
#######################################################
#                                                     #
#                        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 T0347TS393_1-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347TS393_1-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    -       -      S     138           -
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    D     134      G     141          4.350
LGA    P     135      A     142           #
LGA    F     136      L     143           -
LGA    R     137      -       -           -
LGA    S     138      R     144           #
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    -       -      Y     149           -
LGA    L     139      A     150           #
LGA    A     140      K     151          4.754
LGA    G     141      V     152          2.823
LGA    A     142      -       -           -
LGA    L     143      -       -           -
LGA    R     144      I     153          4.697
LGA    M     145      I     154           -
LGA    A     146      P     155           -
LGA    G     147      F     156           -
LGA    G     148      S     157           -
LGA    Y     149      -       -           -
LGA    A     150      -       -           -
LGA    K     151      -       -           -
LGA    V     152      -       -           -
LGA    I     153      -       -           -
LGA    I     154      -       -           -
LGA    P     155      E     158          4.459
LGA    F     156      F     159          3.445
LGA    S     157      G     160          2.820
LGA    E     158      W     161          3.167
LGA    F     159      A     162          2.758
LGA    G     160      D     163          1.914
LGA    W     161      F     164          2.172
LGA    A     162      L     165          2.230
LGA    D     163      R     166          1.561
LGA    F     164      R     167          1.126
LGA    L     165      R     168          2.014
LGA    R     166      I     169          3.673
LGA    R     167      D     170          4.158
LGA    R     168      R     171          1.354
LGA    I     169      D     172          5.051
LGA    D     170      L     173          2.292
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    R     171      F     178          1.736
LGA    D     172      D     179          1.191
LGA    L     173      D     180          0.910
LGA    L     174      A     181          0.421
LGA    S     175      L     182          0.822
LGA    D     176      A     183          0.962
LGA    S     177      E     184          1.181
LGA    F     178      A     185          1.514
LGA    D     179      M     186          1.977
LGA    D     180      K     187          2.268
LGA    A     181      L     188          2.235
LGA    L     182      A     189          2.266
LGA    A     183      K     190          2.524
LGA    E     184      S     191          2.733
LGA    -       -      R     192           -
LGA    -       -      E     193           -
LGA    A     185      A     194          2.716
LGA    -       -      R     195           -
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    M     186      W     200          1.864
LGA    K     187      C     201          4.391
LGA    L     188      G     202           #
LGA    A     189      -       -           -
LGA    K     190      V     203           #
LGA    S     191      E     204          3.198
LGA    R     192      -       -           -
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     38    2.80    10.53     38.467     1.311

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.831549 * X  +  -0.172393 * Y  +  -0.528021 * Z  +  20.332756
  Y_new =  -0.169846 * X  +   0.984002 * Y  +  -0.053784 * Z  +  59.586655
  Z_new =   0.528846 * X  +   0.044958 * Y  +  -0.847526 * Z  +   9.846883 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.088596   -0.052997  [ DEG:   176.9635     -3.0365 ]
  Theta =  -0.557240   -2.584352  [ DEG:   -31.9275   -148.0725 ]
  Phi   =  -2.940111    0.201482  [ DEG:  -168.4560     11.5440 ]
 
# 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: T0347TS393_1-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS393_1-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   38   2.80   10.53  38.467
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS393_1-D2
PFRMAT TS
TARGET T0347
MODEL 1
PARENT N/A
ATOM    134  CA  ASP   134      15.040  49.093  -4.391  1.00 25.00           C
ATOM    135  CA  PRO   135      15.217  49.673  -0.669  1.00 25.00           C
ATOM    136  CA  PHE   136      15.144  46.167   0.871  1.00 25.00           C
ATOM    137  CA  ARG   137      17.721  44.961  -1.693  1.00 25.00           C
ATOM    138  CA  SER   138      19.965  47.957  -0.884  1.00 25.00           C
ATOM    139  CA  LEU   139      19.676  47.193   2.858  1.00 25.00           C
ATOM    140  CA  ALA   140      20.599  43.533   2.208  1.00 25.00           C
ATOM    141  CA  GLY   141      23.635  44.640   0.151  1.00 25.00           C
