    -       -      A     293           -
LGA    -       -      F     294           -
LGA    -       -      A     295           -
LGA    -       -      K     296           -
LGA    -       -      T     297           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   33   74    5.0     32    1.92    50.00     38.774     1.582

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.426189 * X  +   0.672635 * Y  +  -0.604917 * Z  + 105.799133
  Y_new =   0.035028 * X  +   0.680456 * Y  +   0.731951 * Z  + -58.223099
  Z_new =   0.903956 * X  +   0.290761 * Y  +  -0.313564 * Z  +  -0.104839 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.393909   -0.747683  [ DEG:   137.1609    -42.8391 ]
  Theta =  -1.128931   -2.012662  [ DEG:   -64.6830   -115.3170 ]
  Phi   =   3.059589   -0.082004  [ DEG:   175.3015     -4.6985 ]
 
# 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: T0289AL243_1-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289AL243_1-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33   74   5.0   32   1.92   50.00  38.774
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL243_1-D2
REMARK Aligment from pdb entry: 1yw4A
ATOM    833  N   ILE   224      26.148  28.903  19.896  1.00  0.00              
ATOM    834  CA  ILE   224      25.561  29.660  20.989  1.00  0.00              
ATOM    835  C   ILE   224      25.332  28.718  22.165  1.00  0.00              
ATOM    836  O   ILE   224      24.913  27.576  21.983  1.00  0.00              
ATOM    837  N   MET   225      25.621  29.196  23.369  1.00  0.00              
ATOM    838  CA  MET   225      25.415  28.399  24.571  1.00  0.00              
ATOM    839  C   MET   225      24.113  28.877  25.211  1.00  0.00              
ATOM    840  O   MET   225      23.249  28.074  25.554  1.00  0.00              
ATOM    841  N   GLU   226      23.987  30.193  25.358  1.00  0.00              
ATOM    842  CA  GLU   226      22.795  30.813  25.934  1.00  0.00              
ATOM    843  C   GLU   226      22.829  32.325  25.698  1.00  0.00              
ATOM    844  O   GLU   226      23.901  32.906  25.511  1.00  0.00              
ATOM    845  N   LYS   227      21.659  32.958  25.708  1.00  0.00              
ATOM    846  CA  LYS   227      21.584  34.399  25.496  1.00  0.00              
ATOM    847  C   LYS   227      21.524  35.144  26.822  1.00  0.00              
ATOM    848  O   LYS   227      21.010  34.631  27.818  1.00  0.00              
ATOM    849  N   VAL   228      22.058  36.361  26.827  1.00  0.00              
ATOM    850  CA  VAL   228      22.055  37.195  28.023  1.00  0.00              
ATOM    851  C   VAL   228      20.762  37.995  28.048  1.00  0.00              
ATOM    852  O   VAL   228      20.724  39.132  27.583  1.00  0.00              
ATOM    853  N   ASP   229      19.704  37.391  28.583  1.00  0.00              
ATOM    854  CA  ASP   229      18.404  38.047  28.664  1.00  0.00              
ATOM    855  C   ASP   229      18.486  39.271  29.575  1.00  0.00              
ATOM    856  O   ASP   229      18.906  39.172  30.726  1.00  0.00              
ATOM    857  N   ARG   232      18.088  40.427  29.057  1.00  0.00              
ATOM    858  CA  ARG   232      18.127  41.648  29.849  1.00  0.00              
ATOM    859  C   ARG   232      16.759  42.105  30.350  1.00  0.00              
ATOM    860  O   ARG   232      15.766  42.080  29.620  1.00  0.00              
ATOM    861  N   ASN   233      16.729  42.515  31.613  1.00  0.00              
ATOM    862  CA  ASN   233      15.521  43.006  32.260  1.00  0.00              
ATOM    863  C   ASN   233      15.904  44.017  33.341  1.00  0.00              
ATOM    864  O   ASN   233      16.918  43.854  34.025  1.00  0.00              
ATOM    865  N   GLU   234      15.092  45.061  33.475  1.00  0.00              
ATOM    866  CA  GLU   234      15.314  46.130  34.449  1.00  0.00              
