
#######################################################
#                                                     #
#                        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   74 (   74),  selected   74 , name T0289TS168_4-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS168_4-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          3.647
LGA    -       -      M     225           -
LGA    M     225      E     226          3.385
LGA    E     226      K     227          1.116
LGA    K     227      V     228          1.453
LGA    V     228      D     229          0.169
LGA    D     229      Y     230          3.198
LGA    Y     230      P     231          2.773
LGA    P     231      R     232          2.005
LGA    R     232      N     233          1.770
LGA    N     233      E     234          5.869
LGA    E     234      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    -       -      V     238           -
LGA    S     235      A     239          2.192
LGA    G     236      A     240          1.316
LGA    D     237      V     241          1.567
LGA    V     238      I     242          2.080
LGA    -       -      H     243           -
LGA    -       -      P     244           -
LGA    -       -      N     245           -
LGA    A     239      L     246          4.614
LGA    A     240      Q     247          3.341
LGA    V     241      D     248           -
LGA    -       -      Q     249           -
LGA    -       -      D     250           -
LGA    -       -      W     251           -
LGA    -       -      K     252           -
LGA    I     242      P     253          4.275
LGA    H     243      L     254          3.138
LGA    P     244      H     255          2.437
LGA    -       -      P     256           -
LGA    -       -      G     257           -
LGA    N     245      D     258           #
LGA    L     246      P     259           -
LGA    Q     247      V     260           -
LGA    D     248      F     261           -
LGA    Q     249      V     262           -
LGA    D     250      S     263           -
LGA    W     251      L     264           -
LGA    K     252      D     265           -
LGA    P     253      G     266           -
LGA    L     254      K     267           -
LGA    H     255      V     268           -
LGA    P     256      I     269           -
LGA    G     257      P     270          4.674
LGA    D     258      L     271          2.166
LGA    P     259      G     272           #
LGA    V     260      G     273           -
LGA    -       -      D     274           -
LGA    -       -      C     275           -
LGA    F     261      T     276           #
LGA    V     262      V     277          5.526
LGA    S     263      Y     278          4.097
LGA    L     264      P     279           #
LGA    D     265      -       -           -
LGA    G     266      -       -           -
LGA    K     267      -       -           -
LGA    V     268      -       -           -
LGA    I     269      -       -           -
LGA    P     270      -       -           -
LGA    L     271      -       -           -
LGA    G     272      -       -           -
LGA    G     273      -       -           -
LGA    D     274      -       -           -
LGA    C     275      -       -           -
LGA    T     276      -       -           -
LGA    V     277      -       -           -
LGA    Y     278      -       -           -
LGA    P     279      V     280          4.819
LGA    V     280      F     281          3.554
LGA    F     281      V     282          4.389
LGA    V     282      N     283           -
LGA    N     283      E     284           -
LGA    E     284      A     285           -
LGA    A     285      A     286           -
LGA    A     286      Y     287           -
LGA    Y     287      Y     288           -
LGA    Y     288      E     289           -
LGA    E     289      K     290           -
LGA    K     290      K     291           -
LGA    K     291      E     292           -
LGA    -       -      A     293           -
LGA    -       -      F     294           -
LGA    -       -      A     295           -
LGA    E     292      K     296          4.700
LGA    A     293      T     297          3.662
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)   74   74    5.0     28    3.44     7.14     21.582     0.790

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.271273 * X  +  -0.745887 * Y  +  -0.608328 * Z  +  31.135408
  Y_new =   0.249886 * X  +   0.664934 * Y  +  -0.703861 * Z  +  35.012936
  Z_new =   0.929499 * X  +   0.038926 * Y  +   0.366766 * Z  +  22.504557 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.105737   -3.035855  [ DEG:     6.0583   -173.9417 ]
  Theta =  -1.193051   -1.948542  [ DEG:   -68.3568   -111.6432 ]
  Phi   =   0.744383   -2.397209  [ DEG:    42.6500   -137.3500 ]
 
# 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: T0289TS168_4-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS168_4-D2.T0289_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   74   74   5.0   28   3.44    7.14  21.582
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS168_4-D2
PFRMAT TS
TARGET T0289
MODEL 4
PARENT N/A
ATOM    224  CA  ILE   224      25.569  32.748  21.110  1.00 25.00           C
ATOM    225  CA  MET   225      25.395  32.171  24.810  1.00 25.00           C
ATOM    226  CA  GLU   226      22.409  34.513  24.688  1.00 25.00           C
ATOM    227  CA  LYS   227      20.719  35.255  28.063  1.00 25.00           C
