
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms   71 (  561),  selected   71 , name T0347_D2.pdb
# PARAMETERS: T0347TS393_4-D2.T0347_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D     134      D     134           -
LGA    -       -      P     135           -
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    -       -      S     138           -
LGA    -       -      L     139           -
LGA    P     135      A     140           #
LGA    F     136      -       -           -
LGA    R     137      -       -           -
LGA    S     138      -       -           -
LGA    L     139      G     141           #
LGA    A     140      A     142           -
LGA    G     141      L     143           -
LGA    A     142      R     144           #
LGA    L     143      M     145           -
LGA    R     144      A     146           -
LGA    M     145      G     147           -
LGA    -       -      G     148           -
LGA    A     146      Y     149          4.903
LGA    G     147      A     150          1.568
LGA    G     148      K     151           #
LGA    Y     149      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    A     150      S     157           #
LGA    K     151      E     158          4.929
LGA    V     152      F     159           -
LGA    I     153      G     160           -
LGA    I     154      W     161          4.015
LGA    -       -      A     162           -
LGA    -       -      D     163           -
LGA    P     155      F     164          1.889
LGA    F     156      L     165          3.065
LGA    S     157      R     166          1.267
LGA    E     158      R     167          3.424
LGA    F     159      R     168           #
LGA    G     160      I     169          4.764
LGA    W     161      -       -           -
LGA    A     162      D     170          2.491
LGA    D     163      R     171          2.966
LGA    F     164      D     172          2.421
LGA    L     165      -       -           -
LGA    R     166      L     173          2.722
LGA    R     167      L     174           -
LGA    R     168      S     175           -
LGA    I     169      D     176          2.879
LGA    D     170      S     177          3.786
LGA    R     171      -       -           -
LGA    D     172      -       -           -
LGA    L     173      -       -           -
LGA    L     174      F     178          1.510
LGA    S     175      D     179          1.248
LGA    D     176      D     180          0.957
LGA    S     177      A     181          1.065
LGA    F     178      L     182          1.336
LGA    D     179      A     183          1.329
LGA    D     180      E     184          0.898
LGA    A     181      A     185          1.071
LGA    L     182      M     186          1.464
LGA    A     183      K     187          1.286
LGA    E     184      L     188          0.816
LGA    A     185      A     189          0.833
LGA    M     186      K     190          0.980
LGA    K     187      S     191          1.175
LGA    L     188      R     192          3.217
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    A     189      C     201          3.688
LGA    K     190      G     202          3.348
LGA    S     191      V     203          2.244
LGA    R     192      E     204           -
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    2.62     9.09     34.428     1.215

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.782102 * X  +  -0.438075 * Y  +  -0.443178 * Z  +  21.580475
  Y_new =  -0.552180 * X  +  -0.816818 * Y  +  -0.167051 * Z  +  65.161392
  Z_new =  -0.288815 * X  +   0.375365 * Y  +  -0.880731 * Z  +   9.344829 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.738709   -0.402884  [ DEG:   156.9165    -23.0835 ]
  Theta =   0.292988    2.848604  [ DEG:    16.7870    163.2130 ]
  Phi   =  -0.614755    2.526838  [ DEG:   -35.2229    144.7771 ]
 
# 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_4-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS393_4-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   2.62    9.09  34.428
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS393_4-D2
PFRMAT TS
TARGET T0347
MODEL 4
PARENT N/A
ATOM    134  CA  ASP   134      13.215  53.138   0.056  1.00 25.00           C
ATOM    135  CA  PRO   135      12.463  52.454   3.696  1.00 25.00           C
ATOM    136  CA  PHE   136      12.957  53.314   7.395  1.00 25.00           C
ATOM    137  CA  ARG   137      14.548  49.885   8.005  1.00 25.00           C
ATOM    138  CA  SER   138      16.892  50.415   5.023  1.00 25.00           C
ATOM    139  CA  LEU   139      17.876  53.859   6.378  1.00 25.00           C
ATOM    140  CA  ALA   140      18.581  52.331   9.818  1.00 25.00           C
ATOM    141  CA  GLY   141      20.741  49.616   8.198  1.00 25.00           C
ATOM    142  CA  ALA   142      22.677  52.285   6.249  1.00 25.00           C
