
#######################################################
#                                                     #
#                        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_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS393_1-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    M     284      Q     292          3.216
LGA    S     285      V     293           #
LGA    T     286      -       -           -
LGA    S     287      -       -           -
LGA    L     288      H     294          2.533
LGA    E     289      F     295          2.755
LGA    A     290      T     296          4.735
LGA    S     291      R     297          4.549
LGA    Q     292      E     298          4.771
LGA    V     293      -       -           -
LGA    H     294      M     299          5.241
LGA    F     295      P     300           -
LGA    T     296      -       -           -
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      -       -           -
LGA    T     308      -       -           -
LGA    A     309      -       -           -
LGA    K     310      -       -           -
LGA    F     311      -       -           -
LGA    R     312      -       -           -
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      E     301           #
LGA    T     329      E     302          0.951
LGA    E     330      F     303          2.224
LGA    V     331      T     304          4.596
LGA    I     332      L     305          3.162
LGA    F     333      E     306          4.514
LGA    A     334      C     307          3.420
LGA    E     335      T     308          3.164
LGA    -       -      A     309           -
LGA    P     336      K     310          3.638
LGA    Q     337      F     311           -
LGA    R     338      R     312           -
LGA    A     339      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           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    -       -      F     333           -
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    -       -      I     340           -
LGA    -       -      T     341           -
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    I     340      Q     344           #
LGA    T     341      A     345          3.663
LGA    -       -      V     346           -
LGA    P     342      V     347          3.068
LGA    G     343      F     348          1.528
LGA    Q     344      Y     349           #
LGA    A     345      D     350           -
LGA    V     346      -       -           -
LGA    V     347      -       -           -
LGA    F     348      -       -           -
LGA    Y     349      -       -           -
LGA    D     350      -       -           -
LGA    G     351      -       -           -
LGA    E     352      -       -           -
LGA    E     353      -       -           -
LGA    C     354      G     351           #
LGA    L     355      E     352          4.100
LGA    -       -      E     353           -
LGA    G     356      C     354          2.711
LGA    G     357      L     355           #
LGA    G     358      G     356          4.718
LGA    L     359      G     357          2.677
LGA    I     360      G     358          1.718
LGA    D     361      L     359          3.171
LGA    N     362      I     360          2.332
LGA    -       -      D     361           -
LGA    A     363      N     362          0.770
LGA    Y     364      A     363          3.201
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    R     365      C     370          3.442
LGA    D     366      Q     371          2.878
LGA    G     367      Y     372          3.654
LGA    Q     368      I     373          3.188
LGA    V     369      -       -           -
LGA    C     370      -       -           -
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     31    3.42     3.23     19.386     0.882

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.438610 * X  +   0.840858 * Y  +   0.317144 * Z  +  25.764826
