
#######################################################
#                                                     #
#                        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 T0289TS393_4-D2
# Molecule2: number of CA atoms   74 (  581),  selected   74 , name T0289_D2.pdb
# PARAMETERS: T0289TS393_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           -
LGA    -       -      M     225           -
LGA    -       -      E     226           -
LGA    -       -      K     227           -
LGA    -       -      V     228           -
LGA    -       -      D     229           -
LGA    I     224      Y     230          4.650
LGA    M     225      P     231          1.602
LGA    E     226      R     232          2.372
LGA    -       -      N     233           -
LGA    -       -      E     234           -
LGA    -       -      S     235           -
LGA    -       -      G     236           -
LGA    -       -      D     237           -
LGA    -       -      V     238           -
LGA    K     227      A     239          3.437
LGA    V     228      A     240          1.994
LGA    D     229      V     241          2.294
LGA    Y     230      I     242           -
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      H     243          6.176
LGA    -       -      P     244           -
LGA    -       -      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    A     240      P     259          2.756
LGA    V     241      V     260          3.452
LGA    I     242      F     261           #
LGA    H     243      V     262           -
LGA    P     244      S     263           -
LGA    N     245      L     264           -
LGA    L     246      D     265           -
LGA    Q     247      G     266           -
LGA    D     248      K     267           -
LGA    Q     249      V     268           -
LGA    D     250      I     269           -
LGA    W     251      P     270           -
LGA    K     252      L     271           -
LGA    P     253      G     272           -
LGA    L     254      G     273           -
LGA    H     255      D     274           -
LGA    P     256      C     275           -
LGA    G     257      T     276           -
LGA    D     258      V     277           -
LGA    P     259      Y     278           -
LGA    V     260      P     279           -
LGA    F     261      V     280          2.962
LGA    V     262      F     281          2.411
LGA    S     263      V     282          2.373
LGA    L     264      N     283          2.952
LGA    D     265      E     284          2.638
LGA    G     266      A     285          1.567
LGA    K     267      A     286           #
LGA    V     268      Y     287          5.255
LGA    I     269      Y     288          3.804
LGA    P     270      E     289          4.520
LGA    L     271      -       -           -
LGA    G     272      -       -           -
LGA    G     273      -       -           -
LGA    D     274      -       -           -
LGA    C     275      -       -           -
LGA    T     276      K     290          3.339
LGA    V     277      K     291          2.446
LGA    Y     278      E     292          1.320
LGA    P     279      A     293          1.810
LGA    V     280      F     294          2.333
LGA    F     281      A     295          2.098
LGA    V     282      -       -           -
LGA    N     283      -       -           -
LGA    E     284      K     296          3.524
LGA    A     285      T     297          3.252
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     26    3.19     3.85     20.446     0.791

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.766086 * X  +   0.526209 * Y  +  -0.369076 * Z  +  25.855515
  Y_new =   0.642262 * X  +  -0.648844 * Y  +   0.408047 * Z  +  37.538170
  Z_new =  -0.024755 * X  +  -0.549642 * Y  +  -0.835033 * Z  +  28.080151 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.559455    0.582138  [ DEG:  -146.6460     33.3540 ]
  Theta =   0.024758    3.116835  [ DEG:     1.4185    178.5815 ]
  Phi   =   0.697702   -2.443891  [ DEG:    39.9754   -140.0246 ]
 
# 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: T0289TS393_4-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS393_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   26   3.19    3.85  20.446
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS393_4-D2
PFRMAT TS
TARGET T0289
MODEL 4
PARENT N/A
ATOM    224  CA  ILE   224      18.201  38.528  33.188  1.00 25.00           C
ATOM    225  CA  MET   225      19.719  41.193  35.540  1.00 25.00           C
ATOM    226  CA  GLU   226      17.709  44.274  34.705  1.00 25.00           C
ATOM    227  CA  LYS   227      20.805  45.857  33.307  1.00 25.00           C
ATOM    228  CA  VAL   228      23.626  48.068  34.708  1.00 25.00           C
ATOM    229  CA  ASP   229      24.795  49.745  31.483  1.00 25.00           C
ATOM    230  CA  TYR   230      23.345  53.161  32.495  1.00 25.00           C
ATOM    231  CA  PRO   231      24.353  56.674  33.378  1.00 25.00           C
ATOM    232  CA  ARG   232      25.171  57.397  36.973  1.00 25.00           C
