
#######################################################
#                                                     #
#                        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  142 (  142),  selected  142 , name T0324TS168_3-D1
# Molecule2: number of CA atoms  142 ( 1080),  selected  142 , name T0324_D1.pdb
# PARAMETERS: T0324TS168_3-D1.T0324_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           #
LGA    T       2      T       2           #
LGA    Y       3      Y       3          3.144
LGA    Q       4      Q       4          3.693
LGA    A       5      A       5          4.563
LGA    L       6      L       6          2.073
LGA    M       7      M       7          5.501
LGA    F       8      F       8          3.521
LGA    D       9      D       9          1.232
LGA    I      10      I      10          1.334
LGA    D      11      D      11          2.260
LGA    G      12      G      12          1.853
LGA    T      13      T      13          1.588
LGA    -       -      L      14           -
LGA    L      14      T      15          3.987
LGA    T      15      N      16          1.731
LGA    N      16      E      82           #
LGA    E      82      -       -           -
LGA    L      83      L      83          2.098
LGA    Y      84      Y      84          2.494
LGA    P      85      P      85          3.240
LGA    G      86      G      86          2.453
LGA    I      87      I      87          1.677
LGA    T      88      T      88          1.575
LGA    S      89      S      89          1.783
LGA    L      90      L      90          2.010
LGA    F      91      F      91          1.821
LGA    E      92      E      92          1.892
LGA    Q      93      Q      93          2.212
LGA    L      94      L      94          2.896
LGA    P      95      P      95           #
LGA    S      96      S      96          0.914
LGA    E      97      E      97          2.157
LGA    L      98      L      98          2.970
LGA    R      99      R      99          3.525
LGA    L     100      L     100          3.360
LGA    G     101      G     101          3.515
LGA    I     102      I     102          3.816
LGA    V     103      V     103          2.018
LGA    T     104      T     104          1.931
LGA    S     105      S     105          2.592
LGA    Q     106      Q     106          4.206
LGA    R     107      R     107          3.687
LGA    R     108      R     108          3.421
LGA    N     109      N     109          4.042
LGA    E     110      E     110          2.857
LGA    L     111      L     111          1.772
LGA    E     112      E     112          4.138
LGA    S     113      S     113          5.183
LGA    G     114      G     114          4.469
LGA    M     115      M     115          4.112
LGA    R     116      R     116          3.565
LGA    S     117      S     117          2.456
LGA    Y     118      -       -           -
LGA    P     119      -       -           -
LGA    F     120      Y     118          2.929
LGA    M     121      P     119          2.139
LGA    M     122      F     120          2.599
LGA    R     123      M     121          3.350
LGA    -       -      M     122           -
LGA    -       -      R     123           -
LGA    M     124      M     124          0.839
LGA    A     125      A     125          3.833
LGA    V     126      V     126          5.220
LGA    T     127      T     127          2.756
LGA    I     128      I     128          2.012
LGA    S     129      S     129          2.163
LGA    A     130      A     130          5.321
LGA    D     131      D     131          3.182
LGA    D     132      D     132          3.660
LGA    T     133      T     133          2.238
LGA    P     134      P     134          1.738
LGA    K     135      K     135          0.786
LGA    R     136      R     136          1.382
LGA    K     137      K     137          1.837
LGA    P     138      P     138          2.087
LGA    D     139      D     139          0.771
