
#######################################################
#                                                     #
#                        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   90 (   90),  selected   90 , name T0316TS393_2-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS393_2-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284           -
LGA    S     285      S     285           -
LGA    T     286      T     286           -
LGA    S     287      S     287           -
LGA    L     288      L     288           -
LGA    E     289      E     289           -
LGA    A     290      A     290           -
LGA    S     291      -       -           -
LGA    Q     292      -       -           -
LGA    V     293      S     291           #
LGA    H     294      Q     292          3.623
LGA    -       -      V     293           -
LGA    F     295      H     294          1.541
LGA    T     296      F     295          4.492
LGA    R     297      -       -           -
LGA    E     298      -       -           -
LGA    M     299      -       -           -
LGA    P     300      -       -           -
LGA    E     301      -       -           -
LGA    E     302      -       -           -
LGA    F     303      -       -           -
LGA    T     304      -       -           -
LGA    L     305      -       -           -
LGA    E     306      -       -           -
LGA    C     307      T     296          3.038
LGA    T     308      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    A     309      A     309           #
LGA    K     310      K     310          3.103
LGA    F     311      F     311          1.492
LGA    R     312      R     312          4.924
LGA    Y     313      -       -           -
LGA    R     314      -       -           -
LGA    Q     315      -       -           -
LGA    P     316      -       -           -
LGA    D     317      -       -           -
LGA    S     318      -       -           -
LGA    K     319      -       -           -
LGA    V     320      -       -           -
LGA    T     321      -       -           -
LGA    V     322      -       -           -
LGA    H     323      -       -           -
LGA    V     324      -       -           -
LGA    K     325      -       -           -
LGA    G     326      -       -           -
LGA    E     327      -       -           -
LGA    K     328      -       -           -
LGA    T     329      -       -           -
LGA    E     330      Y     313           #
LGA    V     331      R     314          2.159
LGA    I     332      Q     315          1.515
LGA    F     333      P     316          2.440
LGA    A     334      D     317          4.399
LGA    E     335      S     318          4.162
LGA    P     336      K     319          2.424
LGA    Q     337      V     320          3.737
LGA    R     338      T     321           #
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    A     339      F     333           #
LGA    I     340      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    T     341      A     339           #
LGA    P     342      I     340          2.875
LGA    G     343      -       -           -
LGA    Q     344      -       -           -
LGA    A     345      -       -           -
LGA    V     346      T     341          2.070
LGA    V     347      P     342          1.163
LGA    F     348      G     343          3.852
LGA    Y     349      Q     344           -
LGA    D     350      A     345           -
LGA    G     351      -       -           -
LGA    E     352      -       -           -
LGA    E     353      V     346           #
LGA    C     354      V     347           #
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    L     355      G     357          3.741
LGA    G     356      G     358          4.791
LGA    G     357      L     359          3.009
LGA    G     358      I     360          3.326
LGA    L     359      -       -           -
LGA    I     360      D     361          2.862
LGA    D     361      N     362          3.333
LGA    N     362      A     363          2.064
LGA    A     363      Y     364          1.993
LGA    Y     364      R     365          3.721
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    R     365      Q     368           #
