
#######################################################
#                                                     #
#                        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 T0324TS393_4-D1
# Molecule2: number of CA atoms  142 ( 1080),  selected  142 , name T0324_D1.pdb
# PARAMETERS: T0324TS393_4-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      -       -           -
LGA    Q       4      Y       3           #
LGA    -       -      Q       4           -
LGA    A       5      A       5          3.436
LGA    L       6      L       6          2.885
LGA    M       7      M       7          2.221
LGA    F       8      F       8          3.650
LGA    D       9      D       9          2.123
LGA    I      10      I      10          0.790
LGA    D      11      D      11          2.839
LGA    G      12      G      12          5.001
LGA    T      13      T      13          4.676
LGA    L      14      L      14          4.665
LGA    T      15      -       -           -
LGA    N      16      T      15          2.406
LGA    E      82      N      16           -
LGA    -       -      E      82           -
LGA    L      83      L      83          3.454
LGA    Y      84      Y      84          3.025
LGA    P      85      P      85          3.128
LGA    G      86      G      86          1.279
LGA    I      87      I      87          1.232
LGA    T      88      T      88          1.638
LGA    S      89      S      89          1.857
LGA    L      90      L      90          1.903
LGA    F      91      F      91          1.789
LGA    E      92      E      92          2.161
LGA    Q      93      Q      93          2.376
LGA    L      94      L      94          2.138
LGA    P      95      P      95          3.889
LGA    S      96      S      96          1.603
LGA    E      97      E      97          1.592
LGA    L      98      L      98          1.427
LGA    R      99      R      99          3.437
LGA    L     100      L     100          3.960
LGA    G     101      G     101          3.241
LGA    I     102      I     102          1.579
LGA    V     103      V     103          3.306
LGA    T     104      T     104          2.847
LGA    S     105      S     105          2.982
LGA    Q     106      Q     106          3.216
LGA    R     107      R     107          4.079
LGA    R     108      R     108          3.735
LGA    N     109      N     109          3.294
LGA    E     110      E     110          2.400
LGA    L     111      L     111          2.830
LGA    E     112      E     112          4.016
LGA    S     113      S     113          3.852
LGA    G     114      G     114          4.622
LGA    M     115      M     115           #
LGA    R     116      R     116          3.188
LGA    S     117      S     117          2.693
LGA    Y     118      Y     118          3.120
LGA    P     119      P     119          3.247
LGA    F     120      F     120          3.136
LGA    M     121      M     121          3.513
LGA    M     122      M     122          1.494
LGA    R     123      R     123          3.316
LGA    M     124      M     124          2.777
LGA    A     125      A     125          1.815
LGA    V     126      V     126          3.619
LGA    T     127      T     127          3.151
LGA    I     128      I     128          2.898
LGA    S     129      S     129           #
LGA    A     130      A     130          3.703
LGA    D     131      D     131          4.370
LGA    D     132      D     132          2.453
LGA    T     133      T     133          4.527
LGA    P     134      P     134          1.608
LGA    K     135      K     135          1.570
LGA    R     136      R     136          1.778
LGA    K     137      K     137          2.534
LGA    P     138      P     138          2.652
LGA    D     139      D     139          1.173
LGA    P     140      P     140          2.339
