
#######################################################
#                                                     #
#                        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 T0316TS168_3-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS168_3-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           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    S     287      E     301          3.689
LGA    -       -      E     302           -
LGA    L     288      F     303          3.471
LGA    E     289      T     304          3.197
LGA    A     290      L     305          2.210
LGA    -       -      E     306           -
LGA    S     291      C     307          1.726
LGA    Q     292      T     308          3.287
LGA    V     293      A     309          3.227
LGA    H     294      K     310          4.345
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    F     295      Q     315          4.056
LGA    T     296      P     316          2.942
LGA    R     297      D     317           -
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      S     318           #
LGA    C     307      K     319           #
LGA    T     308      V     320          2.897
LGA    A     309      T     321          2.297
LGA    K     310      V     322          5.127
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    F     311      V     331          2.886
LGA    R     312      I     332          3.409
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      F     333          4.031
LGA    V     331      A     334          2.614
LGA    I     332      E     335          3.661
LGA    F     333      P     336          4.547
LGA    A     334      Q     337          3.356
LGA    E     335      R     338          2.262
LGA    P     336      A     339          0.798
LGA    Q     337      I     340          1.175
LGA    R     338      T     341          3.253
LGA    A     339      P     342          2.842
LGA    I     340      G     343          4.402
LGA    T     341      Q     344          2.655
LGA    P     342      A     345          2.917
LGA    G     343      -       -           -
LGA    Q     344      V     346          1.430
LGA    A     345      V     347          2.559
LGA    V     346      F     348          1.410
LGA    V     347      Y     349          2.633
LGA    F     348      D     350          3.503
LGA    Y     349      G     351           -
LGA    D     350      -       -           -
LGA    G     351      -       -           -
LGA    E     352      E     352          4.155
LGA    E     353      E     353          2.614
LGA    C     354      C     354          4.747
LGA    L     355      L     355           -
LGA    G     356      -       -           -
LGA    G     357      G     356           #
LGA    G     358      G     357          2.459
LGA    L     359      G     358          2.336
LGA    I     360      -       -           -
LGA    D     361      L     359          5.332
LGA    N     362      I     360           -
LGA    A     363      D     361           -
LGA    Y     364      N     362           -
LGA    R     365      A     363           -
LGA    D     366      Y     364           -
LGA    G     367      R     365           -
LGA    Q     368      D     366           -
LGA    V     369      G     367           -
LGA    C     370      Q     368           -
LGA    Q     371      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    Y     372      I     373           #
LGA    I     373      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   90   90    5.0     39    3.26    10.26     23.632     1.161

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.998750 * X  +   0.040109 * Y  +  -0.029834 * Z  +  30.987711
  Y_new =   0.004821 * X  +  -0.516747 * Y  +  -0.856124 * Z  +  10.561182
