
#######################################################
#                                                     #
#                        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   81 (   81),  selected   81 , name T0386TS393_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS393_4-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219           -
LGA    P     220      P     220           -
LGA    E     221      E     221           -
LGA    K     222      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    I     223      K     234           #
LGA    -       -      N     235           -
LGA    R     224      T     236          4.288
LGA    L     225      G     237          2.327
LGA    L     226      R     238          4.800
LGA    K     227      -       -           -
LGA    E     228      N     239          1.602
LGA    F     229      V     240          3.740
LGA    M     230      -       -           -
LGA    H     231      -       -           -
LGA    T     232      N     241          2.482
LGA    M     233      -       -           -
LGA    K     234      -       -           -
LGA    N     235      -       -           -
LGA    T     236      D     242          3.175
LGA    G     237      R     243          3.656
LGA    R     238      P     244          1.995
LGA    N     239      V     245          3.471
LGA    V     240      M     246          1.746
LGA    N     241      -       -           -
LGA    D     242      -       -           -
LGA    R     243      V     247          0.787
LGA    P     244      A     248          2.956
LGA    V     245      K     249           -
LGA    M     246      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    V     247      T     255           #
LGA    A     248      G     256          2.721
LGA    K     249      T     257          2.951
LGA    E     250      -       -           -
LGA    G     251      -       -           -
LGA    E     252      -       -           -
LGA    T     253      Y     258          3.838
LGA    Y     254      R     259          3.552
LGA    T     255      G     260          3.558
LGA    G     256      A     261          4.364
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    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    T     257      G     277          4.773
LGA    Y     258      N     278          2.069
LGA    -       -      I     279           -
LGA    R     259      D     280          3.099
LGA    G     260      H     281          2.905
LGA    A     261      L     282           -
LGA    G     262      P     283           -
LGA    L     263      -       -           -
LGA    E     264      -       -           -
LGA    G     265      -       -           -
LGA    F     266      P     284          3.386
LGA    A     267      -       -           -
LGA    L     268      -       -           -
LGA    N     269      -       -           -
LGA    V     270      -       -           -
LGA    K     271      E     285           #
LGA    G     272      Q     286          1.433
LGA    A     273      L     287          2.993
LGA    Y     274      K     288          2.443
LGA    -       -      I     289           -
LGA    I     275      L     290          3.254
LGA    I     276      K     291          1.765
LGA    G     277      P     292          1.088
LGA    N     278      G     293          2.569
LGA    I     279      D     294          4.077
LGA    D     280      K     295           -
LGA    H     281      I     296           -
LGA    L     282      T     297           -
LGA    P     283      -       -           -
LGA    P     284      -       -           -
LGA    E     285      -       -           -
LGA    Q     286      -       -           -
LGA    L     287      -       -           -
LGA    K     288      -       -           -
