
#######################################################
#                                                     #
#                        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_5-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS168_5-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      I     224          1.946
LGA    E     226      M     225          2.705
LGA    K     227      E     226          3.090
LGA    V     228      K     227          2.692
LGA    D     229      V     228          0.979
LGA    Y     230      D     229          1.483
LGA    -       -      Y     230           -
LGA    P     231      P     231          2.607
LGA    R     232      R     232          2.181
LGA    N     233      N     233          3.408
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    -       -      V     238           -
LGA    E     234      A     239          2.084
LGA    S     235      A     240          0.931
LGA    G     236      V     241          1.731
LGA    D     237      I     242          0.818
LGA    V     238      H     243          5.163
LGA    -       -      P     244           -
LGA    A     239      N     245          4.965
LGA    A     240      L     246          1.976
LGA    V     241      Q     247           -
LGA    -       -      D     248           -
LGA    -       -      Q     249           -
LGA    -       -      D     250           -
LGA    -       -      W     251           -
LGA    -       -      K     252           -
LGA    I     242      P     253          2.997
LGA    H     243      L     254          1.796
LGA    -       -      H     255           -
LGA    P     244      P     256          2.476
LGA    N     245      G     257          2.168
LGA    L     246      D     258           -
LGA    Q     247      P     259           -
LGA    D     248      V     260           -
LGA    Q     249      F     261           -
LGA    D     250      V     262           -
LGA    W     251      S     263           -
LGA    K     252      L     264           -
LGA    P     253      D     265           -
LGA    L     254      G     266           -
LGA    H     255      K     267           -
LGA    -       -      V     268           -
LGA    -       -      I     269           -
LGA    -       -      P     270           -
LGA    -       -      L     271           -
LGA    -       -      G     272           -
LGA    P     256      G     273          4.338
LGA    G     257      D     274          1.744
LGA    D     258      C     275          3.319
LGA    P     259      T     276          2.749
LGA    V     260      V     277          3.011
LGA    F     261      Y     278          2.651
LGA    V     262      P     279           -
LGA    S     263      V     280           -
LGA    L     264      F     281           -
LGA    D     265      V     282           -
LGA    G     266      N     283           -
LGA    K     267      E     284           -
LGA    V     268      A     285           -
LGA    I     269      A     286           -
LGA    P     270      Y     287           -
LGA    L     271      Y     288           -
LGA    G     272      E     289           -
LGA    G     273      K     290           -
LGA    D     274      K     291           -
LGA    C     275      E     292           -
LGA    T     276      A     293           -
LGA    V     277      F     294           -
LGA    Y     278      A     295           -
LGA    P     279      K     296           -
LGA    V     280      T     297          4.772
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)   74   74    5.0     27    2.86    18.52     23.159     0.913

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.448088 * X  +   0.556166 * Y  +  -0.699926 * Z  +  34.535057
  Y_new =   0.280515 * X  +   0.830854 * Y  +   0.480618 * Z  +  33.554699
  Z_new =   0.848840 * X  +   0.019019 * Y  +  -0.528308 * Z  +  21.996382 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.105608   -0.035985  [ DEG:   177.9382     -2.0618 ]
  Theta =  -1.013786   -2.127806  [ DEG:   -58.0857   -121.9143 ]
  Phi   =   2.582255   -0.559337  [ DEG:   147.9523    -32.0477 ]
 
# 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_5-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS168_5-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   27   2.86   18.52  23.159
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS168_5-D2
PFRMAT TS
TARGET T0289
MODEL 5
PARENT N/A
ATOM    224  CA  ILE   224      28.758  29.745  16.103  1.00 25.00           C
ATOM    225  CA  MET   225      25.485  29.562  18.058  1.00 25.00           C
ATOM    226  CA  GLU   226      23.685  29.109  21.426  1.00 25.00           C
ATOM    227  CA  LYS   227      25.105  31.787  23.652  1.00 25.00           C
ATOM    228  CA  VAL   228      23.854  34.577  25.837  1.00 25.00           C
ATOM    229  CA  ASP   229      21.800  36.959  28.046  1.00 25.00           C
ATOM    230  CA  TYR   230      19.421  39.148  30.069  1.00 25.00           C
ATOM    231  CA  PRO   231      17.235  40.519  32.863  1.00 25.00           C
ATOM    232  CA  ARG   232      15.405  41.878  35.890  1.00 25.00           C