LGA    P     140      P     140          1.186
LGA    L     141      L     141          1.386
LGA    P     142      P     142          1.389
LGA    L     143      L     143          1.006
LGA    L     144      L     144          1.691
LGA    T     145      T     145          2.310
LGA    A     146      A     146          2.166
LGA    L     147      L     147          1.795
LGA    E     148      E     148          3.020
LGA    K     149      K     149          3.564
LGA    V     150      V     150          3.303
LGA    N     151      N     151          3.911
LGA    V     152      -       -           -
LGA    A     153      V     152          1.816
LGA    P     154      A     153          2.890
LGA    Q     155      P     154          2.536
LGA    -       -      Q     155           -
LGA    N     156      N     156          2.535
LGA    A     157      A     157          2.667
LGA    L     158      L     158          2.807
LGA    F     159      F     159          1.966
LGA    I     160      I     160          2.620
LGA    G     161      G     161          2.001
LGA    D     162      D     162          1.735
LGA    S     163      S     163          1.486
LGA    V     164      V     164          1.858
LGA    S     165      S     165          1.191
LGA    D     166      D     166          0.551
LGA    E     167      E     167          0.862
LGA    Q     168      Q     168          0.409
LGA    T     169      T     169          0.822
LGA    A     170      A     170          1.425
LGA    Q     171      Q     171          0.841
LGA    A     172      A     172          1.787
LGA    A     173      A     173          1.487
LGA    N     174      N     174          3.015
LGA    V     175      V     175          0.410
LGA    D     176      D     176          0.451
LGA    F     177      F     177          1.104
LGA    G     178      G     178          4.235
LGA    L     179      L     179          1.269
LGA    A     180      A     180          2.618
LGA    V     181      V     181          3.895
LGA    W     182      W     182          1.389
LGA    G     183      G     183          2.884
LGA    -       -      M     184           -
LGA    -       -      D     185           -
LGA    -       -      P     186           -
LGA    -       -      N     187           -
LGA    -       -      A     188           -
LGA    M     184      D     189           #
LGA    D     185      H     190           -
LGA    P     186      -       -           -
LGA    N     187      -       -           -
LGA    A     188      -       -           -
LGA    D     189      -       -           -
LGA    H     190      Q     191           #
LGA    Q     191      -       -           -
LGA    K     192      K     192          3.747
LGA    V     193      V     193          2.419
LGA    A     194      A     194           -
LGA    H     195      H     195           -
LGA    R     196      R     196           #
LGA    F     197      F     197           -
LGA    Q     198      -       -           -
LGA    K     199      -       -           -
LGA    P     200      -       -           -
LGA    L     201      -       -           -
LGA    D     202      Q     198           #
LGA    I     203      K     199           -
LGA    L     204      P     200           -
LGA    E     205      L     201           -
LGA    L     206      D     202           -
LGA    F     207      I     203           -
LGA    -       -      L     204           -
LGA    -       -      E     205           -
LGA    -       -      L     206           -
LGA    -       -      F     207           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  142  142    5.0    112    2.71    91.96     49.416     3.987

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.390677 * X  +  -0.494923 * Y  +  -0.776159 * Z  +  25.197947
  Y_new =  -0.426056 * X  +  -0.650201 * Y  +   0.629059 * Z  +  20.491203