LGA    L     141      L     141          0.932
LGA    P     142      P     142          2.339
LGA    L     143      L     143          2.308
LGA    L     144      L     144          1.267
LGA    T     145      T     145          1.367
LGA    A     146      A     146          1.885
LGA    L     147      L     147          1.926
LGA    E     148      E     148          1.580
LGA    K     149      K     149          0.880
LGA    V     150      V     150          2.056
LGA    N     151      N     151          4.479
LGA    V     152      V     152          4.993
LGA    A     153      A     153           -
LGA    -       -      P     154           -
LGA    -       -      Q     155           -
LGA    P     154      N     156          4.160
LGA    Q     155      A     157          2.882
LGA    N     156      -       -           -
LGA    A     157      L     158          1.427
LGA    L     158      -       -           -
LGA    F     159      F     159          2.644
LGA    I     160      I     160          1.621
LGA    G     161      G     161          1.345
LGA    D     162      D     162          1.650
LGA    S     163      S     163          3.269
LGA    V     164      V     164          2.474
LGA    S     165      S     165          1.456
LGA    D     166      D     166          2.896
LGA    E     167      E     167          3.316
LGA    Q     168      Q     168          2.171
LGA    T     169      T     169          1.687
LGA    A     170      A     170          3.411
LGA    Q     171      Q     171          3.633
LGA    A     172      A     172          2.575
LGA    A     173      A     173          1.721
LGA    N     174      N     174          3.197
LGA    V     175      V     175          1.457
LGA    D     176      D     176          1.193
LGA    F     177      F     177          2.109
LGA    G     178      G     178          1.935
LGA    L     179      L     179          3.209
LGA    A     180      A     180          2.778
LGA    -       -      V     181           -
LGA    V     181      W     182          3.909
LGA    W     182      G     183          1.318
LGA    G     183      M     184          3.055
LGA    M     184      D     185          4.238
LGA    -       -      P     186           -
LGA    D     185      N     187          1.967
LGA    P     186      A     188          4.957
LGA    N     187      D     189          4.467
LGA    A     188      H     190          3.730
LGA    D     189      -       -           -
LGA    H     190      Q     191          1.637
LGA    Q     191      K     192          2.846
LGA    K     192      -       -           -
LGA    V     193      -       -           -
LGA    A     194      V     193          2.278
LGA    H     195      A     194          5.004
LGA    R     196      H     195          3.348
LGA    F     197      R     196          0.719
LGA    Q     198      -       -           -
LGA    K     199      -       -           -
LGA    P     200      F     197          3.458
LGA    L     201      Q     198          3.770
LGA    D     202      K     199          2.688
LGA    I     203      P     200           #
LGA    L     204      L     201           -
LGA    E     205      D     202           -
LGA    L     206      I     203           -
LGA    F     207      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    121    2.92    82.64     47.754     4.011

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.351300 * X  +  -0.931299 * Y  +   0.096282 * Z  +  25.776886
  Y_new =   0.397528 * X  +   0.241474 * Y  +   0.885247 * Z  +  21.190802
  Z_new =  -0.847679 * X  +  -0.272712 * Y  +   0.455048 * Z  +  20.718285 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.539908    2.601685  [ DEG:   -30.9344    149.0656 ]
  Theta =   1.011595    2.129997  [ DEG:    57.9601    122.0399 ]
  Phi   =   0.847055   -2.294538  [ DEG:    48.5327   -131.4673 ]
 