  Y_new =   0.723775 * X  +   0.121333 * Y  +   0.679285 * Z  +  11.083368
  Z_new =   0.532702 * X  +   0.527482 * Y  +  -0.661810 * Z  +  19.852942 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.468666   -0.672927  [ DEG:   141.4441    -38.5559 ]
  Theta =  -0.561790   -2.579803  [ DEG:   -32.1882   -147.8118 ]
  Phi   =   2.115618   -1.025975  [ DEG:   121.2160    -58.7840 ]
 
# 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_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS393_1-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   31   3.42    3.23  19.386
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS393_1-D3
PFRMAT TS
TARGET T0316
MODEL 1
PARENT N/A
ATOM    284  CA  MET   284      34.891  11.622   9.123  1.00 25.00           C
ATOM    285  CA  SER   285      35.847  11.853   5.422  1.00 25.00           C
ATOM    286  CA  THR   286      33.384  14.655   6.038  1.00 25.00           C
ATOM    287  CA  SER   287      31.737  15.115   9.419  1.00 25.00           C
ATOM    288  CA  LEU   288      29.625  13.076  11.785  1.00 25.00           C
ATOM    289  CA  GLU   289      28.486  10.355  14.178  1.00 25.00           C
ATOM    290  CA  ALA   290      26.961   9.761  17.577  1.00 25.00           C
ATOM    291  CA  SER   291      26.298   6.988  20.040  1.00 25.00           C
ATOM    292  CA  GLN   292      22.735   8.417  19.972  1.00 25.00           C
ATOM    293  CA  VAL   293      21.812   4.984  18.529  1.00 25.00           C
ATOM    294  CA  HIS   294      21.122   2.406  15.852  1.00 25.00           C
ATOM    295  CA  PHE   295      18.542   2.544  13.125  1.00 25.00           C
ATOM    296  CA  THR   296      17.301  -0.719  11.646  1.00 25.00           C
ATOM    297  CA  ARG   297      15.403  -3.369   9.736  1.00 25.00           C
ATOM    298  CA  GLU   298      12.850  -5.998   8.746  1.00 25.00           C
ATOM    299  CA  MET   299      10.932  -8.498   6.581  1.00 25.00           C
ATOM    300  CA  PRO   300       9.757  -8.246   2.946  1.00 25.00           C
ATOM    301  CA  GLU   301      12.332  -6.490   0.676  1.00 25.00           C
ATOM    302  CA  GLU   302      14.180  -5.400  -2.468  1.00 25.00           C
ATOM    303  CA  PHE   303      13.308  -1.691  -2.879  1.00 25.00           C
ATOM    304  CA  THR   304      16.809  -0.950  -1.595  1.00 25.00           C
ATOM    305  CA  LEU   305      18.337   1.485   0.886  1.00 25.00           C
ATOM    306  CA  GLU   306      21.331   2.988   2.749  1.00 25.00           C
ATOM    307  CA  CYS   307      24.328   4.251   4.624  1.00 25.00           C
ATOM    308  CA  THR   308      26.765   5.212   7.344  1.00 25.00           C
ATOM    309  CA  ALA   309      26.157   7.661  10.225  1.00 25.00           C
ATOM    310  CA  LYS   310      29.843   7.419  11.216  1.00 25.00           C
ATOM    311  CA  PHE   311      32.772   5.033  11.569  1.00 25.00           C
ATOM    312  CA  ARG   312      36.220   3.600  11.996  1.00 25.00           C
ATOM    313  CA  TYR   313      37.718   2.064   8.809  1.00 25.00           C
ATOM    314  CA  ARG   314      38.567   1.087   5.205  1.00 25.00           C
ATOM    315  CA  GLN   315      41.048   0.908   2.344  1.00 25.00           C
ATOM    316  CA  PRO   316      44.350  -0.688   1.323  1.00 25.00           C
ATOM    317  CA  ASP   317      45.781  -2.549  -1.680  1.00 25.00           C
ATOM    318  CA  SER   318      46.670  -5.474   0.608  1.00 25.00           C
ATOM    319  CA  LYS   319      44.525  -8.573  -0.021  1.00 25.00           C
ATOM    320  CA  VAL   320      41.704 -10.057  -1.980  1.00 25.00           C
ATOM    321  CA  THR   321      39.835 -13.399  -2.119  1.00 25.00           C
ATOM    322  CA  VAL   322      37.336 -15.393  -0.107  1.00 25.00           C
ATOM    323  CA  HIS   323      34.176 -17.167   1.203  1.00 25.00           C