  Z_new =  -0.815995 * X  +   0.576446 * Y  +   0.043153 * Z  +  21.061934 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.496075   -1.645518  [ DEG:    85.7188    -94.2812 ]
  Theta =   0.954448    2.187145  [ DEG:    54.6859    125.3141 ]
  Phi   =  -2.312903    0.828689  [ DEG:  -132.5196     47.4804 ]
 
# 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: T0324TS168_3-D1                               
REMARK     2: T0324_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0324TS168_3-D1.T0324_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  142  142   5.0  112   2.71   91.96  49.416
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS168_3-D1
PFRMAT TS
TARGET T0324
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      37.672  33.985  41.044  1.00 25.00           C
ATOM      2  CA  THR     2      33.908  33.572  40.762  1.00 25.00           C
ATOM      3  CA  TYR     3      33.039  31.625  37.610  1.00 25.00           C
ATOM      4  CA  GLN     4      32.599  28.670  35.350  1.00 25.00           C
ATOM      5  CA  ALA     5      31.929  30.990  32.435  1.00 25.00           C
ATOM      6  CA  LEU     6      29.896  28.673  30.159  1.00 25.00           C
ATOM      7  CA  MET     7      29.704  28.429  26.351  1.00 25.00           C
ATOM      8  CA  PHE     8      29.290  25.616  23.738  1.00 25.00           C
ATOM      9  CA  ASP     9      26.840  22.739  24.246  1.00 25.00           C
ATOM     10  CA  ILE    10      27.587  19.789  21.961  1.00 25.00           C
ATOM     11  CA  ASP    11      24.410  20.725  20.134  1.00 25.00           C
ATOM     12  CA  GLY    12      25.350  23.923  18.270  1.00 25.00           C
ATOM     13  CA  THR    13      28.974  24.958  18.652  1.00 25.00           C
ATOM     14  CA  LEU    14      29.182  24.767  14.841  1.00 25.00           C
ATOM     15  CA  THR    15      30.831  21.402  13.953  1.00 25.00           C
ATOM     16  CA  ASN    16      30.915  19.491  17.282  1.00 25.00           C
ATOM     82  CA  GLU    82      39.532  20.831  14.689  1.00 25.00           C
ATOM     83  CA  LEU    83      36.762  21.990  17.000  1.00 25.00           C
ATOM     84  CA  TYR    84      36.651  25.689  16.177  1.00 25.00           C
ATOM     85  CA  PRO    85      39.691  27.617  17.337  1.00 25.00           C
ATOM     86  CA  GLY    86      37.262  29.094  19.878  1.00 25.00           C
ATOM     87  CA  ILE    87      36.048  25.783  21.228  1.00 25.00           C
ATOM     88  CA  THR    88      39.395  24.104  22.026  1.00 25.00           C
ATOM     89  CA  SER    89      40.922  27.506  22.901  1.00 25.00           C
ATOM     90  CA  LEU    90      37.950  28.278  25.190  1.00 25.00           C
ATOM     91  CA  PHE    91      38.363  24.881  26.912  1.00 25.00           C
ATOM     92  CA  GLU    92      42.097  25.563  27.416  1.00 25.00           C
ATOM     93  CA  GLN    93      41.295  28.996  28.911  1.00 25.00           C
ATOM     94  CA  LEU    94      38.745  27.395  31.279  1.00 25.00           C
ATOM     95  CA  PRO    95      41.341  24.792  32.353  1.00 25.00           C
ATOM     96  CA  SER    96      41.700  26.206  35.917  1.00 25.00           C
ATOM     97  CA  GLU    97      38.319  27.816  36.506  1.00 25.00           C
ATOM     98  CA  LEU    98      35.900  24.893  35.901  1.00 25.00           C
ATOM     99  CA  ARG    99      33.485  23.571  33.218  1.00 25.00           C
ATOM    100  CA  LEU   100      33.082  24.435  29.569  1.00 25.00           C
ATOM    101  CA  GLY   101      29.271  24.048  29.493  1.00 25.00           C
ATOM    102  CA  ILE   102      25.627  23.128  29.175  1.00 25.00           C
ATOM    103  CA  VAL   103      22.927  20.934  27.680  1.00 25.00           C
ATOM    104  CA  THR   104      22.465  19.523  24.160  1.00 25.00           C
ATOM    105  CA  SER   105      18.917  18.749  25.394  1.00 25.00           C
ATOM    106  CA  GLN   106      18.949  16.428  22.347  1.00 25.00           C
ATOM    107  CA  ARG   107      21.696  14.359  23.981  1.00 25.00           C