# 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: T0324TS393_4-D1                               
REMARK     2: T0324_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0324TS393_4-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  121   2.92   82.64  47.754
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS393_4-D1
PFRMAT TS
TARGET T0324
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      33.134  31.449  48.955  1.00 25.00           C
ATOM      2  CA  THR     2      30.908  29.855  46.327  1.00 25.00           C
ATOM      3  CA  TYR     3      28.733  28.123  43.715  1.00 25.00           C
ATOM      4  CA  GLN     4      27.089  27.010  40.480  1.00 25.00           C
ATOM      5  CA  ALA     5      27.694  26.832  36.705  1.00 25.00           C
ATOM      6  CA  LEU     6      28.179  26.327  33.030  1.00 25.00           C
ATOM      7  CA  MET     7      25.919  24.621  30.566  1.00 25.00           C
ATOM      8  CA  PHE     8      24.412  25.130  27.129  1.00 25.00           C
ATOM      9  CA  ASP     9      27.401  24.252  24.950  1.00 25.00           C
ATOM     10  CA  ILE    10      27.700  21.726  22.107  1.00 25.00           C
ATOM     11  CA  ASP    11      27.121  23.693  18.924  1.00 25.00           C
ATOM     12  CA  GLY    12      29.342  26.613  19.927  1.00 25.00           C
ATOM     13  CA  THR    13      31.674  25.375  22.617  1.00 25.00           C
ATOM     14  CA  LEU    14      32.341  21.983  24.162  1.00 25.00           C
ATOM     15  CA  THR    15      32.088  19.038  21.813  1.00 25.00           C
ATOM     16  CA  ASN    16      32.148  20.261  18.176  1.00 25.00           C
ATOM     82  CA  GLU    82      41.147  20.369  17.038  1.00 25.00           C
ATOM     83  CA  LEU    83      37.576  21.305  18.079  1.00 25.00           C
ATOM     84  CA  TYR    84      36.868  24.644  16.532  1.00 25.00           C
ATOM     85  CA  PRO    85      39.976  26.887  16.861  1.00 25.00           C
ATOM     86  CA  GLY    86      37.976  29.399  18.899  1.00 25.00           C
ATOM     87  CA  ILE    87      36.251  26.739  21.000  1.00 25.00           C
ATOM     88  CA  THR    88      39.506  25.116  22.203  1.00 25.00           C
ATOM     89  CA  SER    89      40.976  28.570  22.962  1.00 25.00           C
ATOM     90  CA  LEU    90      37.825  29.508  24.925  1.00 25.00           C
ATOM     91  CA  PHE    91      38.061  26.243  26.913  1.00 25.00           C
ATOM     92  CA  GLU    92      41.744  26.954  27.688  1.00 25.00           C
ATOM     93  CA  GLN    93      40.840  30.487  28.859  1.00 25.00           C
ATOM     94  CA  LEU    94      38.085  29.064  31.106  1.00 25.00           C
ATOM     95  CA  PRO    95      40.558  26.540  32.584  1.00 25.00           C
ATOM     96  CA  SER    96      42.676  27.846  35.384  1.00 25.00           C
ATOM     97  CA  GLU    97      39.358  28.787  36.946  1.00 25.00           C
ATOM     98  CA  LEU    98      36.481  26.585  35.699  1.00 25.00           C
ATOM     99  CA  ARG    99      33.499  26.224  33.337  1.00 25.00           C
ATOM    100  CA  LEU   100      32.731  25.988  29.560  1.00 25.00           C
ATOM    101  CA  GLY   101      30.586  22.959  28.691  1.00 25.00           C
ATOM    102  CA  ILE   102      28.583  20.002  27.375  1.00 25.00           C
ATOM    103  CA  VAL   103      25.229  19.706  25.652  1.00 25.00           C
ATOM    104  CA  THR   104      21.917  20.338  23.859  1.00 25.00           C
ATOM    105  CA  SER   105      19.300  18.466  21.858  1.00 25.00           C
ATOM    106  CA  GLN   106      22.331  16.600  20.467  1.00 25.00           C
ATOM    107  CA  ARG   107      22.304  14.776  23.859  1.00 25.00           C
ATOM    108  CA  ARG   108      22.477  12.174  26.676  1.00 25.00           C
ATOM    109  CA  ASN   109      24.243   9.161  25.105  1.00 25.00           C
