
#######################################################
#                                                     #
#                        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_5-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347TS393_5-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          4.512
LGA    P     135      A     142           -
LGA    F     136      L     143           -
LGA    R     137      -       -           -
LGA    S     138      -       -           -
LGA    L     139      -       -           -
LGA    A     140      -       -           -
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           #
LGA    A     150      M     145           -
LGA    K     151      A     146          4.316
LGA    V     152      G     147          2.466
LGA    I     153      G     148          3.876
LGA    I     154      Y     149           #
LGA    P     155      A     150           #
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    F     156      E     158          4.924
LGA    S     157      F     159           -
LGA    -       -      G     160           -
LGA    E     158      W     161          3.921
LGA    F     159      A     162          1.839
LGA    G     160      D     163          4.531
LGA    W     161      F     164          5.059
LGA    A     162      L     165          2.787
LGA    D     163      R     166          0.774
LGA    -       -      R     167           -
LGA    F     164      R     168          1.076
LGA    L     165      I     169          0.647
LGA    R     166      D     170          3.265
LGA    R     167      R     171          1.325
LGA    R     168      D     172          2.695
LGA    I     169      L     173          2.510
LGA    -       -      L     174           -
LGA    -       -      S     175           -
LGA    -       -      D     176           -
LGA    -       -      S     177           -
LGA    D     170      F     178          2.258
LGA    R     171      D     179          2.730
LGA    D     172      D     180          2.081
LGA    L     173      A     181          2.037
LGA    L     174      L     182          1.799
LGA    S     175      A     183          0.485
LGA    D     176      E     184          0.401
LGA    S     177      A     185          1.109
LGA    F     178      M     186          1.540
LGA    D     179      K     187          1.390
LGA    D     180      L     188          1.045
LGA    A     181      A     189          1.641
LGA    L     182      K     190          2.331
LGA    A     183      S     191          2.160
LGA    E     184      R     192           #
LGA    -       -      E     193           -
LGA    A     185      A     194           #
LGA    -       -      R     195           -
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    M     186      C     201          4.155
LGA    K     187      G     202           #
LGA    L     188      -       -           -
LGA    A     189      V     203           #
LGA    K     190      E     204          3.596
LGA    S     191      -       -           -
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     33    2.80    12.12     35.162     1.136

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.878696 * X  +   0.383226 * Y  +   0.284659 * Z  +  19.298752
  Y_new =   0.315274 * X  +  -0.913607 * Y  +   0.256756 * Z  +  61.898418
  Z_new =   0.358463 * X  +  -0.135864 * Y  +  -0.923605 * Z  +  10.281732 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.995538    0.146055  [ DEG:  -171.6317      8.3683 ]
  Theta =  -0.366620   -2.774972  [ DEG:   -21.0058   -158.9942 ]
  Phi   =   0.344491   -2.797102  [ DEG:    19.7379   -160.2621 ]
 
# 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_5-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS393_5-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   33   2.80   12.12  35.162
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS393_5-D2
PFRMAT TS
TARGET T0347
MODEL 5
PARENT N/A
ATOM    134  CA  ASP   134      15.935  48.920  -2.296  1.00 25.00           C
ATOM    135  CA  PRO   135      18.416  47.438   0.113  1.00 25.00           C
ATOM    136  CA  PHE   136      18.156  45.669   3.499  1.00 25.00           C
ATOM    137  CA  ARG   137      21.001  43.305   2.510  1.00 25.00           C
ATOM    138  CA  SER   138      23.151  46.293   1.455  1.00 25.00           C
ATOM    139  CA  LEU   139      22.438  48.017   4.799  1.00 25.00           C
ATOM    140  CA  ALA   140      23.414  44.827   6.681  1.00 25.00           C
ATOM    141  CA  GLY   141      26.667  44.609   4.671  1.00 25.00           C
ATOM    142  CA  ALA   142      27.440  48.272   5.476  1.00 25.00           C
ATOM    143  CA  LEU   143      26.797  47.616   9.195  1.00 25.00           C
