
#######################################################
#                                                     #
#                        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   31 (  132),  selected   31 , name T0386AL380_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386AL380_3-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      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    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    E     228      N     239           #
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    F     229      R     243          4.189
LGA    -       -      P     244           -
LGA    -       -      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    -       -      V     270           -
LGA    M     230      K     271          3.910
LGA    H     231      G     272          3.048
LGA    T     232      A     273          3.712
LGA    M     233      Y     274          2.384
LGA    K     234      -       -           -
LGA    N     235      -       -           -
LGA    T     236      I     275          1.449
LGA    G     237      I     276          3.085
LGA    R     238      G     277          3.593
LGA    N     239      N     278          1.706
LGA    V     240      -       -           -
LGA    N     241      I     279          2.824
LGA    D     242      D     280          1.095
LGA    R     243      H     281           #
LGA    M     246      L     282          2.135
LGA    V     247      P     283          5.824
LGA    A     248      P     284           #
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    K     249      L     287          0.986
LGA    E     250      K     288           #
LGA    G     251      -       -           -
LGA    E     252      -       -           -
LGA    T     253      I     289          2.530
LGA    Y     254      L     290          3.239
LGA    T     255      K     291          1.916
LGA    G     256      -       -           -
LGA    T     257      P     292           #
LGA    Y     258      G     293          3.963
LGA    R     259      D     294           -
LGA    G     260      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)   31   81    5.0     18    3.11    11.11     14.197     0.561

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.614140 * X  +   0.332698 * Y  +  -0.715643 * Z  + -11.348837
  Y_new =  -0.452401 * X  +   0.594606 * Y  +   0.664663 * Z  +  26.404150
  Z_new =   0.646657 * X  +   0.731954 * Y  +  -0.214658 * Z  +  51.144691 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.856065   -1.285528  [ DEG:   106.3447    -73.6553 ]
  Theta =  -0.703194   -2.438398  [ DEG:   -40.2901   -139.7099 ]
  Phi   =  -2.506696    0.634897  [ DEG:  -143.6231     36.3769 ]
 
# 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_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL380_3-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31   81   5.0   18   3.11   11.11  14.197
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL380_3-D2
REMARK Aligment from pdb entry: 2g03A
ATOM    569  N   GLU   228      28.563  64.193  75.660  1.00  0.00              
ATOM    570  CA  GLU   228      27.369  64.491  76.428  1.00  0.00              
ATOM    571  C   GLU   228      26.120  63.765  75.901  1.00  0.00              
ATOM    572  O   GLU   228      25.316  63.246  76.681  1.00  0.00              
ATOM    573  N   PHE   229      25.921  63.747  74.590  1.00  0.00              
ATOM    574  CA  PHE   229      24.778  62.995  74.019  1.00  0.00              
ATOM    575  C   PHE   229      24.845  61.506  74.315  1.00  0.00              
ATOM    576  O   PHE   229      23.835  60.915  74.679  1.00  0.00              
ATOM    577  N  AMET   230      26.024  60.900  74.133  1.00  0.00              
ATOM    578  N  BMET   230      26.028  60.914  74.197  1.00  0.00              
ATOM    579  CA AMET   230      26.253  59.489  74.467  1.00  0.00              
ATOM    580  CA BMET   230      26.168  59.488  74.453  1.00  0.00              
ATOM    581  C  AMET   230      25.804  59.261  75.909  1.00  0.00              
ATOM    582  C  BMET   230      26.029  59.120  75.928  1.00  0.00              
ATOM    583  O  AMET   230      24.922  58.440  76.186  1.00  0.00              
ATOM    584  O  BMET   230      25.577  58.026  76.257  1.00  0.00              
ATOM    585  N   HIS   231      26.370  60.048  76.821  1.00  0.00              
ATOM    586  CA  HIS   231      26.196  59.816  78.242  1.00  0.00              
ATOM    587  C   HIS   231      24.758  60.017  78.671  1.00  0.00              