ATOM    110  CA  GLU   110      25.848  11.439  22.479  1.00 25.00           C
ATOM    111  CA  LEU   111      27.032  13.822  25.232  1.00 25.00           C
ATOM    112  CA  GLU   112      28.522  10.877  27.174  1.00 25.00           C
ATOM    113  CA  SER   113      30.328   9.677  24.017  1.00 25.00           C
ATOM    114  CA  GLY   114      31.717  13.200  23.444  1.00 25.00           C
ATOM    115  CA  MET   115      32.935  13.336  27.071  1.00 25.00           C
ATOM    116  CA  ARG   116      34.630   9.928  26.656  1.00 25.00           C
ATOM    117  CA  SER   117      36.329  11.135  23.444  1.00 25.00           C
ATOM    118  CA  TYR   118      36.272  14.062  21.000  1.00 25.00           C
ATOM    119  CA  PRO   119      39.520  15.828  22.046  1.00 25.00           C
ATOM    120  CA  PHE   120      37.400  17.333  24.822  1.00 25.00           C
ATOM    121  CA  MET   121      39.553  15.099  27.035  1.00 25.00           C
ATOM    122  CA  MET   122      39.232  17.804  29.649  1.00 25.00           C
ATOM    123  CA  ARG   123      35.894  19.506  29.300  1.00 25.00           C
ATOM    124  CA  MET   124      32.972  17.440  30.547  1.00 25.00           C
ATOM    125  CA  ALA   125      33.038  17.594  34.314  1.00 25.00           C
ATOM    126  CA  VAL   126      31.346  20.991  33.708  1.00 25.00           C
ATOM    127  CA  THR   127      28.118  19.184  32.685  1.00 25.00           C
ATOM    128  CA  ILE   128      24.926  18.890  30.635  1.00 25.00           C
ATOM    129  CA  SER   129      21.550  19.548  28.946  1.00 25.00           C
ATOM    130  CA  ALA   130      20.354  16.023  29.761  1.00 25.00           C
ATOM    131  CA  ASP   131      22.149  13.271  31.621  1.00 25.00           C
ATOM    132  CA  ASP   132      18.587  12.467  32.855  1.00 25.00           C
ATOM    133  CA  THR   133      16.778  11.716  29.603  1.00 25.00           C
ATOM    134  CA  PRO   134      13.500  12.149  31.493  1.00 25.00           C
ATOM    135  CA  LYS   135      13.561  15.761  32.837  1.00 25.00           C
ATOM    136  CA  ARG   136      15.356  16.871  29.665  1.00 25.00           C
ATOM    137  CA  LYS   137      16.769  18.919  26.809  1.00 25.00           C
ATOM    138  CA  PRO   138      13.702  21.101  26.372  1.00 25.00           C
ATOM    139  CA  ASP   139      13.829  21.990  30.055  1.00 25.00           C
ATOM    140  CA  PRO   140      16.996  22.413  32.077  1.00 25.00           C
ATOM    141  CA  LEU   141      16.541  20.982  35.601  1.00 25.00           C
ATOM    142  CA  PRO   142      18.882  18.072  34.749  1.00 25.00           C
ATOM    143  CA  LEU   143      21.495  20.534  33.411  1.00 25.00           C
ATOM    144  CA  LEU   144      21.217  22.608  36.619  1.00 25.00           C
ATOM    145  CA  THR   145      21.671  19.447  38.732  1.00 25.00           C
ATOM    146  CA  ALA   146      24.761  18.491  36.682  1.00 25.00           C
ATOM    147  CA  LEU   147      26.204  22.004  37.171  1.00 25.00           C
ATOM    148  CA  GLU   148      25.583  21.760  40.942  1.00 25.00           C
ATOM    149  CA  LYS   149      27.327  18.351  41.033  1.00 25.00           C
ATOM    150  CA  VAL   150      30.312  19.799  39.121  1.00 25.00           C
ATOM    151  CA  ASN   151      32.151  21.985  41.647  1.00 25.00           C
ATOM    152  CA  VAL   152      31.896  25.085  39.506  1.00 25.00           C
ATOM    153  CA  ALA   153      32.263  28.901  39.888  1.00 25.00           C
ATOM    154  CA  PRO   154      30.332  30.849  37.271  1.00 25.00           C
ATOM    155  CA  GLN   155      26.799  31.817  38.391  1.00 25.00           C
ATOM    156  CA  ASN   156      26.408  34.053  35.307  1.00 25.00           C
ATOM    157  CA  ALA   157      27.765  31.716  32.577  1.00 25.00           C
ATOM    158  CA  LEU   158      28.510  32.600  28.910  1.00 25.00           C