ATOM    233  CA  ASN   233      16.849  45.284  36.801  1.00 25.00           C
ATOM    234  CA  GLU   234      18.954  48.400  36.764  1.00 25.00           C
ATOM    235  CA  SER   235      22.010  46.847  35.247  1.00 25.00           C
ATOM    236  CA  GLY   236      24.724  46.700  32.597  1.00 25.00           C
ATOM    237  CA  ASP   237      27.530  46.303  29.996  1.00 25.00           C
ATOM    238  CA  VAL   238      29.225  47.477  26.818  1.00 25.00           C
ATOM    239  CA  ALA   239      31.199  44.318  27.631  1.00 25.00           C
ATOM    240  CA  ALA   240      33.509  41.498  28.710  1.00 25.00           C
ATOM    241  CA  VAL   241      36.138  38.903  27.801  1.00 25.00           C
ATOM    242  CA  ILE   242      38.117  35.837  28.658  1.00 25.00           C
ATOM    243  CA  HIS   243      35.150  35.275  30.979  1.00 25.00           C
ATOM    244  CA  PRO   244      32.410  34.394  33.536  1.00 25.00           C
ATOM    245  CA  ASN   245      32.545  34.376  37.294  1.00 25.00           C
ATOM    246  CA  LEU   246      29.726  32.372  38.830  1.00 25.00           C
ATOM    247  CA  GLN   247      28.371  31.993  42.361  1.00 25.00           C
ATOM    248  CA  ASP   248      27.519  33.417  45.758  1.00 25.00           C
ATOM    249  CA  GLN   249      29.967  35.513  47.643  1.00 25.00           C
ATOM    250  CA  ASP   250      32.343  32.854  46.406  1.00 25.00           C
ATOM    251  CA  TRP   251      33.900  29.392  46.172  1.00 25.00           C
ATOM    252  CA  LYS   252      32.995  26.497  48.507  1.00 25.00           C
ATOM    253  CA  PRO   253      32.292  23.460  46.256  1.00 25.00           C
ATOM    254  CA  LEU   254      29.265  23.881  43.992  1.00 25.00           C
ATOM    255  CA  HIS   255      28.069  23.313  40.424  1.00 25.00           C
ATOM    256  CA  PRO   256      29.484  25.719  37.848  1.00 25.00           C
ATOM    257  CA  GLY   257      30.415  28.177  35.070  1.00 25.00           C
ATOM    258  CA  ASP   258      30.535  29.529  31.548  1.00 25.00           C
ATOM    259  CA  PRO   259      32.727  31.310  29.017  1.00 25.00           C
ATOM    260  CA  VAL   260      34.882  33.098  26.434  1.00 25.00           C
ATOM    261  CA  PHE   261      33.624  30.829  23.603  1.00 25.00           C
ATOM    262  CA  VAL   262      36.759  29.748  21.816  1.00 25.00           C
ATOM    263  CA  SER   263      39.652  28.160  19.936  1.00 25.00           C
ATOM    264  CA  LEU   264      41.984  25.817  17.981  1.00 25.00           C
ATOM    265  CA  ASP   265      40.465  22.784  16.259  1.00 25.00           C
ATOM    266  CA  GLY   266      39.056  22.816  12.700  1.00 25.00           C
ATOM    267  CA  LYS   267      35.946  20.988  13.913  1.00 25.00           C
ATOM    268  CA  VAL   268      32.131  21.052  13.970  1.00 25.00           C
ATOM    269  CA  ILE   269      29.574  23.421  12.556  1.00 25.00           C
ATOM    270  CA  PRO   270      28.844  27.048  11.768  1.00 25.00           C
ATOM    271  CA  LEU   271      28.191  28.869   8.458  1.00 25.00           C
ATOM    272  CA  GLY   272      27.981  28.071   4.812  1.00 25.00           C
ATOM    273  CA  GLY   273      29.998  25.121   3.530  1.00 25.00           C
ATOM    274  CA  ASP   274      30.538  23.621   6.970  1.00 25.00           C
ATOM    275  CA  CYS   275      32.870  26.486   7.927  1.00 25.00           C
ATOM    276  CA  THR   276      35.288  25.442  10.653  1.00 25.00           C
ATOM    277  CA  VAL   277      33.319  25.655  13.895  1.00 25.00           C
ATOM    278  CA  TYR   278      31.354  25.012  17.056  1.00 25.00           C
ATOM    279  CA  PRO   279      30.824  24.735  20.787  1.00 25.00           C
ATOM    280  CA  VAL   280      31.570  26.566  24.000  1.00 25.00           C
ATOM    281  CA  PHE   281      28.762  28.033  26.135  1.00 25.00           C
ATOM    282  CA  VAL   282      25.056  28.444  26.948  1.00 25.00           C
ATOM    283  CA  ASN   283      21.720  30.018  25.962  1.00 25.00           C
ATOM    284  CA  GLU   284      20.033  32.078  23.215  1.00 25.00           C
ATOM    285  CA  ALA   285      19.595  29.911  20.088  1.00 25.00           C
ATOM    286  CA  ALA   286      17.566  32.695  18.412  1.00 25.00           C
ATOM    287  CA  TYR   287      20.296  35.238  19.279  1.00 25.00           C
ATOM    288  CA  TYR   288      22.963  32.914  17.811  1.00 25.00           C
ATOM    289  CA  GLU   289      20.894  32.521  14.612  1.00 25.00           C
ATOM    290  CA  LYS   290      20.533  36.324  14.349  1.00 25.00           C
ATOM    291  CA  LYS   291      22.677  37.474  11.409  1.00 25.00           C
ATOM    292  CA  GLU   292      26.414  36.789  11.875  1.00 25.00           C
ATOM    293  CA  ALA   293      25.778  33.423  13.615  1.00 25.00           C
ATOM    294  CA  PHE   294      24.970  29.718  13.265  1.00 25.00           C
ATOM    295  CA  ALA   295      25.360  26.248  14.759  1.00 25.00           C
ATOM    296  CA  LYS   296      26.012  24.586  18.140  1.00 25.00           C
ATOM    297  CA  THR   297      22.386  24.475  19.199  1.00 25.00           C
TER
END
