
#######################################################
#                                                     #
#                        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_2-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347TS168_2-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    D     134      R     137           #
LGA    -       -      S     138           -
LGA    -       -      L     139           -
LGA    -       -      A     140           -
LGA    P     135      G     141           #
LGA    F     136      A     142           -
LGA    R     137      L     143           -
LGA    S     138      R     144          4.012
LGA    -       -      M     145           -
LGA    -       -      A     146           -
LGA    -       -      G     147           -
LGA    -       -      G     148           -
LGA    L     139      Y     149          2.692
LGA    A     140      A     150          2.858
LGA    G     141      K     151          4.703
LGA    A     142      V     152           -
LGA    L     143      I     153           -
LGA    R     144      I     154           -
LGA    M     145      P     155           -
LGA    A     146      F     156           -
LGA    G     147      S     157           -
LGA    G     148      -       -           -
LGA    Y     149      -       -           -
LGA    A     150      -       -           -
LGA    K     151      -       -           -
LGA    V     152      -       -           -
LGA    I     153      -       -           -
LGA    I     154      -       -           -
LGA    P     155      E     158          4.619
LGA    -       -      F     159           -
LGA    F     156      G     160          4.574
LGA    S     157      W     161          3.035
LGA    E     158      A     162          4.949
LGA    F     159      D     163          5.007
LGA    G     160      F     164          2.739
LGA    W     161      L     165          2.483
LGA    A     162      R     166          3.789
LGA    D     163      R     167          2.664
LGA    F     164      R     168          0.679
LGA    L     165      I     169          2.353
LGA    R     166      D     170          3.267
LGA    R     167      R     171          4.369
LGA    R     168      D     172          3.718
LGA    -       -      L     173           -
LGA    I     169      L     174          3.010
LGA    D     170      S     175          0.304
LGA    R     171      D     176          4.671
LGA    D     172      S     177          1.795
LGA    L     173      -       -           -
LGA    L     174      F     178          3.162
LGA    S     175      D     179          2.754
LGA    D     176      D     180          1.434
LGA    S     177      A     181          1.899
LGA    F     178      L     182          2.576
LGA    D     179      A     183          2.367
LGA    D     180      E     184          1.412
LGA    A     181      A     185          1.702
LGA    L     182      M     186          2.288
LGA    A     183      K     187          2.264
LGA    E     184      L     188          1.755
LGA    A     185      A     189          1.566
LGA    M     186      K     190          1.800
LGA    K     187      S     191          2.984
LGA    L     188      R     192          2.423
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    A     189      G     202          2.612
LGA    K     190      V     203          0.945
LGA    S     191      E     204          3.021
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     40    3.02    12.50     37.646     1.282

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.546887 * X  +  -0.792814 * Y  +  -0.269000 * Z  +  20.411873
  Y_new =  -0.799188 * X  +  -0.590096 * Y  +   0.114391 * Z  +  62.187920
  Z_new =  -0.249427 * X  +   0.152423 * Y  +  -0.956323 * Z  +   7.365699 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.983537   -0.158055  [ DEG:   170.9441     -9.0559 ]
  Theta =   0.252088    2.889504  [ DEG:    14.4436    165.5564 ]
  Phi   =  -0.970683    2.170910  [ DEG:   -55.6160    124.3840 ]
 
# 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_2-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS168_2-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   40   3.02   12.50  37.646
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS168_2-D2
PFRMAT TS
TARGET T0347
MODEL 2
PARENT N/A
ATOM    134  CA  ASP   134      14.191  48.341  -1.924  1.00 25.00           C
ATOM    135  CA  PRO   135      17.174  49.714  -0.069  1.00 25.00           C
ATOM    136  CA  PHE   136      18.950  48.537   3.114  1.00 25.00           C
ATOM    137  CA  ARG   137      21.589  46.733   1.003  1.00 25.00           C
ATOM    138  CA  SER   138      22.121  49.901  -1.084  1.00 25.00           C
ATOM    139  CA  LEU   139      22.523  51.969   2.115  1.00 25.00           C
ATOM    140  CA  ALA   140      25.077  49.448   3.454  1.00 25.00           C
ATOM    141  CA  GLY   141      27.013  49.619   0.154  1.00 25.00           C