ATOM    142  CA  ALA   142      24.724  46.986   2.974  1.00 25.00           C
ATOM    143  CA  LEU   143      24.378  44.137   5.510  1.00 25.00           C
ATOM    144  CA  ARG   144      26.475  41.851   3.264  1.00 25.00           C
ATOM    145  CA  MET   145      29.160  44.565   2.968  1.00 25.00           C
ATOM    146  CA  ALA   146      29.852  48.044   1.516  1.00 25.00           C
ATOM    147  CA  GLY   147      27.779  48.195  -1.630  1.00 25.00           C
ATOM    148  CA  GLY   148      27.152  50.896  -4.209  1.00 25.00           C
ATOM    149  CA  TYR   149      23.623  50.877  -2.745  1.00 25.00           C
ATOM    150  CA  ALA   150      24.861  52.466   0.520  1.00 25.00           C
ATOM    151  CA  LYS   151      26.835  55.643  -0.303  1.00 25.00           C
ATOM    152  CA  VAL   152      24.650  56.260  -3.359  1.00 25.00           C
ATOM    153  CA  ILE   153      21.302  55.405  -1.729  1.00 25.00           C
ATOM    154  CA  ILE   154      17.985  56.298   0.033  1.00 25.00           C
ATOM    155  CA  PRO   155      18.901  53.222   2.104  1.00 25.00           C
ATOM    156  CA  PHE   156      15.329  52.491   3.276  1.00 25.00           C
ATOM    157  CA  SER   157      16.192  53.761   6.783  1.00 25.00           C
ATOM    158  CA  GLU   158      17.684  56.955   5.285  1.00 25.00           C
ATOM    159  CA  PHE   159      14.521  57.478   3.190  1.00 25.00           C
ATOM    160  CA  GLY   160      12.348  57.007   6.308  1.00 25.00           C
ATOM    161  CA  TRP   161      14.485  59.552   8.212  1.00 25.00           C
ATOM    162  CA  ALA   162      14.135  62.043   5.325  1.00 25.00           C
ATOM    163  CA  ASP   163      10.339  61.537   5.315  1.00 25.00           C
ATOM    164  CA  PHE   164      10.226  62.125   9.098  1.00 25.00           C
ATOM    165  CA  LEU   165      12.281  65.330   8.686  1.00 25.00           C
ATOM    166  CA  ARG   166       9.899  66.533   5.938  1.00 25.00           C
ATOM    167  CA  ARG   167       6.281  65.659   5.070  1.00 25.00           C
ATOM    168  CA  ARG   168       7.594  66.596   1.626  1.00 25.00           C
ATOM    169  CA  ILE   169      10.998  65.624   0.233  1.00 25.00           C
ATOM    170  CA  ASP   170      11.091  67.197  -3.196  1.00 25.00           C
ATOM    171  CA  ARG   171      13.079  66.309  -6.262  1.00 25.00           C
ATOM    172  CA  ASP   172      16.839  66.550  -6.948  1.00 25.00           C
ATOM    173  CA  LEU   173      17.359  68.336  -3.600  1.00 25.00           C
ATOM    174  CA  LEU   174      15.357  65.609  -1.805  1.00 25.00           C
ATOM    175  CA  SER   175      17.469  62.904  -3.504  1.00 25.00           C
ATOM    176  CA  ASP   176      20.676  64.705  -2.437  1.00 25.00           C
ATOM    177  CA  SER   177      19.388  64.918   1.163  1.00 25.00           C
ATOM    178  CA  PHE   178      18.566  61.178   1.117  1.00 25.00           C
ATOM    179  CA  ASP   179      22.079  60.398  -0.195  1.00 25.00           C
ATOM    180  CA  ASP   180      23.618  62.544   2.579  1.00 25.00           C
ATOM    181  CA  ALA   181      21.510  60.714   5.199  1.00 25.00           C
ATOM    182  CA  LEU   182      22.640  57.338   3.786  1.00 25.00           C
ATOM    183  CA  ALA   183      26.295  58.476   3.928  1.00 25.00           C
ATOM    184  CA  GLU   184      25.833  59.591   7.563  1.00 25.00           C
ATOM    185  CA  ALA   185      24.276  56.200   8.431  1.00 25.00           C
ATOM    186  CA  MET   186      27.217  54.397   6.766  1.00 25.00           C
ATOM    187  CA  LYS   187      29.690  56.548   8.748  1.00 25.00           C
ATOM    188  CA  LEU   188      27.829  55.738  11.996  1.00 25.00           C
ATOM    189  CA  ALA   189      27.941  52.003  11.158  1.00 25.00           C
ATOM    190  CA  LYS   190      31.701  52.244  10.473  1.00 25.00           C
ATOM    191  CA  SER   191      32.805  54.731  13.200  1.00 25.00           C
ATOM    192  CA  ARG   192      34.288  56.722  16.026  1.00 25.00           C
ATOM    193  CA  GLU   193      36.721  57.807  13.274  1.00 25.00           C
ATOM    194  CA  ALA   194      34.979  61.210  13.041  1.00 25.00           C
ATOM    195  CA  ARG   195      35.222  61.622  16.841  1.00 25.00           C
ATOM    196  CA  HIS   196      37.950  59.731  18.689  1.00 25.00           C
ATOM    197  CA  LEU   197      36.025  60.907  21.770  1.00 25.00           C
ATOM    198  CA  PRO   198      35.836  63.807  24.119  1.00 25.00           C
ATOM    199  CA  GLY   199      38.036  66.485  22.612  1.00 25.00           C
ATOM    200  CA  TRP   200      35.126  68.050  20.775  1.00 25.00           C
ATOM    201  CA  CYS   201      34.277  71.786  20.957  1.00 25.00           C
ATOM    202  CA  GLY   202      35.765  73.451  24.022  1.00 25.00           C
ATOM    203  CA  VAL   203      35.912  76.663  21.989  1.00 25.00           C
ATOM    204  CA  GLU   204      32.998  78.170  23.803  1.00 25.00           C
TER
END