LGA    I     289      -       -           -
LGA    L     290      -       -           -
LGA    K     291      -       -           -
LGA    P     292      F     298           #
LGA    G     293      T     299           #
LGA    D     294      -       -           -
LGA    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)   81   81    5.0     32    3.10     0.00     22.529     0.999

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.068887 * X  +   0.260731 * Y  +   0.962951 * Z  +  11.218559
  Y_new =   0.970204 * X  +   0.242259 * Y  +   0.003811 * Z  +  75.927856
  Z_new =  -0.232290 * X  +   0.934521 * Y  +  -0.269651 * Z  +  89.392883 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.851710   -1.289882  [ DEG:   106.0952    -73.9048 ]
  Theta =   0.234432    2.907161  [ DEG:    13.4319    166.5681 ]
  Phi   =   1.641680   -1.499913  [ DEG:    94.0613    -85.9387 ]
 
# 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: T0386TS393_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS393_4-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   81   81   5.0   32   3.10    0.00  22.529
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS393_4-D2
PFRMAT TS
TARGET T0386
MODEL 4
PARENT N/A
ATOM    219  CA  ASN   219      24.484  86.666  74.128  1.00 25.00           C
ATOM    220  CA  PRO   220      21.661  84.268  73.306  1.00 25.00           C
ATOM    221  CA  GLU   221      24.371  81.609  73.808  1.00 25.00           C
ATOM    222  CA  LYS   222      22.158  79.801  76.359  1.00 25.00           C
ATOM    223  CA  ILE   223      19.219  79.884  73.905  1.00 25.00           C
ATOM    224  CA  ARG   224      21.455  78.459  71.142  1.00 25.00           C
ATOM    225  CA  LEU   225      22.619  75.667  73.489  1.00 25.00           C
ATOM    226  CA  LEU   226      18.982  74.858  74.372  1.00 25.00           C
ATOM    227  CA  LYS   227      18.082  74.727  70.652  1.00 25.00           C
ATOM    228  CA  GLU   228      21.034  72.377  69.996  1.00 25.00           C
ATOM    229  CA  PHE   229      19.911  70.121  72.879  1.00 25.00           C
ATOM    230  CA  MET   230      16.351  70.050  71.469  1.00 25.00           C
ATOM    231  CA  HIS   231      17.713  69.127  68.010  1.00 25.00           C
ATOM    232  CA  THR   232      19.802  66.314  69.556  1.00 25.00           C
ATOM    233  CA  MET   233      16.716  65.010  71.412  1.00 25.00           C
ATOM    234  CA  LYS   234      14.702  65.071  68.156  1.00 25.00           C
ATOM    235  CA  ASN   235      17.489  63.150  66.366  1.00 25.00           C
ATOM    236  CA  THR   236      21.104  62.422  65.734  1.00 25.00           C
ATOM    237  CA  GLY   237      24.242  61.133  67.423  1.00 25.00           C
ATOM    238  CA  ARG   238      22.429  60.084  70.554  1.00 25.00           C
ATOM    239  CA  ASN   239      19.436  58.074  71.948  1.00 25.00           C
ATOM    240  CA  VAL   240      15.968  57.551  73.339  1.00 25.00           C
ATOM    241  CA  ASN   241      14.148  54.318  72.811  1.00 25.00           C
ATOM    242  CA  ASP   242      10.929  55.755  74.355  1.00 25.00           C
ATOM    243  CA  ARG   243      12.382  57.120  77.612  1.00 25.00           C
ATOM    244  CA  PRO   244      12.525  55.970  81.279  1.00 25.00           C
ATOM    245  CA  VAL   245      14.059  56.765  84.619  1.00 25.00           C
ATOM    246  CA  MET   246      16.209  59.575  83.355  1.00 25.00           C
ATOM    247  CA  VAL   247      20.052  59.582  83.428  1.00 25.00           C
ATOM    248  CA  ALA   248      23.744  59.356  84.352  1.00 25.00           C
ATOM    249  CA  LYS   249      27.542  59.140  84.352  1.00 25.00           C
ATOM    250  CA  GLU   250      30.739  57.199  84.960  1.00 25.00           C
ATOM    251  CA  GLY   251      29.587  56.612  88.543  1.00 25.00           C