ATOM    228  CA  VAL   228      19.452  38.790  28.558  1.00 25.00           C
ATOM    229  CA  ASP   229      17.017  41.620  29.329  1.00 25.00           C
ATOM    230  CA  TYR   230      16.633  42.552  32.994  1.00 25.00           C
ATOM    231  CA  PRO   231      13.784  43.413  35.366  1.00 25.00           C
ATOM    232  CA  ARG   232      13.412  45.214  38.633  1.00 25.00           C
ATOM    233  CA  ASN   233      12.980  48.641  40.238  1.00 25.00           C
ATOM    234  CA  GLU   234      16.636  49.619  39.535  1.00 25.00           C
ATOM    235  CA  SER   235      18.209  49.118  36.156  1.00 25.00           C
ATOM    236  CA  GLY   236      21.479  48.187  34.494  1.00 25.00           C
ATOM    237  CA  ASP   237      23.235  46.339  31.675  1.00 25.00           C
ATOM    238  CA  VAL   238      25.244  45.831  28.513  1.00 25.00           C
ATOM    239  CA  ALA   239      28.307  43.696  28.444  1.00 25.00           C
ATOM    240  CA  ALA   240      31.422  42.910  26.463  1.00 25.00           C
ATOM    241  CA  VAL   241      32.112  39.358  27.637  1.00 25.00           C
ATOM    242  CA  ILE   242      33.997  36.116  28.400  1.00 25.00           C
ATOM    243  CA  HIS   243      36.585  37.395  30.940  1.00 25.00           C
ATOM    244  CA  PRO   244      36.617  35.040  33.926  1.00 25.00           C
ATOM    245  CA  ASN   245      40.264  35.987  34.462  1.00 25.00           C
ATOM    246  CA  LEU   246      41.006  35.298  38.123  1.00 25.00           C
ATOM    247  CA  GLN   247      43.268  32.473  39.362  1.00 25.00           C
ATOM    248  CA  ASP   248      42.853  32.226  43.106  1.00 25.00           C
ATOM    249  CA  GLN   249      42.194  28.526  43.613  1.00 25.00           C
ATOM    250  CA  ASP   250      40.168  28.764  46.829  1.00 25.00           C
ATOM    251  CA  TRP   251      37.256  26.268  47.035  1.00 25.00           C
ATOM    252  CA  LYS   252      33.719  27.558  46.921  1.00 25.00           C
ATOM    253  CA  PRO   253      32.993  31.216  47.643  1.00 25.00           C
ATOM    254  CA  LEU   254      33.965  34.661  46.249  1.00 25.00           C
ATOM    255  CA  HIS   255      30.288  34.618  45.276  1.00 25.00           C
ATOM    256  CA  PRO   256      29.855  33.022  41.823  1.00 25.00           C
ATOM    257  CA  GLY   257      30.364  34.010  38.186  1.00 25.00           C
ATOM    258  CA  ASP   258      31.088  34.394  34.458  1.00 25.00           C
ATOM    259  CA  PRO   259      30.703  37.350  32.165  1.00 25.00           C
ATOM    260  CA  VAL   260      29.282  34.881  29.676  1.00 25.00           C
ATOM    261  CA  PHE   261      30.509  33.173  26.470  1.00 25.00           C
ATOM    262  CA  VAL   262      29.965  33.792  22.823  1.00 25.00           C
ATOM    263  CA  SER   263      32.280  33.216  19.869  1.00 25.00           C
ATOM    264  CA  LEU   264      29.305  32.958  17.532  1.00 25.00           C
ATOM    265  CA  ASP   265      25.874  31.859  16.279  1.00 25.00           C
ATOM    266  CA  GLY   266      26.659  31.361  12.605  1.00 25.00           C
ATOM    267  CA  LYS   267      25.885  32.204   8.981  1.00 25.00           C
ATOM    268  CA  VAL   268      29.562  32.377   8.131  1.00 25.00           C
ATOM    269  CA  ILE   269      29.530  35.545  10.188  1.00 25.00           C
ATOM    270  CA  PRO   270      30.040  39.013   8.793  1.00 25.00           C
ATOM    271  CA  LEU   271      28.560  40.510   5.604  1.00 25.00           C
ATOM    272  CA  GLY   272      26.430  41.778   2.703  1.00 25.00           C
ATOM    273  CA  GLY   273      23.042  43.340   3.520  1.00 25.00           C
ATOM    274  CA  ASP   274      20.894  41.239   5.888  1.00 25.00           C
ATOM    275  CA  CYS   275      24.127  40.875   7.884  1.00 25.00           C
ATOM    276  CA  THR   276      25.482  37.361   7.203  1.00 25.00           C
ATOM    277  CA  VAL   277      25.655  37.324  11.041  1.00 25.00           C
ATOM    278  CA  TYR   278      27.275  36.317  14.338  1.00 25.00           C
ATOM    279  CA  PRO   279      30.501  37.625  15.854  1.00 25.00           C
ATOM    280  CA  VAL   280      29.282  37.763  19.477  1.00 25.00           C
ATOM    281  CA  PHE   281      30.580  38.818  22.865  1.00 25.00           C
ATOM    282  CA  VAL   282      33.471  36.452  23.563  1.00 25.00           C
ATOM    283  CA  ASN   283      36.421  38.050  25.368  1.00 25.00           C
ATOM    284  CA  GLU   284      36.871  34.308  24.757  1.00 25.00           C
ATOM    285  CA  ALA   285      39.509  32.222  26.590  1.00 25.00           C
ATOM    286  CA  ALA   286      36.944  31.298  29.281  1.00 25.00           C
ATOM    287  CA  TYR   287      34.439  30.268  26.573  1.00 25.00           C
ATOM    288  CA  TYR   288      37.115  28.112  24.883  1.00 25.00           C
ATOM    289  CA  GLU   289      37.932  26.453  28.237  1.00 25.00           C
ATOM    290  CA  LYS   290      34.214  25.748  28.822  1.00 25.00           C
ATOM    291  CA  LYS   291      32.064  25.691  25.717  1.00 25.00           C
ATOM    292  CA  GLU   292      30.132  28.810  24.902  1.00 25.00           C
ATOM    293  CA  ALA   293      32.623  28.670  22.079  1.00 25.00           C
ATOM    294  CA  PHE   294      33.413  29.141  18.410  1.00 25.00           C
ATOM    295  CA  ALA   295      33.865  31.913  15.878  1.00 25.00           C
ATOM    296  CA  LYS   296      33.340  31.121  12.164  1.00 25.00           C
ATOM    297  CA  THR   297      33.719  28.195   9.826  1.00 25.00           C
TER
END