ATOM    233  CA  ASN   233      26.309  59.453  40.016  1.00 25.00           C
ATOM    234  CA  GLU   234      29.011  57.645  42.008  1.00 25.00           C
ATOM    235  CA  SER   235      29.157  54.817  44.548  1.00 25.00           C
ATOM    236  CA  GLY   236      27.949  51.430  43.352  1.00 25.00           C
ATOM    237  CA  ASP   237      28.060  48.077  41.550  1.00 25.00           C
ATOM    238  CA  VAL   238      27.148  44.904  39.747  1.00 25.00           C
ATOM    239  CA  ALA   239      27.880  43.067  36.564  1.00 25.00           C
ATOM    240  CA  ALA   240      29.869  41.492  33.740  1.00 25.00           C
ATOM    241  CA  VAL   241      32.141  42.787  30.918  1.00 25.00           C
ATOM    242  CA  ILE   242      35.446  43.320  29.147  1.00 25.00           C
ATOM    243  CA  HIS   243      35.203  46.945  30.303  1.00 25.00           C
ATOM    244  CA  PRO   244      37.157  50.150  29.706  1.00 25.00           C
ATOM    245  CA  ASN   245      37.975  53.514  28.127  1.00 25.00           C
ATOM    246  CA  LEU   246      37.988  56.378  25.708  1.00 25.00           C
ATOM    247  CA  GLN   247      41.173  57.240  23.806  1.00 25.00           C
ATOM    248  CA  ASP   248      44.835  56.716  22.741  1.00 25.00           C
ATOM    249  CA  GLN   249      46.041  54.469  19.977  1.00 25.00           C
ATOM    250  CA  ASP   250      46.227  56.076  16.556  1.00 25.00           C
ATOM    251  CA  TRP   251      44.362  57.955  13.829  1.00 25.00           C
ATOM    252  CA  LYS   252      41.453  56.655  11.794  1.00 25.00           C
ATOM    253  CA  PRO   253      43.455  54.000  10.094  1.00 25.00           C
ATOM    254  CA  LEU   254      42.178  53.496   6.578  1.00 25.00           C
ATOM    255  CA  HIS   255      41.495  49.754   6.551  1.00 25.00           C
ATOM    256  CA  PRO   256      39.174  46.981   7.802  1.00 25.00           C
ATOM    257  CA  GLY   257      36.822  44.608   9.706  1.00 25.00           C
ATOM    258  CA  ASP   258      34.030  42.706  11.453  1.00 25.00           C
ATOM    259  CA  PRO   259      31.438  40.040  12.263  1.00 25.00           C
ATOM    260  CA  VAL   260      32.096  36.984  14.420  1.00 25.00           C
ATOM    261  CA  PHE   261      30.508  36.850  17.896  1.00 25.00           C
ATOM    262  CA  VAL   262      28.081  38.382  20.347  1.00 25.00           C
ATOM    263  CA  SER   263      25.805  40.657  22.356  1.00 25.00           C
ATOM    264  CA  LEU   264      24.829  43.722  20.316  1.00 25.00           C
ATOM    265  CA  ASP   265      24.297  47.200  18.778  1.00 25.00           C
ATOM    266  CA  GLY   266      21.086  47.264  20.746  1.00 25.00           C
ATOM    267  CA  LYS   267      20.402  44.606  23.372  1.00 25.00           C
ATOM    268  CA  VAL   268      16.929  46.222  23.666  1.00 25.00           C
ATOM    269  CA  ILE   269      14.684  45.392  20.710  1.00 25.00           C
ATOM    270  CA  PRO   270      12.032  44.304  18.172  1.00 25.00           C
ATOM    271  CA  LEU   271      11.658  40.689  17.047  1.00 25.00           C
ATOM    272  CA  GLY   272       8.088  40.839  18.390  1.00 25.00           C
ATOM    273  CA  GLY   273       6.124  39.888  21.453  1.00 25.00           C
ATOM    274  CA  ASP   274       7.329  40.605  24.967  1.00 25.00           C
ATOM    275  CA  CYS   275      10.711  42.370  25.343  1.00 25.00           C
ATOM    276  CA  THR   276      11.667  40.321  22.366  1.00 25.00           C
ATOM    277  CA  VAL   277      15.201  41.184  23.450  1.00 25.00           C
ATOM    278  CA  TYR   278      18.576  39.777  24.454  1.00 25.00           C
ATOM    279  CA  PRO   279      22.362  40.248  24.431  1.00 25.00           C
ATOM    280  CA  VAL   280      23.930  37.006  23.248  1.00 25.00           C
ATOM    281  CA  PHE   281      26.839  34.808  24.317  1.00 25.00           C
ATOM    282  CA  VAL   282      29.532  36.906  25.937  1.00 25.00           C
ATOM    283  CA  ASN   283      29.413  35.604  29.481  1.00 25.00           C
ATOM    284  CA  GLU   284      30.290  33.060  26.838  1.00 25.00           C
ATOM    285  CA  ALA   285      32.139  31.232  24.025  1.00 25.00           C
ATOM    286  CA  ALA   286      34.035  34.442  23.152  1.00 25.00           C
ATOM    287  CA  TYR   287      34.996  34.905  26.830  1.00 25.00           C
ATOM    288  CA  TYR   288      36.232  31.283  26.989  1.00 25.00           C
ATOM    289  CA  GLU   289      38.309  31.829  23.818  1.00 25.00           C
ATOM    290  CA  LYS   290      39.818  35.010  25.324  1.00 25.00           C
ATOM    291  CA  LYS   291      38.333  36.940  28.268  1.00 25.00           C
ATOM    292  CA  GLU   292      35.427  38.024  30.492  1.00 25.00           C
ATOM    293  CA  ALA   293      32.983  38.934  27.703  1.00 25.00           C
ATOM    294  CA  PHE   294      32.755  40.288  24.131  1.00 25.00           C
ATOM    295  CA  ALA   295      31.548  41.217  20.632  1.00 25.00           C
ATOM    296  CA  LYS   296      30.548  42.247  17.084  1.00 25.00           C
ATOM    297  CA  THR   297      34.187  41.327  16.265  1.00 25.00           C
TER
END