ATOM    324  CA  VAL   324      31.815 -15.317   3.548  1.00 25.00           C
ATOM    325  CA  LYS   325      29.162 -15.664   6.215  1.00 25.00           C
ATOM    326  CA  GLY   326      27.777 -12.176   5.579  1.00 25.00           C
ATOM    327  CA  GLU   327      27.526  -9.089   7.685  1.00 25.00           C
ATOM    328  CA  LYS   328      27.662  -5.682   9.409  1.00 25.00           C
ATOM    329  CA  THR   329      27.645  -2.010  10.260  1.00 25.00           C
ATOM    330  CA  GLU   330      25.310   0.893   9.575  1.00 25.00           C
ATOM    331  CA  VAL   331      22.288   3.268   9.370  1.00 25.00           C
ATOM    332  CA  ILE   332      20.515   6.080   7.465  1.00 25.00           C
ATOM    333  CA  PHE   333      18.689   8.277   4.938  1.00 25.00           C
ATOM    334  CA  ALA   334      18.181   9.380   1.301  1.00 25.00           C
ATOM    335  CA  GLU   335      18.169  12.583  -0.744  1.00 25.00           C
ATOM    336  CA  PRO   336      17.821  16.230   0.450  1.00 25.00           C
ATOM    337  CA  GLN   337      19.046  19.407   2.203  1.00 25.00           C
ATOM    338  CA  ARG   338      20.195  22.068   4.566  1.00 25.00           C
ATOM    339  CA  ALA   339      23.595  20.390   4.046  1.00 25.00           C
ATOM    340  CA  ILE   340      26.908  19.344   2.586  1.00 25.00           C
ATOM    341  CA  THR   341      25.519  16.557   0.395  1.00 25.00           C
ATOM    342  CA  PRO   342      24.427  13.066   1.295  1.00 25.00           C
ATOM    343  CA  GLY   343      22.361  11.727   4.179  1.00 25.00           C
ATOM    344  CA  GLN   344      24.765   9.588   6.125  1.00 25.00           C
ATOM    345  CA  ALA   345      26.410  12.355   8.097  1.00 25.00           C
ATOM    346  CA  VAL   346      26.740  16.043   8.946  1.00 25.00           C
ATOM    347  CA  VAL   347      26.114  19.622   7.835  1.00 25.00           C
ATOM    348  CA  PHE   348      25.768  23.443   7.596  1.00 25.00           C
ATOM    349  CA  TYR   349      25.486  27.211   7.913  1.00 25.00           C
ATOM    350  CA  ASP   350      21.941  27.236   6.566  1.00 25.00           C
ATOM    351  CA  GLY   351      19.087  25.785   8.639  1.00 25.00           C
ATOM    352  CA  GLU   352      17.070  22.529   8.611  1.00 25.00           C
ATOM    353  CA  GLU   353      16.096  21.400  12.145  1.00 25.00           C
ATOM    354  CA  CYS   354      17.122  17.933  11.127  1.00 25.00           C
ATOM    355  CA  LEU   355      15.972  14.442  10.321  1.00 25.00           C
ATOM    356  CA  GLY   356      18.979  14.177   8.036  1.00 25.00           C
ATOM    357  CA  GLY   357      20.948  16.296   5.550  1.00 25.00           C
ATOM    358  CA  GLY   358      24.635  15.551   5.070  1.00 25.00           C
ATOM    359  CA  LEU   359      28.270  14.833   4.326  1.00 25.00           C
ATOM    360  CA  ILE   360      29.384  11.193   4.011  1.00 25.00           C
ATOM    361  CA  ASP   361      30.271  11.588   0.327  1.00 25.00           C
ATOM    362  CA  ASN   362      31.146  10.392  -3.155  1.00 25.00           C
ATOM    363  CA  ALA   363      32.321   9.435  -6.643  1.00 25.00           C
ATOM    364  CA  TYR   364      32.360   9.872 -10.482  1.00 25.00           C
ATOM    365  CA  ARG   365      30.852  11.662 -13.517  1.00 25.00           C
ATOM    366  CA  ASP   366      32.893  12.312 -16.645  1.00 25.00           C
ATOM    367  CA  GLY   367      35.781  10.484 -14.932  1.00 25.00           C
ATOM    368  CA  GLN   368      38.879  12.601 -14.616  1.00 25.00           C
ATOM    369  CA  VAL   369      40.310  11.979 -11.187  1.00 25.00           C
ATOM    370  CA  CYS   370      41.704  15.295  -9.905  1.00 25.00           C
ATOM    371  CA  GLN   371      45.096  16.973  -9.431  1.00 25.00           C
ATOM    372  CA  TYR   372      45.520  20.734  -9.042  1.00 25.00           C
ATOM    373  CA  ILE   373      44.090  24.167  -9.670  1.00 25.00           C
TER
END