ATOM    142  CA  ALA   142      27.013  53.446   0.324  1.00 25.00           C
ATOM    143  CA  LEU   143      28.302  53.309   3.929  1.00 25.00           C
ATOM    144  CA  ARG   144      31.080  50.895   2.870  1.00 25.00           C
ATOM    145  CA  MET   145      32.052  53.235  -0.003  1.00 25.00           C
ATOM    146  CA  ALA   146      31.317  51.747  -3.408  1.00 25.00           C
ATOM    147  CA  GLY   147      28.433  53.770  -4.884  1.00 25.00           C
ATOM    148  CA  GLY   148      29.554  56.748  -2.741  1.00 25.00           C
ATOM    149  CA  TYR   149      25.918  57.891  -3.125  1.00 25.00           C
ATOM    150  CA  ALA   150      23.086  58.464  -5.605  1.00 25.00           C
ATOM    151  CA  LYS   151      24.244  55.380  -7.540  1.00 25.00           C
ATOM    152  CA  VAL   152      23.257  52.789  -4.852  1.00 25.00           C
ATOM    153  CA  ILE   153      21.829  55.017  -2.097  1.00 25.00           C
ATOM    154  CA  ILE   154      18.063  55.676  -2.150  1.00 25.00           C
ATOM    155  CA  PRO   155      15.127  53.584  -0.941  1.00 25.00           C
ATOM    156  CA  PHE   156      15.005  53.393   2.882  1.00 25.00           C
ATOM    157  CA  SER   157      17.532  56.259   3.130  1.00 25.00           C
ATOM    158  CA  GLU   158      15.435  58.352   0.705  1.00 25.00           C
ATOM    159  CA  PHE   159      12.294  57.657   2.782  1.00 25.00           C
ATOM    160  CA  GLY   160      14.140  58.703   5.970  1.00 25.00           C
ATOM    161  CA  TRP   161      15.299  61.933   4.268  1.00 25.00           C
ATOM    162  CA  ALA   162      11.708  62.662   3.154  1.00 25.00           C
ATOM    163  CA  ASP   163      10.455  62.077   6.725  1.00 25.00           C
ATOM    164  CA  PHE   164      13.139  64.449   8.082  1.00 25.00           C
ATOM    165  CA  LEU   165      12.117  67.108   5.522  1.00 25.00           C
ATOM    166  CA  ARG   166       8.446  66.710   6.539  1.00 25.00           C
ATOM    167  CA  ARG   167       5.982  64.174   5.139  1.00 25.00           C
ATOM    168  CA  ARG   168       5.999  66.035   1.856  1.00 25.00           C
ATOM    169  CA  ILE   169       7.980  66.273  -1.331  1.00 25.00           C
ATOM    170  CA  ASP   170       7.935  66.008  -5.173  1.00 25.00           C
ATOM    171  CA  ARG   171      10.081  65.437  -8.208  1.00 25.00           C
ATOM    172  CA  ASP   172      13.239  67.604  -8.267  1.00 25.00           C
ATOM    173  CA  LEU   173      12.663  68.586  -4.611  1.00 25.00           C
ATOM    174  CA  LEU   174      12.227  64.901  -3.664  1.00 25.00           C
ATOM    175  CA  SER   175      15.476  64.023  -5.491  1.00 25.00           C
ATOM    176  CA  ASP   176      17.305  66.836  -3.646  1.00 25.00           C
ATOM    177  CA  SER   177      15.942  65.561  -0.302  1.00 25.00           C
ATOM    178  CA  PHE   178      17.108  62.014  -1.152  1.00 25.00           C
ATOM    179  CA  ASP   179      20.587  63.344  -2.043  1.00 25.00           C
ATOM    180  CA  ASP   180      20.733  65.253   1.274  1.00 25.00           C
ATOM    181  CA  ALA   181      19.725  62.083   3.171  1.00 25.00           C
ATOM    182  CA  LEU   182      22.449  60.098   1.353  1.00 25.00           C
ATOM    183  CA  ALA   183      25.033  62.781   2.245  1.00 25.00           C
ATOM    184  CA  GLU   184      23.933  62.657   5.911  1.00 25.00           C
ATOM    185  CA  ALA   185      24.252  58.840   5.904  1.00 25.00           C
ATOM    186  CA  MET   186      27.763  59.113   4.398  1.00 25.00           C
ATOM    187  CA  LYS   187      28.746  61.658   7.086  1.00 25.00           C
ATOM    188  CA  LEU   188      27.415  59.325   9.816  1.00 25.00           C
ATOM    189  CA  ALA   189      29.416  56.413   8.337  1.00 25.00           C
ATOM    190  CA  LYS   190      32.573  58.581   8.279  1.00 25.00           C
ATOM    191  CA  SER   191      32.947  60.430  11.577  1.00 25.00           C
ATOM    192  CA  ARG   192      32.648  63.988  12.931  1.00 25.00           C
ATOM    193  CA  GLU   193      33.054  64.183  16.734  1.00 25.00           C
ATOM    194  CA  ALA   194      36.858  63.942  16.366  1.00 25.00           C
ATOM    195  CA  ARG   195      36.806  66.741  13.751  1.00 25.00           C
ATOM    196  CA  HIS   196      40.093  66.401  12.009  1.00 25.00           C
ATOM    197  CA  LEU   197      39.314  65.864   8.350  1.00 25.00           C
ATOM    198  CA  PRO   198      42.914  66.841   7.730  1.00 25.00           C
ATOM    199  CA  GLY   199      43.344  70.296   6.124  1.00 25.00           C
ATOM    200  CA  TRP   200      39.773  70.792   4.948  1.00 25.00           C
ATOM    201  CA  CYS   201      38.675  71.817   1.454  1.00 25.00           C
ATOM    202  CA  GLY   202      41.575  73.185  -0.488  1.00 25.00           C
ATOM    203  CA  VAL   203      41.335  76.814  -1.431  1.00 25.00           C
ATOM    204  CA  GLU   204      38.447  77.255  -3.864  1.00 25.00           C
TER
END