  Z_new =  -0.049755 * X  +  -0.855198 * Y  +   0.515908 * Z  +   3.134651 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.027982    2.113610  [ DEG:   -58.8990    121.1010 ]
  Theta =   0.049776    3.091817  [ DEG:     2.8519    177.1481 ]
  Phi   =   3.136765   -0.004827  [ DEG:   179.7234     -0.2766 ]
 
# 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: T0316TS168_3-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS168_3-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   39   3.26   10.26  23.632
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS168_3-D3
PFRMAT TS
TARGET T0316
MODEL 3
PARENT N/A
ATOM    284  CA  MET   284      23.361  -3.991   8.602  1.00 25.00           C
ATOM    285  CA  SER   285      25.994  -2.705   6.138  1.00 25.00           C
ATOM    286  CA  THR   286      28.762  -1.956   8.669  1.00 25.00           C
ATOM    287  CA  SER   287      26.180  -0.512  11.019  1.00 25.00           C
ATOM    288  CA  LEU   288      24.873   2.653   9.373  1.00 25.00           C
ATOM    289  CA  GLU   289      22.583   3.242   6.385  1.00 25.00           C
ATOM    290  CA  ALA   290      19.693   5.688   5.896  1.00 25.00           C
ATOM    291  CA  SER   291      16.983   8.301   5.589  1.00 25.00           C
ATOM    292  CA  GLN   292      16.065  11.896   4.999  1.00 25.00           C
ATOM    293  CA  VAL   293      16.867  13.020   1.493  1.00 25.00           C
ATOM    294  CA  HIS   294      17.100  16.654   0.471  1.00 25.00           C
ATOM    295  CA  PHE   295      16.483  18.285  -2.885  1.00 25.00           C
ATOM    296  CA  THR   296      13.190  20.146  -3.509  1.00 25.00           C
ATOM    297  CA  ARG   297      10.566  22.615  -4.597  1.00 25.00           C
ATOM    298  CA  GLU   298       7.012  22.722  -5.828  1.00 25.00           C
ATOM    299  CA  MET   299       3.549  21.560  -6.746  1.00 25.00           C
ATOM    300  CA  PRO   300       0.672  19.489  -5.352  1.00 25.00           C
ATOM    301  CA  GLU   301      -1.035  18.030  -2.277  1.00 25.00           C
ATOM    302  CA  GLU   302       0.490  14.774  -3.406  1.00 25.00           C
ATOM    303  CA  PHE   303       0.169  13.141  -0.051  1.00 25.00           C
ATOM    304  CA  THR   304       3.642  11.735   0.399  1.00 25.00           C
ATOM    305  CA  LEU   305       7.371  11.386   1.146  1.00 25.00           C
ATOM    306  CA  GLU   306      10.314   9.062   1.095  1.00 25.00           C
ATOM    307  CA  CYS   307      13.137   7.020   2.640  1.00 25.00           C
ATOM    308  CA  THR   308      15.989   8.164   0.455  1.00 25.00           C
ATOM    309  CA  ALA   309      18.539   5.638   1.571  1.00 25.00           C
ATOM    310  CA  LYS   310      20.178   6.523  -1.728  1.00 25.00           C
ATOM    311  CA  PHE   311      23.048   5.873  -4.166  1.00 25.00           C
ATOM    312  CA  ARG   312      24.510   2.317  -4.003  1.00 25.00           C
ATOM    313  CA  TYR   313      24.204  -0.949  -5.873  1.00 25.00           C
ATOM    314  CA  ARG   314      23.513  -3.391  -8.667  1.00 25.00           C
ATOM    315  CA  GLN   315      23.226  -6.081 -11.351  1.00 25.00           C
ATOM    316  CA  PRO   316      24.439  -8.979 -13.469  1.00 25.00           C
ATOM    317  CA  ASP   317      25.990 -11.663 -15.628  1.00 25.00           C
ATOM    318  CA  SER   318      22.514 -12.234 -17.139  1.00 25.00           C
ATOM    319  CA  LYS   319      20.556 -11.604 -20.312  1.00 25.00           C
ATOM    320  CA  VAL   320      18.178  -9.010 -21.718  1.00 25.00           C
ATOM    321  CA  THR   321      14.524  -9.939 -21.656  1.00 25.00           C
ATOM    322  CA  VAL   322      11.185  -9.056 -20.074  1.00 25.00           C
ATOM    323  CA  HIS   323       7.751  -7.705 -19.294  1.00 25.00           C
ATOM    324  CA  VAL   324       6.542  -5.159 -16.793  1.00 25.00           C
