
#######################################################
#                                                     #
#                        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   71 (   71),  selected   71 , name T0347TS168_3-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347TS168_3-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D     134           -
LGA    -       -      P     135           -
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    D     134      S     138           #
LGA    -       -      L     139           -
LGA    P     135      A     140          5.544
LGA    F     136      -       -           -
LGA    R     137      -       -           -
LGA    S     138      G     141           #
LGA    L     139      A     142           -
LGA    A     140      L     143           -
LGA    G     141      -       -           -
LGA    A     142      -       -           -
LGA    L     143      -       -           -
LGA    R     144      -       -           -
LGA    M     145      -       -           -
LGA    A     146      -       -           -
LGA    G     147      -       -           -
LGA    G     148      -       -           -
LGA    Y     149      R     144          5.543
LGA    A     150      M     145           -
LGA    K     151      A     146           -
LGA    -       -      G     147           -
LGA    V     152      G     148          0.730
LGA    I     153      Y     149          4.660
LGA    I     154      A     150           #
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    P     155      E     158          3.524
LGA    -       -      F     159           -
LGA    F     156      G     160          1.940
LGA    S     157      W     161          3.358
LGA    E     158      A     162          4.677
LGA    F     159      D     163          3.873
LGA    G     160      F     164          2.005
LGA    W     161      L     165          1.587
LGA    A     162      R     166          4.066
LGA    D     163      R     167          4.584
LGA    F     164      R     168          2.734
LGA    L     165      I     169          1.915
LGA    R     166      D     170          3.209
LGA    -       -      R     171           -
LGA    R     167      D     172          3.216
LGA    R     168      L     173          2.898
LGA    I     169      L     174          2.789
LGA    D     170      S     175          3.532
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    R     171      F     178          1.130
LGA    D     172      D     179          0.909
LGA    L     173      D     180          0.649
LGA    L     174      A     181          0.801
LGA    S     175      L     182          0.490
LGA    D     176      A     183          0.986
LGA    S     177      E     184          1.658
LGA    F     178      A     185          1.593
LGA    D     179      M     186          1.351
LGA    D     180      K     187          2.184
LGA    A     181      L     188          2.502
LGA    L     182      A     189          1.560
LGA    A     183      K     190          1.769
LGA    E     184      S     191          2.561
LGA    -       -      R     192           -
LGA    A     185      E     193          3.729
LGA    M     186      A     194          4.098
LGA    K     187      R     195          4.357
LGA    L     188      -       -           -
LGA    A     189      H     196          3.964
LGA    K     190      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    -       -      C     201           -
LGA    -       -      G     202           -
LGA    S     191      V     203           #
LGA    R     192      E     204          3.342
LGA    E     193      -       -           -
LGA    A     194      -       -           -
LGA    R     195      -       -           -
LGA    H     196      -       -           -
LGA    L     197      -       -           -
LGA    P     198      -       -           -
LGA    G     199      -       -           -
LGA    W     200      -       -           -
LGA    C     201      -       -           -
LGA    G     202      -       -           -
LGA    V     203      -       -           -
LGA    E     204      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   71   71    5.0     39    3.05     2.56     37.887     1.236

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.399582 * X  +  -0.865657 * Y  +  -0.301614 * Z  +  20.011097
  Y_new =  -0.205841 * X  +   0.405350 * Y  +  -0.890686 * Z  +  60.367790
  Z_new =   0.893288 * X  +  -0.293818 * Y  +  -0.340158 * Z  +  12.021745 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.429160    0.712433  [ DEG:  -139.1806     40.8194 ]
  Theta =  -1.104608   -2.036985  [ DEG:   -63.2894   -116.7106 ]
  Phi   =  -2.665907    0.475686  [ DEG:  -152.7452     27.2548 ]
 
# 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: T0347TS168_3-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS168_3-D2.T0347_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   71   71   5.0   39   3.05    2.56  37.887
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS168_3-D2
PFRMAT TS
TARGET T0347
MODEL 3
PARENT N/A
ATOM    134  CA  ASP   134      12.836  49.065  -1.029  1.00 25.00           C
ATOM    135  CA  PRO   135      12.717  51.460   1.923  1.00 25.00           C
ATOM    136  CA  PHE   136      10.842  49.363   4.521  1.00 25.00           C