ATOM    252  CA  GLU   252      27.835  59.352  90.432  1.00 25.00           C
ATOM    253  CA  THR   253      25.055  61.618  89.345  1.00 25.00           C
ATOM    254  CA  TYR   254      23.169  63.671  86.767  1.00 25.00           C
ATOM    255  CA  THR   255      19.516  64.134  85.651  1.00 25.00           C
ATOM    256  CA  GLY   256      16.749  63.040  87.995  1.00 25.00           C
ATOM    257  CA  THR   257      13.461  61.219  87.351  1.00 25.00           C
ATOM    258  CA  TYR   258       9.785  60.645  86.571  1.00 25.00           C
ATOM    259  CA  ARG   259       7.508  57.804  87.675  1.00 25.00           C
ATOM    260  CA  GLY   260       8.579  54.242  88.139  1.00 25.00           C
ATOM    261  CA  ALA   261       7.393  52.847  91.479  1.00 25.00           C
ATOM    262  CA  GLY   262       3.601  52.260  91.779  1.00 25.00           C
ATOM    263  CA  LEU   263       3.285  55.440  93.762  1.00 25.00           C
ATOM    264  CA  GLU   264       5.933  55.874  96.431  1.00 25.00           C
ATOM    265  CA  GLY   265       7.848  58.360  94.286  1.00 25.00           C
ATOM    266  CA  PHE   266      10.494  61.024  94.719  1.00 25.00           C
ATOM    267  CA  ALA   267      12.411  62.928  92.140  1.00 25.00           C
ATOM    268  CA  LEU   268      15.573  60.905  92.524  1.00 25.00           C
ATOM    269  CA  ASN   269      19.362  60.948  92.193  1.00 25.00           C
ATOM    270  CA  VAL   270      21.989  61.795  94.845  1.00 25.00           C
ATOM    271  CA  LYS   271      21.416  59.466  97.850  1.00 25.00           C
ATOM    272  CA  GLY   272      17.652  59.318  97.330  1.00 25.00           C
ATOM    273  CA  ALA   273      17.266  63.100  97.166  1.00 25.00           C
ATOM    274  CA  TYR   274      15.633  66.298  95.928  1.00 25.00           C
ATOM    275  CA  ILE   275      18.803  66.795  93.847  1.00 25.00           C
ATOM    276  CA  ILE   276      21.715  67.077  91.462  1.00 25.00           C
ATOM    277  CA  GLY   277      23.600  68.642  88.567  1.00 25.00           C
ATOM    278  CA  ASN   278      26.932  67.154  89.657  1.00 25.00           C
ATOM    279  CA  ILE   279      29.191  64.293  88.448  1.00 25.00           C
ATOM    280  CA  ASP   280      31.298  67.020  86.929  1.00 25.00           C
ATOM    281  CA  HIS   281      33.088  66.571  83.610  1.00 25.00           C
ATOM    282  CA  LEU   282      30.890  63.941  81.876  1.00 25.00           C
ATOM    283  CA  PRO   283      30.527  65.317  78.349  1.00 25.00           C
ATOM    284  CA  PRO   284      27.248  64.807  76.440  1.00 25.00           C
ATOM    285  CA  GLU   285      26.232  64.496  80.120  1.00 25.00           C
ATOM    286  CA  GLN   286      23.046  66.509  79.435  1.00 25.00           C
ATOM    287  CA  LEU   287      22.226  64.243  76.458  1.00 25.00           C
ATOM    288  CA  LYS   288      22.754  61.141  78.640  1.00 25.00           C
ATOM    289  CA  ILE   289      24.402  59.308  75.743  1.00 25.00           C
ATOM    290  CA  LEU   290      23.553  55.807  77.002  1.00 25.00           C
ATOM    291  CA  LYS   291      23.725  52.991  79.490  1.00 25.00           C
ATOM    292  CA  PRO   292      20.768  52.646  81.823  1.00 25.00           C
ATOM    293  CA  GLY   293      17.258  52.648  80.280  1.00 25.00           C
ATOM    294  CA  ASP   294      17.885  55.505  77.952  1.00 25.00           C
ATOM    295  CA  LYS   295      17.056  59.177  78.434  1.00 25.00           C
ATOM    296  CA  ILE   296      16.258  62.750  79.428  1.00 25.00           C
ATOM    297  CA  THR   297      14.407  65.641  77.766  1.00 25.00           C
ATOM    298  CA  PHE   298      13.095  67.159  80.983  1.00 25.00           C
ATOM    299  CA  THR   299      13.014  70.128  83.374  1.00 25.00           C
TER
END