ATOM    325  CA  LYS   325       5.990  -1.951 -14.761  1.00 25.00           C
ATOM    326  CA  GLY   326       6.675  -3.071 -11.154  1.00 25.00           C
ATOM    327  CA  GLU   327       9.389  -1.468  -9.070  1.00 25.00           C
ATOM    328  CA  LYS   328      12.096  -0.411  -6.690  1.00 25.00           C
ATOM    329  CA  THR   329      15.201   0.823  -4.898  1.00 25.00           C
ATOM    330  CA  GLU   330      17.314   3.918  -5.382  1.00 25.00           C
ATOM    331  CA  VAL   331      18.340   7.370  -6.581  1.00 25.00           C
ATOM    332  CA  ILE   332      19.639   9.583  -9.413  1.00 25.00           C
ATOM    333  CA  PHE   333      22.820  11.646  -9.951  1.00 25.00           C
ATOM    334  CA  ALA   334      22.027  13.075 -13.444  1.00 25.00           C
ATOM    335  CA  GLU   335      22.394  16.846 -13.815  1.00 25.00           C
ATOM    336  CA  PRO   336      25.831  16.120 -12.284  1.00 25.00           C
ATOM    337  CA  GLN   337      27.037  15.657  -8.708  1.00 25.00           C
ATOM    338  CA  ARG   338      29.657  13.049  -7.839  1.00 25.00           C
ATOM    339  CA  ALA   339      31.094  14.691  -4.688  1.00 25.00           C
ATOM    340  CA  ILE   340      31.915  13.596  -1.192  1.00 25.00           C
ATOM    341  CA  THR   341      31.894  17.139   0.118  1.00 25.00           C
ATOM    342  CA  PRO   342      29.064  19.670  -0.387  1.00 25.00           C
ATOM    343  CA  GLY   343      27.322  16.646  -1.953  1.00 25.00           C
ATOM    344  CA  GLN   344      27.802  14.148   0.858  1.00 25.00           C
ATOM    345  CA  ALA   345      24.554  12.894   2.276  1.00 25.00           C
ATOM    346  CA  VAL   346      20.973  12.991   3.664  1.00 25.00           C
ATOM    347  CA  VAL   347      20.188  12.562   7.389  1.00 25.00           C
ATOM    348  CA  PHE   348      17.900  10.387   9.490  1.00 25.00           C
ATOM    349  CA  TYR   349      20.146   9.572  12.453  1.00 25.00           C
ATOM    350  CA  ASP   350      18.345  10.256  15.743  1.00 25.00           C
ATOM    351  CA  GLY   351      15.237  11.579  13.963  1.00 25.00           C
ATOM    352  CA  GLU   352      15.315  14.342  11.325  1.00 25.00           C
ATOM    353  CA  GLU   353      17.649  15.880   8.837  1.00 25.00           C
ATOM    354  CA  CYS   354      18.420  16.734   5.182  1.00 25.00           C
ATOM    355  CA  LEU   355      21.999  16.883   3.980  1.00 25.00           C
ATOM    356  CA  GLY   356      24.480  18.689   1.650  1.00 25.00           C
ATOM    357  CA  GLY   357      27.284  17.170   3.729  1.00 25.00           C
ATOM    358  CA  GLY   358      29.118  14.334   5.422  1.00 25.00           C
ATOM    359  CA  LEU   359      31.170  11.134   5.626  1.00 25.00           C
ATOM    360  CA  ILE   360      34.100  11.900   3.421  1.00 25.00           C
ATOM    361  CA  ASP   361      37.474  13.220   2.204  1.00 25.00           C
ATOM    362  CA  ASN   362      40.793  14.848   1.477  1.00 25.00           C
ATOM    363  CA  ALA   363      44.469  15.653   1.920  1.00 25.00           C
ATOM    364  CA  TYR   364      47.763  17.371   0.912  1.00 25.00           C
ATOM    365  CA  ARG   365      49.980  19.408  -1.457  1.00 25.00           C
ATOM    366  CA  ASP   366      52.567  20.568  -4.008  1.00 25.00           C
ATOM    367  CA  GLY   367      53.762  17.632  -6.165  1.00 25.00           C
ATOM    368  CA  GLN   368      53.290  16.148  -9.632  1.00 25.00           C
ATOM    369  CA  VAL   369      49.615  16.737 -10.627  1.00 25.00           C
ATOM    370  CA  CYS   370      47.208  13.872 -11.443  1.00 25.00           C
ATOM    371  CA  GLN   371      45.142  13.916 -14.560  1.00 25.00           C
ATOM    372  CA  TYR   372      42.869  12.921 -17.477  1.00 25.00           C
ATOM    373  CA  ILE   373      43.697  10.723 -20.443  1.00 25.00           C
TER
END