ATOM    588  O   HIS   231      24.242  59.236  79.438  1.00  0.00              
ATOM    589  N   THR   232      24.114  61.093  78.231  1.00  0.00              
ATOM    590  CA  THR   232      22.748  61.355  78.710  1.00  0.00              
ATOM    591  C   THR   232      21.701  60.446  78.049  1.00  0.00              
ATOM    592  O   THR   232      20.771  59.995  78.704  1.00  0.00              
ATOM    593  N   MET   233      21.876  60.152  76.766  1.00  0.00              
ATOM    594  CA  MET   233      20.959  59.295  76.038  1.00  0.00              
ATOM    595  C   MET   233      20.903  57.900  76.644  1.00  0.00              
ATOM    596  O   MET   233      19.855  57.289  76.688  1.00  0.00              
ATOM    597  N   LYS   234      22.054  57.396  77.079  1.00  0.00              
ATOM    598  CA  LYS   234      22.155  56.143  77.841  1.00  0.00              
ATOM    599  C   LYS   234      21.380  56.147  79.164  1.00  0.00              
ATOM    600  O   LYS   234      21.170  55.100  79.768  1.00  0.00              
ATOM    601  N   ASN   235      21.000  57.325  79.635  1.00  0.00              
ATOM    602  CA  ASN   235      20.512  57.431  80.983  1.00  0.00              
ATOM    603  C   ASN   235      19.186  58.180  81.077  1.00  0.00              
ATOM    604  O   ASN   235      18.884  58.751  82.105  1.00  0.00              
ATOM    605  N   THR   236      18.376  58.150  80.023  1.00  0.00              
ATOM    606  CA  THR   236      17.042  58.744  80.107  1.00  0.00              
ATOM    607  C   THR   236      16.120  57.736  80.757  1.00  0.00              
ATOM    608  O   THR   236      16.396  56.534  80.716  1.00  0.00              
ATOM    609  N   GLY   237      15.042  58.219  81.378  1.00  0.00              
ATOM    610  CA  GLY   237      13.994  57.354  81.907  1.00  0.00              
ATOM    611  C   GLY   237      12.672  58.022  81.594  1.00  0.00              
ATOM    612  O   GLY   237      12.588  59.240  81.605  1.00  0.00              
ATOM    613  N   ARG   238      11.625  57.256  81.309  1.00  0.00              
ATOM    614  CA  ARG   238      10.328  57.903  81.180  1.00  0.00              
ATOM    615  C   ARG   238       9.507  57.862  82.457  1.00  0.00              
ATOM    616  O   ARG   238       8.350  58.257  82.460  1.00  0.00              
ATOM    617  N   ASN   239      10.130  57.434  83.546  1.00  0.00              
ATOM    618  CA  ASN   239       9.460  57.409  84.843  1.00  0.00              
ATOM    619  C   ASN   239       9.692  58.778  85.511  1.00  0.00              
ATOM    620  O   ASN   239      10.402  58.875  86.506  1.00  0.00              
ATOM    621  N   VAL   240       9.080  59.823  84.954  1.00  0.00              
ATOM    622  CA  VAL   240       9.526  61.207  85.163  1.00  0.00              
ATOM    623  C   VAL   240       9.158  61.766  86.546  1.00  0.00              
ATOM    624  O   VAL   240       9.698  62.810  86.959  1.00  0.00              
ATOM    625  N   ASN   241       8.257  61.077  87.245  1.00  0.00              
ATOM    626  CA  ASN   241       7.730  61.553  88.519  1.00  0.00              
ATOM    627  C   ASN   241       8.032  60.597  89.665  1.00  0.00              
ATOM    628  O   ASN   241       7.474  60.717  90.744  1.00  0.00              
ATOM    629  N   ASP   242       8.916  59.649  89.417  1.00  0.00              
ATOM    630  CA  ASP   242       9.295  58.677  90.418  1.00  0.00              
ATOM    631  C   ASP   242      10.117  59.329  91.545  1.00  0.00              
ATOM    632  O   ASP   242      11.109  60.010  91.289  1.00  0.00              
ATOM    633  N   ARG   243       9.676  59.152  92.788  1.00  0.00              
ATOM    634  CA  ARG   243      10.345  59.762  93.938  1.00  0.00              
ATOM    635  C   ARG   243      11.848  59.421  94.028  1.00  0.00              
ATOM    636  O   ARG   243      12.659  60.292  94.324  1.00  0.00              
ATOM    637  N   MET   246      12.216  58.176  93.748  1.00  0.00              
ATOM    638  CA  MET   246      13.602  57.754  93.863  1.00  0.00              
ATOM    639  C   MET   246      14.494  58.393  92.790  1.00  0.00              
ATOM    640  O   MET   246      15.613  58.851  93.078  1.00  0.00              
ATOM    641  N   VAL   247      13.997  58.437  91.554  1.00  0.00              
ATOM    642  CA  VAL   247      14.696  59.096  90.458  1.00  0.00              
ATOM    643  C   VAL   247      14.832  60.584  90.742  1.00  0.00              