ATOM    867  C   GLU   234      16.619  46.864  34.159  1.00  0.00              
ATOM    868  O   GLU   234      16.735  47.582  33.165  1.00  0.00              
ATOM    869  N   TRP   251      20.704  45.804  36.058  1.00  0.00              
ATOM    870  CA  TRP   251      21.313  45.506  34.768  1.00  0.00              
ATOM    871  C   TRP   251      22.641  46.229  34.582  1.00  0.00              
ATOM    872  O   TRP   251      22.706  47.457  34.650  1.00  0.00              
ATOM    873  N   LYS   252      23.692  45.451  34.338  1.00  0.00              
ATOM    874  CA  LYS   252      25.040  45.984  34.138  1.00  0.00              
ATOM    875  C   LYS   252      25.890  45.010  33.330  1.00  0.00              
ATOM    876  O   LYS   252      26.007  43.835  33.681  1.00  0.00              
ATOM    877  N   LEU   254      26.484  45.513  32.252  1.00  0.00              
ATOM    878  CA  LEU   254      27.337  44.708  31.379  1.00  0.00              
ATOM    879  C   LEU   254      28.793  44.895  31.810  1.00  0.00              
ATOM    880  O   LEU   254      29.380  45.955  31.597  1.00  0.00              
ATOM    881  N   HIS   255      29.369  43.858  32.410  1.00  0.00              
ATOM    882  CA  HIS   255      30.739  43.914  32.909  1.00  0.00              
ATOM    883  C   HIS   255      31.849  43.850  31.860  1.00  0.00              
ATOM    884  O   HIS   255      32.893  43.236  32.084  1.00  0.00              
ATOM    885  N   PRO   256      35.547  43.477  22.008  1.00  0.00              
ATOM    886  CA  PRO   256      35.563  42.777  20.723  1.00  0.00              
ATOM    887  C   PRO   256      34.746  41.492  20.746  1.00  0.00              
ATOM    888  O   PRO   256      34.576  40.869  21.795  1.00  0.00              
ATOM    889  N   GLY   257      34.240  41.096  19.579  1.00  0.00              
ATOM    890  CA  GLY   257      33.471  39.866  19.483  1.00  0.00              
ATOM    891  C   GLY   257      34.408  38.688  19.717  1.00  0.00              
ATOM    892  O   GLY   257      35.595  38.746  19.379  1.00  0.00              
ATOM    893  N   PHE   261      33.854  37.624  20.288  1.00  0.00              
ATOM    894  CA  PHE   261      34.582  36.396  20.596  1.00  0.00              
ATOM    895  C   PHE   261      35.574  36.580  21.734  1.00  0.00              
ATOM    896  O   PHE   261      36.505  35.792  21.889  1.00  0.00              
ATOM    897  N   VAL   262      35.377  37.627  22.531  1.00  0.00              
ATOM    898  CA  VAL   262      36.260  37.861  23.668  1.00  0.00              
ATOM    899  C   VAL   262      36.064  36.718  24.661  1.00  0.00              
ATOM    900  O   VAL   262      34.939  36.432  25.066  1.00  0.00              
ATOM    901  N   SER   263      37.166  36.074  25.044  1.00  0.00              
ATOM    902  CA  SER   263      37.149  34.952  25.980  1.00  0.00              
ATOM    903  C   SER   263      36.725  35.366  27.391  1.00  0.00              
ATOM    904  O   SER   263      37.221  36.357  27.933  1.00  0.00              
ATOM    905  N   LEU   264      35.808  34.604  27.981  1.00  0.00              
ATOM    906  CA  LEU   264      35.326  34.881  29.331  1.00  0.00              
ATOM    907  C   LEU   264      35.976  33.908  30.320  1.00  0.00              
ATOM    908  O   LEU   264      35.668  32.725  30.332  1.00  0.00              
ATOM    909  N   ASP   265      36.881  34.405  31.174  1.00  0.00              
ATOM    910  CA  ASP   265      37.554  33.535  32.147  1.00  0.00              
ATOM    911  C   ASP   265      36.626  32.879  33.159  1.00  0.00              
ATOM    912  O   ASP   265      35.531  33.371  33.428  1.00  0.00              
ATOM    913  N   GLY   266      34.908  32.279  36.276  1.00  0.00              
ATOM    914  CA  GLY   266      34.650  33.134  37.421  1.00  0.00              
ATOM    915  C   GLY   266      33.517  34.107  37.140  1.00  0.00              