ATOM    144  CA  ARG   144      29.126  44.577   9.087  1.00 25.00           C
ATOM    145  CA  MET   145      31.839  46.687   7.394  1.00 25.00           C
ATOM    146  CA  ALA   146      32.262  48.476   4.069  1.00 25.00           C
ATOM    147  CA  GLY   147      31.278  50.206   0.810  1.00 25.00           C
ATOM    148  CA  GLY   148      27.600  49.593   0.561  1.00 25.00           C
ATOM    149  CA  TYR   149      24.885  52.124   1.274  1.00 25.00           C
ATOM    150  CA  ALA   150      27.586  54.616   0.386  1.00 25.00           C
ATOM    151  CA  LYS   151      26.592  56.891  -2.537  1.00 25.00           C
ATOM    152  CA  VAL   152      24.314  54.021  -3.511  1.00 25.00           C
ATOM    153  CA  ILE   153      21.380  55.624  -1.697  1.00 25.00           C
ATOM    154  CA  ILE   154      18.426  53.406  -1.058  1.00 25.00           C
ATOM    155  CA  PRO   155      19.168  51.433   2.050  1.00 25.00           C
ATOM    156  CA  PHE   156      18.181  52.107   5.689  1.00 25.00           C
ATOM    157  CA  SER   157      20.088  55.428   5.616  1.00 25.00           C
ATOM    158  CA  GLU   158      18.314  56.403   2.365  1.00 25.00           C
ATOM    159  CA  PHE   159      14.925  55.548   3.929  1.00 25.00           C
ATOM    160  CA  GLY   160      15.777  57.673   6.998  1.00 25.00           C
ATOM    161  CA  TRP   161      16.771  60.594   4.730  1.00 25.00           C
ATOM    162  CA  ALA   162      13.475  60.258   2.811  1.00 25.00           C
ATOM    163  CA  ASP   163      11.527  60.257   6.108  1.00 25.00           C
ATOM    164  CA  PHE   164      13.400  63.397   7.245  1.00 25.00           C
ATOM    165  CA  LEU   165      12.600  65.111   3.915  1.00 25.00           C
ATOM    166  CA  ARG   166       8.904  64.179   4.297  1.00 25.00           C
ATOM    167  CA  ARG   167       7.693  64.119   0.694  1.00 25.00           C
ATOM    168  CA  ARG   168       9.192  67.610   0.581  1.00 25.00           C
ATOM    169  CA  ILE   169      10.681  66.480  -2.744  1.00 25.00           C
ATOM    170  CA  ASP   170      13.162  66.641  -5.548  1.00 25.00           C
ATOM    171  CA  ARG   171      16.513  68.028  -6.666  1.00 25.00           C
ATOM    172  CA  ASP   172      17.534  69.821  -3.441  1.00 25.00           C
ATOM    173  CA  LEU   173      15.432  67.369  -1.382  1.00 25.00           C
ATOM    174  CA  LEU   174      17.076  64.414  -3.180  1.00 25.00           C
ATOM    175  CA  SER   175      20.543  65.878  -2.469  1.00 25.00           C
ATOM    176  CA  ASP   176      19.630  66.312   1.224  1.00 25.00           C
ATOM    177  CA  SER   177      18.416  62.683   1.375  1.00 25.00           C
ATOM    178  CA  PHE   178      21.685  61.496  -0.227  1.00 25.00           C
ATOM    179  CA  ASP   179      23.699  63.524   2.323  1.00 25.00           C
ATOM    180  CA  ASP   180      21.666  61.992   5.183  1.00 25.00           C
ATOM    181  CA  ALA   181      22.293  58.482   3.785  1.00 25.00           C
ATOM    182  CA  LEU   182      26.045  59.219   3.553  1.00 25.00           C
ATOM    183  CA  ALA   183      26.050  60.459   7.177  1.00 25.00           C
ATOM    184  CA  GLU   184      24.231  57.279   8.293  1.00 25.00           C
ATOM    185  CA  ALA   185      26.793  55.130   6.426  1.00 25.00           C
ATOM    186  CA  MET   186      29.657  57.042   8.102  1.00 25.00           C
ATOM    187  CA  LYS   187      28.036  56.514  11.531  1.00 25.00           C
ATOM    188  CA  LEU   188      27.671  52.771  10.809  1.00 25.00           C
ATOM    189  CA  ALA   189      31.354  52.586   9.774  1.00 25.00           C
ATOM    190  CA  LYS   190      32.375  54.380  13.000  1.00 25.00           C
ATOM    191  CA  SER   191      33.263  55.097  16.667  1.00 25.00           C
ATOM    192  CA  ARG   192      35.186  58.420  16.423  1.00 25.00           C
ATOM    193  CA  GLU   193      35.972  61.488  14.268  1.00 25.00           C
ATOM    194  CA  ALA   194      34.663  63.794  17.031  1.00 25.00           C
ATOM    195  CA  ARG   195      36.836  61.979  19.610  1.00 25.00           C
ATOM    196  CA  HIS   196      37.742  65.523  20.650  1.00 25.00           C
ATOM    197  CA  LEU   197      34.188  66.818  21.014  1.00 25.00           C
ATOM    198  CA  PRO   198      35.488  68.495  24.135  1.00 25.00           C
ATOM    199  CA  GLY   199      32.753  70.987  24.983  1.00 25.00           C
ATOM    200  CA  TRP   200      29.365  72.282  23.842  1.00 25.00           C
ATOM    201  CA  CYS   201      30.328  75.274  21.724  1.00 25.00           C
ATOM    202  CA  GLY   202      31.751  76.527  25.010  1.00 25.00           C
ATOM    203  CA  VAL   203      29.892  79.860  24.520  1.00 25.00           C
ATOM    204  CA  GLU   204      26.249  79.071  25.268  1.00 25.00           C
TER
END