ATOM    644  O   VAL   247      15.911  61.150  90.556  1.00  0.00              
ATOM    645  N   ALA   248      13.758  61.228  91.196  1.00  0.00              
ATOM    646  CA  ALA   248      13.835  62.656  91.514  1.00  0.00              
ATOM    647  C   ALA   248      14.864  62.914  92.650  1.00  0.00              
ATOM    648  O   ALA   248      15.831  63.649  92.472  1.00  0.00              
ATOM    649  N   LYS   249      14.690  62.272  93.790  1.00  0.00              
ATOM    650  CA  LYS   249      15.524  62.585  94.944  1.00  0.00              
ATOM    651  C   LYS   249      16.983  62.096  94.896  1.00  0.00              
ATOM    652  O   LYS   249      17.865  62.832  95.314  1.00  0.00              
ATOM    653  N   GLU   250      17.231  60.888  94.391  1.00  0.00              
ATOM    654  CA  GLU   250      18.602  60.424  94.173  1.00  0.00              
ATOM    655  C   GLU   250      19.278  61.252  93.088  1.00  0.00              
ATOM    656  O   GLU   250      20.497  61.438  93.118  1.00  0.00              
ATOM    657  N   GLY   251      18.481  61.754  92.141  1.00  0.00              
ATOM    658  CA  GLY   251      18.955  62.636  91.093  1.00  0.00              
ATOM    659  C   GLY   251      19.395  63.995  91.601  1.00  0.00              
ATOM    660  O   GLY   251      20.441  64.495  91.204  1.00  0.00              
ATOM    661  N   GLU   252      18.576  64.619  92.444  1.00  0.00              
ATOM    662  CA  GLU   252      18.930  65.862  93.129  1.00  0.00              
ATOM    663  C   GLU   252      20.216  65.682  93.944  1.00  0.00              
ATOM    664  O   GLU   252      21.098  66.528  93.897  1.00  0.00              
ATOM    665  N   THR   253      20.318  64.596  94.700  1.00  0.00              
ATOM    666  CA  THR   253      21.561  64.313  95.410  1.00  0.00              
ATOM    667  C   THR   253      22.784  64.202  94.496  1.00  0.00              
ATOM    668  O   THR   253      23.852  64.679  94.853  1.00  0.00              
ATOM    669  N   TYR   254      22.632  63.567  93.338  1.00  0.00              
ATOM    670  CA  TYR   254      23.753  63.402  92.420  1.00  0.00              
ATOM    671  C   TYR   254      24.112  64.748  91.795  1.00  0.00              
ATOM    672  O   TYR   254      25.273  65.106  91.728  1.00  0.00              
ATOM    673  N   THR   255      23.103  65.499  91.355  1.00  0.00              
ATOM    674  CA  THR   255      23.277  66.837  90.819  1.00  0.00              
ATOM    675  C   THR   255      24.086  67.756  91.740  1.00  0.00              
ATOM    676  O   THR   255      24.976  68.489  91.281  1.00  0.00              
ATOM    677  N  AGLY   256      23.759  67.731  93.030  1.00  0.00              
ATOM    678  N  BGLY   256      23.745  67.725  93.016  1.00  0.00              
ATOM    679  CA AGLY   256      24.441  68.549  94.044  1.00  0.00              
ATOM    680  CA BGLY   256      24.404  68.528  94.019  1.00  0.00              
ATOM    681  C  AGLY   256      25.865  68.064  94.326  1.00  0.00              
ATOM    682  C  BGLY   256      25.859  68.085  94.212  1.00  0.00              
ATOM    683  O  AGLY   256      26.730  68.844  94.764  1.00  0.00              
ATOM    684  O  BGLY   256      26.733  68.913  94.501  1.00  0.00              
ATOM    685  N   THR   257      26.099  66.779  94.075  1.00  0.00              
ATOM    686  CA  THR   257      27.435  66.185  94.187  1.00  0.00              
ATOM    687  C   THR   257      28.395  66.645  93.049  1.00  0.00              
ATOM    688  O   THR   257      29.596  66.798  93.268  1.00  0.00              
ATOM    689  N   TYR   258      27.854  66.903  91.860  1.00  0.00              
ATOM    690  CA  TYR   258      28.657  67.265  90.699  1.00  0.00              
ATOM    691  C   TYR   258      29.480  68.500  90.978  1.00  0.00              
ATOM    692  O   TYR   258      30.593  68.639  90.467  1.00  0.00              
ATOM    693  N   ARG   259      28.964  69.405  91.801  1.00  0.00              
ATOM    694  CA  ARG   259      29.744  70.624  92.030  1.00  0.00              
ATOM    695  C   ARG   259      30.133  70.822  93.478  1.00  0.00              
ATOM    696  O   ARG   259      30.385  71.942  93.883  1.00  0.00              
ATOM    697  N   GLY   260      30.245  69.733  94.236  1.00  0.00              
ATOM    698  CA  GLY   260      30.591  69.814  95.665  1.00  0.00              
ATOM    699  C   GLY   260      30.921  68.462  96.272  1.00  0.00              
ATOM    700  O   GLY   260      30.798  68.252  97.492  1.00  0.00              
END