LGA    D     366      V     369           -
LGA    G     367      C     370           -
LGA    Q     368      Q     371           -
LGA    V     369      Y     372           -
LGA    C     370      I     373           -
LGA    Q     371      -       -           -
LGA    Y     372      -       -           -
LGA    I     373      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   90   90    5.0     27    3.21    14.81     17.412     0.817

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.280897 * X  +  -0.645583 * Y  +   0.710155 * Z  +  28.448244
  Y_new =   0.769592 * X  +  -0.290595 * Y  +  -0.568579 * Z  +  26.286133
  Z_new =   0.573433 * X  +   0.706242 * Y  +   0.415208 * Z  +   4.618129 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.039312   -2.102281  [ DEG:    59.5482   -120.4518 ]
  Theta =  -0.610690   -2.530903  [ DEG:   -34.9899   -145.0101 ]
  Phi   =   1.220827   -1.920766  [ DEG:    69.9482   -110.0518 ]
 
# 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: T0316TS393_2-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS393_2-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   90   90   5.0   27   3.21   14.81  17.412
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS393_2-D3
PFRMAT TS
TARGET T0316
MODEL 2
PARENT N/A
ATOM    284  CA  MET   284      18.802  18.423   1.819  1.00 25.00           C
ATOM    285  CA  SER   285      16.725  21.640   1.788  1.00 25.00           C
ATOM    286  CA  THR   286      15.472  24.705   3.673  1.00 25.00           C
ATOM    287  CA  SER   287      19.287  24.595   3.748  1.00 25.00           C
ATOM    288  CA  LEU   288      22.490  22.642   3.304  1.00 25.00           C
ATOM    289  CA  GLU   289      24.004  19.871   5.340  1.00 25.00           C
ATOM    290  CA  ALA   290      26.902  17.463   5.346  1.00 25.00           C
ATOM    291  CA  SER   291      27.520  15.678   8.621  1.00 25.00           C
ATOM    292  CA  GLN   292      29.932  16.948  11.244  1.00 25.00           C
ATOM    293  CA  VAL   293      33.063  16.586   9.062  1.00 25.00           C
ATOM    294  CA  HIS   294      33.325  12.837   8.868  1.00 25.00           C
ATOM    295  CA  PHE   295      30.727  11.787  11.378  1.00 25.00           C
ATOM    296  CA  THR   296      30.312   8.308  12.762  1.00 25.00           C
ATOM    297  CA  ARG   297      30.768   5.474  15.266  1.00 25.00           C
ATOM    298  CA  GLU   298      31.741   3.041  18.029  1.00 25.00           C
ATOM    299  CA  MET   299      28.871   0.969  19.322  1.00 25.00           C
ATOM    300  CA  PRO   300      25.834   0.002  21.289  1.00 25.00           C
ATOM    301  CA  GLU   301      22.746  -0.942  19.337  1.00 25.00           C
ATOM    302  CA  GLU   302      19.580   0.883  20.445  1.00 25.00           C
ATOM    303  CA  PHE   303      19.327   4.610  20.121  1.00 25.00           C
ATOM    304  CA  THR   304      19.938   8.206  19.015  1.00 25.00           C
ATOM    305  CA  LEU   305      21.199  10.569  16.361  1.00 25.00           C
ATOM    306  CA  GLU   306      21.380  13.771  14.400  1.00 25.00           C
ATOM    307  CA  CYS   307      24.432  15.110  12.599  1.00 25.00           C
ATOM    308  CA  THR   308      23.118  16.119   9.155  1.00 25.00           C
ATOM    309  CA  ALA   309      22.411  15.220   5.482  1.00 25.00           C
ATOM    310  CA  LYS   310      23.217  16.435   1.999  1.00 25.00           C
ATOM    311  CA  PHE   311      23.256  16.456  -1.776  1.00 25.00           C
ATOM    312  CA  ARG   312      21.298  16.902  -5.016  1.00 25.00           C
ATOM    313  CA  TYR   313      19.322  17.094  -8.242  1.00 25.00           C
ATOM    314  CA  ARG   314      16.842  17.056 -11.093  1.00 25.00           C
ATOM    315  CA  GLN   315      14.310  16.981 -13.971  1.00 25.00           C
ATOM    316  CA  PRO   316      13.885  17.111 -17.726  1.00 25.00           C
ATOM    317  CA  ASP   317      12.314  19.482 -20.228  1.00 25.00           C
ATOM    318  CA  SER   318      10.388  22.684 -20.734  1.00 25.00           C
ATOM    319  CA  LYS   319       9.823  24.118 -17.262  1.00 25.00           C
ATOM    320  CA  VAL   320       8.325  27.580 -17.254  1.00 25.00           C