ATOM    108  CA  ARG   108      24.743  12.926  25.784  1.00 25.00           C
ATOM    109  CA  ASN   109      26.644   9.700  26.592  1.00 25.00           C
ATOM    110  CA  GLU   110      28.234   9.736  23.107  1.00 25.00           C
ATOM    111  CA  LEU   111      29.273  13.391  23.592  1.00 25.00           C
ATOM    112  CA  GLU   112      30.814  12.528  26.989  1.00 25.00           C
ATOM    113  CA  SER   113      32.732   9.615  25.408  1.00 25.00           C
ATOM    114  CA  GLY   114      34.017  11.931  22.641  1.00 25.00           C
ATOM    115  CA  MET   115      35.144  14.482  25.266  1.00 25.00           C
ATOM    116  CA  ARG   116      36.961  11.721  27.203  1.00 25.00           C
ATOM    117  CA  SER   117      38.694  10.572  23.987  1.00 25.00           C
ATOM    118  CA  TYR   118      38.754  12.284  20.527  1.00 25.00           C
ATOM    119  CA  PRO   119      41.584  14.844  20.697  1.00 25.00           C
ATOM    120  CA  PHE   120      39.498  18.032  20.379  1.00 25.00           C
ATOM    121  CA  MET   121      39.677  18.024  24.179  1.00 25.00           C
ATOM    122  CA  MET   122      40.278  18.380  27.917  1.00 25.00           C
ATOM    123  CA  ARG   123      37.029  19.983  28.972  1.00 25.00           C
ATOM    124  CA  MET   124      35.400  18.845  32.164  1.00 25.00           C
ATOM    125  CA  ALA   125      32.021  17.021  32.454  1.00 25.00           C
ATOM    126  CA  VAL   126      31.658  19.654  29.793  1.00 25.00           C
ATOM    127  CA  THR   127      27.986  18.676  29.749  1.00 25.00           C
ATOM    128  CA  ILE   128      24.857  16.549  29.241  1.00 25.00           C
ATOM    129  CA  SER   129      21.456  15.002  29.285  1.00 25.00           C
ATOM    130  CA  ALA   130      22.701  12.327  31.644  1.00 25.00           C
ATOM    131  CA  ASP   131      19.007  11.602  32.016  1.00 25.00           C
ATOM    132  CA  ASP   132      19.037  11.944  35.836  1.00 25.00           C
ATOM    133  CA  THR   133      16.669  14.829  35.161  1.00 25.00           C
ATOM    134  CA  PRO   134      13.306  14.041  33.569  1.00 25.00           C
ATOM    135  CA  LYS   135      13.370  16.518  30.755  1.00 25.00           C
ATOM    136  CA  ARG   136      14.829  16.484  27.294  1.00 25.00           C
ATOM    137  CA  LYS   137      14.119  20.145  26.555  1.00 25.00           C
ATOM    138  CA  PRO   138      11.838  22.998  27.603  1.00 25.00           C
ATOM    139  CA  ASP   139      12.421  21.990  31.235  1.00 25.00           C
ATOM    140  CA  PRO   140      15.850  23.114  32.245  1.00 25.00           C
ATOM    141  CA  LEU   141      16.291  19.653  33.826  1.00 25.00           C
ATOM    142  CA  PRO   142      19.244  18.938  31.494  1.00 25.00           C
ATOM    143  CA  LEU   143      20.833  22.293  32.437  1.00 25.00           C
ATOM    144  CA  LEU   144      20.383  21.488  36.154  1.00 25.00           C
ATOM    145  CA  THR   145      22.006  18.059  35.633  1.00 25.00           C
ATOM    146  CA  ALA   146      24.948  19.699  33.811  1.00 25.00           C
ATOM    147  CA  LEU   147      25.359  22.205  36.678  1.00 25.00           C
ATOM    148  CA  GLU   148      25.330  19.340  39.219  1.00 25.00           C
ATOM    149  CA  LYS   149      27.984  17.475  37.183  1.00 25.00           C
ATOM    150  CA  VAL   150      30.146  20.633  37.062  1.00 25.00           C
ATOM    151  CA  ASN   151      30.667  21.784  40.641  1.00 25.00           C
ATOM    152  CA  VAL   152      30.836  25.473  39.583  1.00 25.00           C
ATOM    153  CA  ALA   153      28.718  25.876  42.770  1.00 25.00           C
ATOM    154  CA  PRO   154      26.039  26.880  40.266  1.00 25.00           C
ATOM    155  CA  GLN   155      24.480  30.371  40.052  1.00 25.00           C
ATOM    156  CA  ASN   156      26.548  31.129  36.920  1.00 25.00           C
ATOM    157  CA  ALA   157      27.171  28.078  34.743  1.00 25.00           C