ATOM    916  O   GLY   266      32.411  33.958  37.672  1.00  0.00              
ATOM    917  N   LYS   267      33.782  35.105  36.301  1.00  0.00              
ATOM    918  CA  LYS   267      32.762  36.095  35.951  1.00  0.00              
ATOM    919  C   LYS   267      31.666  35.436  35.123  1.00  0.00              
ATOM    920  O   LYS   267      31.944  34.766  34.130  1.00  0.00              
ATOM    921  N   VAL   268      30.417  35.613  35.535  1.00  0.00              
ATOM    922  CA  VAL   268      29.300  35.036  34.793  1.00  0.00              
ATOM    923  C   VAL   268      28.066  35.917  34.972  1.00  0.00              
ATOM    924  O   VAL   268      28.165  37.038  35.476  1.00  0.00              
ATOM    925  N   ILE   269      26.906  35.430  34.558  1.00  0.00              
ATOM    926  CA  ILE   269      25.698  36.229  34.695  1.00  0.00              
ATOM    927  C   ILE   269      24.882  35.809  35.915  1.00  0.00              
ATOM    928  O   ILE   269      24.766  34.618  36.217  1.00  0.00              
ATOM    929  N   PRO   270      24.335  36.794  36.622  1.00  0.00              
ATOM    930  CA  PRO   270      23.521  36.543  37.809  1.00  0.00              
ATOM    931  C   PRO   270      22.622  37.747  38.089  1.00  0.00              
ATOM    932  O   PRO   270      21.461  37.587  38.474  1.00  0.00              
ATOM    933  N   THR   276      36.140  28.742  28.644  1.00  0.00              
ATOM    934  CA  THR   276      35.993  28.361  27.243  1.00  0.00              
ATOM    935  C   THR   276      34.983  29.238  26.504  1.00  0.00              
ATOM    936  O   THR   276      35.033  29.359  25.281  1.00  0.00              
ATOM    937  N   VAL   277      34.069  29.851  27.251  1.00  0.00              
ATOM    938  CA  VAL   277      33.051  30.691  26.642  1.00  0.00              
ATOM    939  C   VAL   277      33.588  32.040  26.154  1.00  0.00              
ATOM    940  O   VAL   277      34.620  32.518  26.616  1.00  0.00              
ATOM    941  N   TYR   278      32.883  32.635  25.198  1.00  0.00              
ATOM    942  CA  TYR   278      33.266  33.926  24.644  1.00  0.00              
ATOM    943  C   TYR   278      31.989  34.726  24.412  1.00  0.00              
ATOM    944  O   TYR   278      30.919  34.156  24.201  1.00  0.00              
ATOM    945  N   PRO   279      32.103  36.045  24.457  1.00  0.00              
ATOM    946  CA  PRO   279      30.952  36.910  24.252  1.00  0.00              
ATOM    947  C   PRO   279      30.865  37.232  22.760  1.00  0.00              
ATOM    948  O   PRO   279      31.886  37.393  22.086  1.00  0.00              
ATOM    949  N   VAL   280      29.651  37.311  22.236  1.00  0.00              
ATOM    950  CA  VAL   280      29.479  37.612  20.823  1.00  0.00              
ATOM    951  C   VAL   280      28.303  38.563  20.630  1.00  0.00              
ATOM    952  O   VAL   280      27.253  38.391  21.244  1.00  0.00              
ATOM    953  N   PHE   281      28.504  39.577  19.794  1.00  0.00              
ATOM    954  CA  PHE   281      27.476  40.574  19.494  1.00  0.00              
ATOM    955  C   PHE   281      26.840  41.226  20.726  1.00  0.00              
ATOM    956  O   PHE   281      25.620  41.290  20.844  1.00  0.00              
ATOM    957  N   VAL   282      27.662  41.730  21.658  1.00  0.00              
ATOM    958  CA  VAL   282      27.120  42.372  22.861  1.00  0.00              
ATOM    959  C   VAL   282      26.371  43.670  22.534  1.00  0.00              
ATOM    960  O   VAL   282      26.839  44.475  21.729  1.00  0.00              
ATOM    961  N   ASN   283      25.215  43.872  23.160  1.00  0.00              
ATOM    962  CA  ASN   283      24.424  45.077  22.926  1.00  0.00              
ATOM    963  C   ASN   283      23.565  45.374  24.151  1.00  0.00              
ATOM    964  O   ASN   283      22.364  45.095  24.163  1.00  0.00              
END