ATOM    137  CA  ARG   137      12.290  46.155   3.011  1.00 25.00           C
ATOM    138  CA  SER   138      15.811  47.654   3.139  1.00 25.00           C
ATOM    139  CA  LEU   139      15.290  48.630   6.806  1.00 25.00           C
ATOM    140  CA  ALA   140      14.099  45.079   7.606  1.00 25.00           C
ATOM    141  CA  GLY   141      17.184  43.625   5.863  1.00 25.00           C
ATOM    142  CA  ALA   142      19.453  45.969   7.869  1.00 25.00           C
ATOM    143  CA  LEU   143      17.730  44.896  11.117  1.00 25.00           C
ATOM    144  CA  ARG   144      18.209  41.214  10.184  1.00 25.00           C
ATOM    145  CA  MET   145      21.915  41.853   9.461  1.00 25.00           C
ATOM    146  CA  ALA   146      22.400  42.344   5.751  1.00 25.00           C
ATOM    147  CA  GLY   147      22.658  43.038   2.065  1.00 25.00           C
ATOM    148  CA  GLY   148      20.802  46.337   2.785  1.00 25.00           C
ATOM    149  CA  TYR   149      20.653  48.765  -0.085  1.00 25.00           C
ATOM    150  CA  ALA   150      24.348  49.435   0.497  1.00 25.00           C
ATOM    151  CA  LYS   151      25.909  52.821   1.321  1.00 25.00           C
ATOM    152  CA  VAL   152      24.767  56.258   0.402  1.00 25.00           C
ATOM    153  CA  ILE   153      21.070  55.480   0.380  1.00 25.00           C
ATOM    154  CA  ILE   154      21.597  53.850   3.751  1.00 25.00           C
ATOM    155  CA  PRO   155      18.261  51.972   3.518  1.00 25.00           C
ATOM    156  CA  PHE   156      16.188  52.712   6.652  1.00 25.00           C
ATOM    157  CA  SER   157      18.087  55.999   7.162  1.00 25.00           C
ATOM    158  CA  GLU   158      17.451  56.961   3.510  1.00 25.00           C
ATOM    159  CA  PHE   159      13.724  56.183   3.927  1.00 25.00           C
ATOM    160  CA  GLY   160      13.605  58.334   7.093  1.00 25.00           C
ATOM    161  CA  TRP   161      15.324  61.208   5.236  1.00 25.00           C
ATOM    162  CA  ALA   162      12.797  60.902   2.374  1.00 25.00           C
ATOM    163  CA  ASP   163       9.906  60.977   4.885  1.00 25.00           C
ATOM    164  CA  PHE   164      11.388  64.100   6.534  1.00 25.00           C
ATOM    165  CA  LEU   165      11.715  65.783   3.108  1.00 25.00           C
ATOM    166  CA  ARG   166       8.071  64.918   2.309  1.00 25.00           C
ATOM    167  CA  ARG   167       7.617  68.678   2.504  1.00 25.00           C
ATOM    168  CA  ARG   168      10.406  70.541   0.710  1.00 25.00           C
ATOM    169  CA  ILE   169      10.872  67.624  -1.600  1.00 25.00           C
ATOM    170  CA  ASP   170      11.057  66.879  -5.277  1.00 25.00           C
ATOM    171  CA  ARG   171      13.747  65.291  -7.443  1.00 25.00           C
ATOM    172  CA  ASP   172      17.442  66.280  -7.240  1.00 25.00           C
ATOM    173  CA  LEU   173      16.788  68.147  -3.960  1.00 25.00           C
ATOM    174  CA  LEU   174      14.983  65.079  -2.546  1.00 25.00           C
ATOM    175  CA  SER   175      17.925  62.848  -3.562  1.00 25.00           C
ATOM    176  CA  ASP   176      20.370  65.261  -1.868  1.00 25.00           C
ATOM    177  CA  SER   177      18.240  65.224   1.314  1.00 25.00           C
ATOM    178  CA  PHE   178      18.197  61.395   1.270  1.00 25.00           C
ATOM    179  CA  ASP   179      22.004  61.332   0.858  1.00 25.00           C
ATOM    180  CA  ASP   180      22.387  63.753   3.801  1.00 25.00           C
ATOM    181  CA  ALA   181      20.109  61.545   5.946  1.00 25.00           C
ATOM    182  CA  LEU   182      22.178  58.461   5.013  1.00 25.00           C
ATOM    183  CA  ALA   183      25.399  60.310   5.947  1.00 25.00           C
ATOM    184  CA  GLU   184      23.872  61.323   9.311  1.00 25.00           C
ATOM    185  CA  ALA   185      22.843  57.692   9.964  1.00 25.00           C
ATOM    186  CA  MET   186      26.389  56.510   9.130  1.00 25.00           C
ATOM    187  CA  LYS   187      27.849  59.121  11.521  1.00 25.00           C
ATOM    188  CA  LEU   188      25.458  57.966  14.281  1.00 25.00           C
ATOM    189  CA  ALA   189      26.490  54.326  13.685  1.00 25.00           C
ATOM    190  CA  LYS   190      30.185  55.316  13.888  1.00 25.00           C
ATOM    191  CA  SER   191      32.537  53.484  11.531  1.00 25.00           C
ATOM    192  CA  ARG   192      35.617  55.019  13.177  1.00 25.00           C
ATOM    193  CA  GLU   193      37.548  51.712  13.191  1.00 25.00           C
ATOM    194  CA  ALA   194      38.584  52.273   9.547  1.00 25.00           C
ATOM    195  CA  ARG   195      39.766  55.814  10.402  1.00 25.00           C
ATOM    196  CA  HIS   196      39.916  57.439   7.029  1.00 25.00           C
ATOM    197  CA  LEU   197      38.259  60.851   6.946  1.00 25.00           C
ATOM    198  CA  PRO   198      40.327  61.675   3.816  1.00 25.00           C
ATOM    199  CA  GLY   199      42.519  64.076   5.875  1.00 25.00           C
ATOM    200  CA  TRP   200      43.454  64.700   9.508  1.00 25.00           C
ATOM    201  CA  CYS   201      43.452  66.469  12.871  1.00 25.00           C
ATOM    202  CA  GLY   202      45.032  69.591  11.456  1.00 25.00           C
ATOM    203  CA  VAL   203      44.238  71.211  14.794  1.00 25.00           C
ATOM    204  CA  GLU   204      41.756  74.040  14.255  1.00 25.00           C
TER
END
