
#######################################################
#                                                     #
#                        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   21 (   84),  selected   21 , name T0289TS550_2-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS550_2-D2.T0289_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    -       -      I     224           -
LGA    -       -      M     225           -
LGA    -       -      E     226           -
LGA    -       -      K     227           -
LGA    -       -      V     228           -
LGA    -       -      D     229           -
LGA    -       -      Y     230           -
LGA    -       -      P     231           -
LGA    -       -      R     232           -
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    -       -      V     238           -
LGA    -       -      A     239           -
LGA    -       -      A     240           -
LGA    -       -      V     241           -
LGA    I     224      I     242          2.564
LGA    M     225      H     243          2.816
LGA    E     226      P     244          4.288
LGA    K     227      N     245           -
LGA    -       -      L     246           -
LGA    -       -      Q     247           -
LGA    -       -      D     248           -
LGA    -       -      Q     249           -
LGA    -       -      D     250           -
LGA    -       -      W     251           -
LGA    -       -      K     252           -
LGA    -       -      P     253           -
LGA    -       -      L     254           -
LGA    -       -      H     255           -
LGA    -       -      P     256           -
LGA    -       -      G     257           -
LGA    -       -      D     258           -
LGA    -       -      P     259           -
LGA    -       -      V     260           -
LGA    -       -      F     261           -
LGA    V     228      V     262          2.245
LGA    D     229      S     263          2.340
LGA    -       -      L     264           -
LGA    Y     230      D     265          1.849
LGA    P     231      G     266          1.690
LGA    R     232      K     267          1.662
LGA    N     233      V     268          1.490
LGA    E     234      I     269          1.740
LGA    S     235      P     270          2.198
LGA    G     236      L     271          0.989
LGA    D     237      G     272           -
LGA    H     255      G     273           -
LGA    P     256      D     274           -
LGA    G     257      C     275           -
LGA    D     258      T     276           -
LGA    P     259      V     277           -
LGA    V     260      Y     278           -
LGA    F     261      P     279           -
LGA    -       -      V     280           -
LGA    -       -      F     281           -
LGA    -       -      V     282           -
LGA    -       -      N     283           -
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)   21   74    5.0     12    2.30    16.67     12.684     0.500

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.975005 * X  +  -0.070874 * Y  +   0.210578 * Z  +  56.189812
  Y_new =   0.215644 * X  +  -0.073593 * Y  +   0.973695 * Z  + -12.309689
  Z_new =  -0.053512 * X  +   0.994767 * Y  +   0.087037 * Z  +  11.517109 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.483524   -1.658069  [ DEG:    84.9997    -95.0003 ]
  Theta =   0.053538    3.088055  [ DEG:     3.0675    176.9325 ]
  Phi   =   2.923924   -0.217669  [ DEG:   167.5285    -12.4715 ]
 
# 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: T0289TS550_2-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS550_2-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21   74   5.0   12   2.30   16.67  12.684
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS550_2-D2
PFRMAT TS
TARGET T0289
MODEL 2
PARENT 2bco_B
ATOM    223  N   ILE   224      28.236  46.837  27.211  1.00  0.00
ATOM    223  CA  ILE   224      28.425  47.622  28.418  1.00  0.00
ATOM    223  C   ILE   224      29.572  47.033  29.251  1.00  0.00
ATOM    223  O   ILE   224      29.358  46.124  30.053  1.00  0.00
ATOM    224  N   MET   225      30.768  47.563  29.043  1.00  0.00
ATOM    224  CA  MET   225      31.946  47.090  29.766  1.00  0.00
ATOM    224  C   MET   225      31.878  47.297  31.284  1.00  0.00
ATOM    224  O   MET   225      32.277  48.347  31.792  1.00  0.00
ATOM    225  N   GLU   226      30.716  47.793  31.897  1.00  0.00
ATOM    225  CA  GLU   226      29.613  47.460  32.794  1.00  0.00
ATOM    225  C   GLU   226      28.348  48.152  32.304  1.00  0.00
ATOM    225  O   GLU   226      28.371  49.292  31.840  1.00  0.00
ATOM    226  N   LYS   227      27.248  47.424  32.387  1.00  0.00
ATOM    226  CA  LYS   227      25.933  48.038  32.220  1.00  0.00