ATOM    158  CA  LEU   158      24.751  29.040  32.011  1.00 25.00           C
ATOM    159  CA  PHE   159      23.500  27.911  28.610  1.00 25.00           C
ATOM    160  CA  ILE   160      24.619  27.852  24.976  1.00 25.00           C
ATOM    161  CA  GLY   161      25.254  28.048  21.245  1.00 25.00           C
ATOM    162  CA  ASP   162      21.594  27.820  20.278  1.00 25.00           C
ATOM    163  CA  SER   163      17.816  27.337  19.729  1.00 25.00           C
ATOM    164  CA  VAL   164      14.442  27.993  21.358  1.00 25.00           C
ATOM    165  CA  SER   165      14.823  25.235  23.988  1.00 25.00           C
ATOM    166  CA  ASP   166      18.357  26.464  24.802  1.00 25.00           C
ATOM    167  CA  GLU   167      17.054  30.047  25.167  1.00 25.00           C
ATOM    168  CA  GLN   168      14.277  28.825  27.503  1.00 25.00           C
ATOM    169  CA  THR   169      16.849  26.917  29.604  1.00 25.00           C
ATOM    170  CA  ALA   170      19.038  30.053  29.815  1.00 25.00           C
ATOM    171  CA  GLN   171      16.009  32.122  30.918  1.00 25.00           C
ATOM    172  CA  ALA   172      15.177  29.519  33.601  1.00 25.00           C
ATOM    173  CA  ALA   173      17.591  26.957  35.070  1.00 25.00           C
ATOM    174  CA  ASN   174      18.874  29.530  37.530  1.00 25.00           C
ATOM    175  CA  VAL   175      20.999  31.188  34.808  1.00 25.00           C
ATOM    176  CA  ASP   176      21.932  33.777  32.182  1.00 25.00           C
ATOM    177  CA  PHE   177      23.658  32.906  28.917  1.00 25.00           C
ATOM    178  CA  GLY   178      21.729  32.064  25.825  1.00 25.00           C
ATOM    179  CA  LEU   179      23.746  32.847  22.714  1.00 25.00           C
ATOM    180  CA  ALA   180      27.473  32.339  22.917  1.00 25.00           C
ATOM    181  CA  VAL   181      29.482  33.872  19.991  1.00 25.00           C
ATOM    182  CA  TRP   182      29.168  32.528  16.481  1.00 25.00           C
ATOM    183  CA  GLY   183      25.587  31.455  16.754  1.00 25.00           C
ATOM    184  CA  MET   184      24.914  34.953  18.209  1.00 25.00           C
ATOM    185  CA  ASP   185      27.228  37.989  18.160  1.00 25.00           C
ATOM    186  CA  PRO   186      27.427  41.807  18.571  1.00 25.00           C
ATOM    187  CA  ASN   187      27.485  41.135  22.270  1.00 25.00           C
ATOM    188  CA  ALA   188      24.681  43.506  23.356  1.00 25.00           C
ATOM    189  CA  ASP   189      22.055  41.006  22.120  1.00 25.00           C
ATOM    190  CA  HIS   190      23.786  38.193  24.060  1.00 25.00           C
ATOM    191  CA  GLN   191      23.824  40.361  27.218  1.00 25.00           C
ATOM    192  CA  LYS   192      20.095  41.111  26.777  1.00 25.00           C
ATOM    193  CA  VAL   193      18.082  38.005  26.130  1.00 25.00           C
ATOM    194  CA  ALA   194      16.863  39.687  22.895  1.00 25.00           C
ATOM    195  CA  HIS   195      16.627  36.125  21.554  1.00 25.00           C
ATOM    196  CA  ARG   196      20.046  36.207  19.887  1.00 25.00           C
ATOM    197  CA  PHE   197      19.268  33.206  17.711  1.00 25.00           C
ATOM    198  CA  GLN   198      16.523  35.383  16.215  1.00 25.00           C
ATOM    199  CA  LYS   199      17.354  38.843  14.998  1.00 25.00           C
ATOM    200  CA  PRO   200      21.039  39.344  15.466  1.00 25.00           C
ATOM    201  CA  LEU   201      21.075  39.359  11.636  1.00 25.00           C
ATOM    202  CA  ASP   202      24.158  37.085  11.633  1.00 25.00           C
ATOM    203  CA  ILE   203      22.424  34.690  14.066  1.00 25.00           C
ATOM    204  CA  LEU   204      19.318  34.625  11.827  1.00 25.00           C
ATOM    205  CA  GLU   205      21.505  33.873   8.774  1.00 25.00           C
ATOM    206  CA  LEU   206      23.226  31.028  10.676  1.00 25.00           C
ATOM    207  CA  PHE   207      19.816  29.598  11.671  1.00 25.00           C
TER
END