ATOM    321  CA  THR   321       5.863  30.110 -15.937  1.00 25.00           C
ATOM    322  CA  VAL   322       5.217  33.489 -14.235  1.00 25.00           C
ATOM    323  CA  HIS   323       5.387  33.285 -10.407  1.00 25.00           C
ATOM    324  CA  VAL   324       3.468  35.035  -7.661  1.00 25.00           C
ATOM    325  CA  LYS   325       4.829  35.508  -4.193  1.00 25.00           C
ATOM    326  CA  GLY   326       8.515  35.759  -3.339  1.00 25.00           C
ATOM    327  CA  GLU   327      10.792  34.446  -0.626  1.00 25.00           C
ATOM    328  CA  LYS   328      13.863  32.767   0.845  1.00 25.00           C
ATOM    329  CA  THR   329      16.830  30.462   1.543  1.00 25.00           C
ATOM    330  CA  GLU   330      17.402  27.176  -0.337  1.00 25.00           C
ATOM    331  CA  VAL   331      19.930  24.375  -1.134  1.00 25.00           C
ATOM    332  CA  ILE   332      18.582  21.127  -2.592  1.00 25.00           C
ATOM    333  CA  PHE   333      17.075  17.607  -2.433  1.00 25.00           C
ATOM    334  CA  ALA   334      13.753  16.547  -3.950  1.00 25.00           C
ATOM    335  CA  GLU   335      11.757  13.424  -3.123  1.00 25.00           C
ATOM    336  CA  PRO   336      14.663  10.962  -3.559  1.00 25.00           C
ATOM    337  CA  GLN   337      18.127  11.005  -2.116  1.00 25.00           C
ATOM    338  CA  ARG   338      20.916  10.417   0.363  1.00 25.00           C
ATOM    339  CA  ALA   339      23.311  11.760  -2.307  1.00 25.00           C
ATOM    340  CA  ILE   340      26.879  12.528  -3.451  1.00 25.00           C
ATOM    341  CA  THR   341      25.537  14.509  -6.392  1.00 25.00           C
ATOM    342  CA  PRO   342      26.405  17.254  -8.810  1.00 25.00           C
ATOM    343  CA  GLY   343      25.279  19.915  -6.278  1.00 25.00           C
ATOM    344  CA  GLN   344      27.071  21.276  -3.177  1.00 25.00           C
ATOM    345  CA  ALA   345      28.713  17.883  -3.590  1.00 25.00           C
ATOM    346  CA  VAL   346      30.819  15.557  -5.744  1.00 25.00           C
ATOM    347  CA  VAL   347      34.561  14.845  -5.610  1.00 25.00           C
ATOM    348  CA  PHE   348      36.439  13.179  -2.733  1.00 25.00           C
ATOM    349  CA  TYR   349      38.206  10.566  -0.577  1.00 25.00           C
ATOM    350  CA  ASP   350      35.389   8.185  -1.209  1.00 25.00           C
ATOM    351  CA  GLY   351      34.300   7.439   2.388  1.00 25.00           C
ATOM    352  CA  GLU   352      30.900   6.110   1.414  1.00 25.00           C
ATOM    353  CA  GLU   353      28.297   8.388   3.112  1.00 25.00           C
ATOM    354  CA  CYS   354      29.643  11.045   5.485  1.00 25.00           C
ATOM    355  CA  LEU   355      30.204  14.718   4.805  1.00 25.00           C
ATOM    356  CA  GLY   356      33.733  15.939   4.061  1.00 25.00           C
ATOM    357  CA  GLY   357      34.638  12.621   2.580  1.00 25.00           C
ATOM    358  CA  GLY   358      31.709  11.011   0.727  1.00 25.00           C
ATOM    359  CA  LEU   359      31.522  13.858  -1.736  1.00 25.00           C
ATOM    360  CA  ILE   360      31.678  10.884  -4.076  1.00 25.00           C
ATOM    361  CA  ASP   361      29.721   9.723  -7.182  1.00 25.00           C
ATOM    362  CA  ASN   362      28.867   8.219 -10.601  1.00 25.00           C
ATOM    363  CA  ALA   363      29.392   4.855 -12.320  1.00 25.00           C
ATOM    364  CA  TYR   364      28.933   2.921 -15.599  1.00 25.00           C
ATOM    365  CA  ARG   365      26.972   0.146 -17.302  1.00 25.00           C
ATOM    366  CA  ASP   366      27.017  -2.120 -14.186  1.00 25.00           C
ATOM    367  CA  GLY   367      25.033  -5.261 -13.263  1.00 25.00           C
ATOM    368  CA  GLN   368      21.405  -5.100 -12.364  1.00 25.00           C
ATOM    369  CA  VAL   369      22.140  -5.373  -8.617  1.00 25.00           C
ATOM    370  CA  CYS   370      19.400  -4.836  -6.087  1.00 25.00           C
ATOM    371  CA  GLN   371      18.151  -7.524  -3.697  1.00 25.00           C
ATOM    372  CA  TYR   372      18.582  -7.368   0.041  1.00 25.00           C
ATOM    373  CA  ILE   373      19.495  -8.462   3.562  1.00 25.00           C
TER
END