ATOM    159  CA  PHE   159      27.223  29.108  28.298  1.00 25.00           C
ATOM    160  CA  ILE   160      26.472  29.199  24.541  1.00 25.00           C
ATOM    161  CA  GLY   161      24.378  27.132  22.183  1.00 25.00           C
ATOM    162  CA  ASP   162      22.056  27.720  19.250  1.00 25.00           C
ATOM    163  CA  SER   163      19.493  24.928  18.773  1.00 25.00           C
ATOM    164  CA  VAL   164      16.931  27.559  19.879  1.00 25.00           C
ATOM    165  CA  SER   165      15.241  25.023  22.198  1.00 25.00           C
ATOM    166  CA  ASP   166      18.635  24.118  23.723  1.00 25.00           C
ATOM    167  CA  GLU   167      19.401  27.829  24.279  1.00 25.00           C
ATOM    168  CA  GLN   168      15.995  28.306  25.965  1.00 25.00           C
ATOM    169  CA  THR   169      16.667  25.289  28.228  1.00 25.00           C
ATOM    170  CA  ALA   170      20.094  26.722  29.161  1.00 25.00           C
ATOM    171  CA  GLN   171      18.487  30.100  29.979  1.00 25.00           C
ATOM    172  CA  ALA   172      15.872  28.355  32.167  1.00 25.00           C
ATOM    173  CA  ALA   173      17.471  26.574  35.155  1.00 25.00           C
ATOM    174  CA  ASN   174      18.966  29.272  37.389  1.00 25.00           C
ATOM    175  CA  VAL   175      21.685  30.273  34.898  1.00 25.00           C
ATOM    176  CA  ASP   176      21.501  33.678  33.086  1.00 25.00           C
ATOM    177  CA  PHE   177      23.302  31.931  30.206  1.00 25.00           C
ATOM    178  CA  GLY   178      23.731  33.517  26.754  1.00 25.00           C
ATOM    179  CA  LEU   179      21.930  32.430  23.586  1.00 25.00           C
ATOM    180  CA  ALA   180      24.519  32.058  20.824  1.00 25.00           C
ATOM    181  CA  VAL   181      27.786  31.879  18.945  1.00 25.00           C
ATOM    182  CA  TRP   182      26.186  29.700  16.331  1.00 25.00           C
ATOM    183  CA  GLY   183      23.764  32.638  15.744  1.00 25.00           C
ATOM    184  CA  MET   184      20.596  32.750  17.769  1.00 25.00           C
ATOM    185  CA  ASP   185      17.411  31.693  15.990  1.00 25.00           C
ATOM    186  CA  PRO   186      15.666  35.006  15.239  1.00 25.00           C
ATOM    187  CA  ASN   187      16.055  38.339  16.880  1.00 25.00           C
ATOM    188  CA  ALA   188      12.962  38.302  19.137  1.00 25.00           C
ATOM    189  CA  ASP   189      14.475  35.458  21.207  1.00 25.00           C
ATOM    190  CA  HIS   190      17.747  37.417  21.553  1.00 25.00           C
ATOM    191  CA  GLN   191      15.801  40.516  22.683  1.00 25.00           C
ATOM    192  CA  LYS   192      13.908  38.414  25.266  1.00 25.00           C
ATOM    193  CA  VAL   193      17.252  36.981  26.288  1.00 25.00           C
ATOM    194  CA  ALA   194      19.757  39.743  26.920  1.00 25.00           C
ATOM    195  CA  HIS   195      21.781  38.056  24.135  1.00 25.00           C
ATOM    196  CA  ARG   196      24.442  40.663  24.848  1.00 25.00           C
ATOM    197  CA  PHE   197      26.407  38.508  22.405  1.00 25.00           C
ATOM    198  CA  GLN   198      26.506  41.257  19.857  1.00 25.00           C
ATOM    199  CA  LYS   199      30.230  41.719  20.030  1.00 25.00           C
ATOM    200  CA  PRO   200      32.271  38.530  20.378  1.00 25.00           C
ATOM    201  CA  LEU   201      33.454  39.389  16.837  1.00 25.00           C
ATOM    202  CA  ASP   202      32.741  35.802  15.702  1.00 25.00           C
ATOM    203  CA  ILE   203      29.237  35.987  17.237  1.00 25.00           C
ATOM    204  CA  LEU   204      28.598  39.308  15.440  1.00 25.00           C
ATOM    205  CA  GLU   205      29.755  37.767  12.130  1.00 25.00           C
ATOM    206  CA  LEU   206      27.423  34.779  12.677  1.00 25.00           C
ATOM    207  CA  PHE   207      24.507  37.155  13.397  1.00 25.00           C
TER
END