ATOM    143  CA  LEU   143      23.235  54.272   9.475  1.00 25.00           C
ATOM    144  CA  ARG   144      24.495  51.111  11.232  1.00 25.00           C
ATOM    145  CA  MET   145      26.890  50.421   8.324  1.00 25.00           C
ATOM    146  CA  ALA   146      26.726  49.768   4.603  1.00 25.00           C
ATOM    147  CA  GLY   147      24.462  49.761   1.508  1.00 25.00           C
ATOM    148  CA  GLY   148      24.209  53.502   0.944  1.00 25.00           C
ATOM    149  CA  TYR   149      22.471  55.764  -1.573  1.00 25.00           C
ATOM    150  CA  ALA   150      20.357  52.722  -2.153  1.00 25.00           C
ATOM    151  CA  LYS   151      18.224  54.109   0.610  1.00 25.00           C
ATOM    152  CA  VAL   152      17.483  57.014  -1.728  1.00 25.00           C
ATOM    153  CA  ILE   153      14.983  58.363   0.798  1.00 25.00           C
ATOM    154  CA  ILE   154      17.628  57.589   3.436  1.00 25.00           C
ATOM    155  CA  PRO   155      15.927  58.059   6.741  1.00 25.00           C
ATOM    156  CA  PHE   156      12.780  57.423   4.653  1.00 25.00           C
ATOM    157  CA  SER   157      10.739  59.653   7.005  1.00 25.00           C
ATOM    158  CA  GLU   158      13.372  62.419   6.705  1.00 25.00           C
ATOM    159  CA  PHE   159      13.275  62.132   2.888  1.00 25.00           C
ATOM    160  CA  GLY   160       9.453  62.371   2.942  1.00 25.00           C
ATOM    161  CA  TRP   161       9.654  65.478   5.171  1.00 25.00           C
ATOM    162  CA  ALA   162      12.182  67.065   2.772  1.00 25.00           C
ATOM    163  CA  ASP   163       9.880  66.310  -0.194  1.00 25.00           C
ATOM    164  CA  PHE   164       6.928  67.891   1.665  1.00 25.00           C
ATOM    165  CA  LEU   165       9.033  71.000   2.414  1.00 25.00           C
ATOM    166  CA  ARG   166      10.030  71.244  -1.275  1.00 25.00           C
ATOM    167  CA  ARG   167      10.235  74.967  -0.571  1.00 25.00           C
ATOM    168  CA  ARG   168      10.960  75.145  -4.339  1.00 25.00           C
ATOM    169  CA  ILE   169       9.526  72.188  -6.339  1.00 25.00           C
ATOM    170  CA  ASP   170       9.515  69.394  -8.918  1.00 25.00           C
ATOM    171  CA  ARG   171      11.114  66.154 -10.097  1.00 25.00           C
ATOM    172  CA  ASP   172      13.593  68.804  -8.869  1.00 25.00           C
ATOM    173  CA  LEU   173      12.141  68.558  -5.334  1.00 25.00           C
ATOM    174  CA  LEU   174      12.469  64.744  -5.437  1.00 25.00           C
ATOM    175  CA  SER   175      16.109  65.063  -6.585  1.00 25.00           C
ATOM    176  CA  ASP   176      16.819  67.516  -3.731  1.00 25.00           C
ATOM    177  CA  SER   177      15.234  65.094  -1.223  1.00 25.00           C
ATOM    178  CA  PHE   178      17.377  62.231  -2.596  1.00 25.00           C
ATOM    179  CA  ASP   179      20.519  64.397  -2.275  1.00 25.00           C
ATOM    180  CA  ASP   180      19.587  65.256   1.340  1.00 25.00           C
ATOM    181  CA  ALA   181      19.071  61.542   2.115  1.00 25.00           C
ATOM    182  CA  LEU   182      22.484  60.722   0.584  1.00 25.00           C
ATOM    183  CA  ALA   183      24.117  63.470   2.693  1.00 25.00           C
ATOM    184  CA  GLU   184      22.439  62.085   5.844  1.00 25.00           C
ATOM    185  CA  ALA   185      23.690  58.567   4.994  1.00 25.00           C
ATOM    186  CA  MET   186      27.236  59.923   4.490  1.00 25.00           C
ATOM    187  CA  LYS   187      27.055  61.720   7.867  1.00 25.00           C
ATOM    188  CA  LEU   188      25.874  58.488   9.550  1.00 25.00           C
ATOM    189  CA  ALA   189      28.767  56.563   7.941  1.00 25.00           C
ATOM    190  CA  LYS   190      31.246  59.212   9.169  1.00 25.00           C
ATOM    191  CA  SER   191      33.865  59.877   6.534  1.00 25.00           C
ATOM    192  CA  ARG   192      36.768  61.360   4.591  1.00 25.00           C
ATOM    193  CA  GLU   193      35.704  63.234   1.425  1.00 25.00           C
ATOM    194  CA  ALA   194      37.916  66.202   2.408  1.00 25.00           C
ATOM    195  CA  ARG   195      40.872  63.837   2.989  1.00 25.00           C
ATOM    196  CA  HIS   196      42.984  61.583   5.209  1.00 25.00           C
ATOM    197  CA  LEU   197      43.790  64.645   7.293  1.00 25.00           C
ATOM    198  CA  PRO   198      46.988  65.410   5.400  1.00 25.00           C
ATOM    199  CA  GLY   199      46.716  69.186   6.086  1.00 25.00           C
ATOM    200  CA  TRP   200      45.111  68.943   9.526  1.00 25.00           C
ATOM    201  CA  CYS   201      46.056  71.116  12.514  1.00 25.00           C
ATOM    202  CA  GLY   202      48.057  74.326  12.410  1.00 25.00           C
ATOM    203  CA  VAL   203      48.728  75.406  16.023  1.00 25.00           C
ATOM    204  CA  GLU   204      46.385  78.120  17.297  1.00 25.00           C
TER
END