ATOM    226  C   LYS   227      25.125  47.935  33.491  1.00  0.00
ATOM    226  O   LYS   227      23.912  48.062  33.462  1.00  0.00
ATOM    227  N   VAL   228      25.794  47.743  34.616  1.00  0.00
ATOM    227  CA  VAL   228      25.122  47.763  35.917  1.00  0.00
ATOM    227  C   VAL   228      24.931  49.204  36.379  1.00  0.00
ATOM    227  O   VAL   228      25.891  49.982  36.431  1.00  0.00
ATOM    228  N   ASP   229      23.689  49.569  36.710  1.00  0.00
ATOM    228  CA  ASP   229      23.364  50.922  37.164  1.00  0.00
ATOM    228  C   ASP   229      24.190  51.328  38.375  1.00  0.00
ATOM    228  O   ASP   229      24.651  52.470  38.459  1.00  0.00
ATOM    229  N   TYR   230      24.389  50.382  39.285  1.00  0.00
ATOM    229  CA  TYR   230      25.186  50.622  40.489  1.00  0.00
ATOM    229  C   TYR   230      26.675  50.315  40.353  1.00  0.00
ATOM    229  O   TYR   230      27.417  50.388  41.334  1.00  0.00
ATOM    230  N   PRO   231      27.090  49.997  39.136  1.00  0.00
ATOM    230  CA  PRO   231      28.485  49.750  38.790  1.00  0.00
ATOM    230  C   PRO   231      29.087  48.593  39.584  1.00  0.00
ATOM    230  O   PRO   231      30.302  48.498  39.717  1.00  0.00
ATOM    231  N   ARG   232      28.252  47.693  40.098  1.00  0.00
ATOM    231  CA  ARG   232      28.763  46.609  40.944  1.00  0.00
ATOM    231  C   ARG   232      28.850  45.317  40.156  1.00  0.00
ATOM    231  O   ARG   232      27.867  44.855  39.585  1.00  0.00
ATOM    232  N   ASN   233      30.041  44.729  40.094  1.00  0.00
ATOM    232  CA  ASN   233      30.251  43.504  39.338  1.00  0.00
ATOM    232  C   ASN   233      29.424  42.332  39.880  1.00  0.00
ATOM    232  O   ASN   233      29.343  42.119  41.088  1.00  0.00
ATOM    233  N   GLU   234      28.819  41.603  38.954  1.00  0.00
ATOM    233  CA  GLU   234      28.192  40.312  39.227  1.00  0.00
ATOM    233  C   GLU   234      28.825  39.233  38.372  1.00  0.00
ATOM    233  O   GLU   234      29.322  39.497  37.284  1.00  0.00
ATOM    234  N   SER   235      28.767  37.999  38.862  1.00  0.00
ATOM    234  CA  SER   235      29.347  36.873  38.161  1.00  0.00
ATOM    234  C   SER   235      28.824  36.825  36.727  1.00  0.00
ATOM    234  O   SER   235      27.619  36.944  36.491  1.00  0.00
ATOM    235  N   GLY   236      29.743  36.711  35.766  1.00  0.00
ATOM    235  CA  GLY   236      29.412  36.723  34.352  1.00  0.00
ATOM    235  C   GLY   236      29.683  38.048  33.653  1.00  0.00
ATOM    235  O   GLY   236      29.790  38.126  32.424  1.00  0.00
ATOM    236  N   ASP   237      29.777  39.118  34.435  1.00  0.00
ATOM    236  CA  ASP   237      30.037  40.435  33.869  1.00  0.00
ATOM    236  C   ASP   237      31.493  40.520  33.389  1.00  0.00
ATOM    236  O   ASP   237      32.350  39.756  33.845  1.00  0.00
ATOM    254  N   HIS   255      39.461  51.795  27.302  1.00  0.00
ATOM    254  CA  HIS   255      39.997  52.085  25.984  1.00  0.00
ATOM    254  C   HIS   255      41.164  51.155  25.637  1.00  0.00
ATOM    254  O   HIS   255      41.950  50.794  26.510  1.00  0.00
ATOM    255  N   PRO   256      41.255  50.786  24.369  1.00  0.00
ATOM    255  CA  PRO   256      42.291  49.877  23.883  1.00  0.00
ATOM    255  C   PRO   256      43.717  50.424  23.844  1.00  0.00
ATOM    255  O   PRO   256      43.990  51.393  23.141  1.00  0.00
ATOM    256  N   GLY   257      44.398  51.207  23.392  1.00  0.00
ATOM    256  CA  GLY   257      45.358  52.234  23.779  1.00  0.00
ATOM    256  C   GLY   257      46.688  51.675  24.244  1.00  0.00
ATOM    256  O   GLY   257      47.623  52.432  24.508  1.00  0.00
ATOM    257  N   ASP   258      46.773  50.354  24.354  1.00  0.00
ATOM    257  CA  ASP   258      48.011  49.681  24.757  1.00  0.00
ATOM    257  C   ASP   258      48.594  48.858  23.604  1.00  0.00
ATOM    257  O   ASP   258      49.363  47.923  23.833  1.00  0.00
ATOM    258  N   PRO   259      48.193  49.229  22.391  1.00  0.00
ATOM    258  CA  PRO   259      48.542  48.573  21.111  1.00  0.00
ATOM    258  C   PRO   259      47.516  47.526  20.702  1.00  0.00
ATOM    258  O   PRO   259      47.430  47.160  19.537  1.00  0.00
ATOM    259  N   VAL   260      46.721  47.140  21.835  1.00  0.00
ATOM    259  CA  VAL   260      45.838  46.090  21.363  1.00  0.00
ATOM    259  C   VAL   260      45.150  45.346  22.495  1.00  0.00
ATOM    259  O   VAL   260      44.665  44.224  22.317  1.00  0.00
ATOM    260  N   PHE   261      45.101  45.971  23.664  1.00  0.00
ATOM    260  CA  PHE   261      44.480  45.354  24.830  1.00  0.00
ATOM    260  C   PHE   261      43.531  46.305  25.567  1.00  0.00
ATOM    260  O   PHE   261      43.875  47.459  25.838  1.00  0.00
TER
END
