
#######################################################
#                                                     #
#                        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  159 (  159),  selected  159 , name T0332TS393_2
# Molecule2: number of CA atoms  159 ( 1235),  selected  159 , name T0332.pdb
# PARAMETERS: T0332TS393_2.T0332.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L       1      L       1           -
LGA    G       2      G       2          2.165
LGA    K       3      K       3          4.546
LGA    S       4      S       4          1.705
LGA    I       5      I       5          3.949
LGA    S       6      S       6          1.974
LGA    R       7      R       7          1.163
LGA    L       8      L       8          0.807
LGA    I       9      I       9          0.845
LGA    V      10      V      10          1.168
LGA    V      11      V      11          1.219
LGA    A      12      A      12          1.953
LGA    S      13      S      13          3.949
LGA    L      14      L      14          1.425
LGA    I      15      I      15          0.878
LGA    D      16      D      16          1.491
LGA    K      17      K      17          1.989
LGA    P      18      P      18          0.811
LGA    T      19      T      19          0.673
LGA    N      20      N      20          0.797
LGA    L      21      L      21          0.667
LGA    G      22      G      22          0.496
LGA    G      23      G      23          1.073
LGA    L      24      L      24          1.143
LGA    C      25      C      25          0.500
LGA    R      26      R      26          0.942
LGA    T      27      T      27          1.066
LGA    C      28      C      28          0.487
LGA    E      29      E      29          0.816
LGA    V      30      V      30          1.127
LGA    F      31      F      31          0.252
LGA    G      32      G      32          0.882
LGA    A      33      A      33          1.297
LGA    S      34      S      34          2.221
LGA    V      35      V      35          1.812
LGA    L      36      L      36          1.812
LGA    V      37      V      37          2.220
LGA    V      38      V      38          2.805
LGA    G      39      G      39          2.598
LGA    S      40      -       -           -
LGA    L      41      -       -           -
LGA    Q      42      -       -           -
LGA    C      43      S      40          3.561
LGA    I      44      L      41          3.684
LGA    S      45      Q      42          3.896
LGA    D      46      -       -           -
LGA    K      47      C      43          4.346
LGA    Q      48      I      44          3.482
LGA    F      49      S      45           #
LGA    Q      50      D      46           #
LGA    -       -      K      47           -
LGA    -       -      Q      48           -
LGA    H      51      F      49           #
LGA    L      52      Q      50          1.556
LGA    -       -      H      51           -
LGA    -       -      L      52           -
LGA    S      53      S      53          3.256
LGA    V      54      V      54          5.421
LGA    S      55      S      55          2.167
LGA    A      56      A      56          2.723
LGA    E      57      E      57          2.996
LGA    -       -      Q      58           -
LGA    Q      58      W      59          0.869
LGA    W      59      L      60          3.229
LGA    L      60      P      61          2.562
LGA    P      61      L      62          1.929
LGA    L      62      V      63          3.194
LGA    V      63      E      64          1.271
LGA    E      64      V      65          1.227
LGA    V      65      K      66          3.939
LGA    K      66      P      67          2.107
LGA    P      67      P      68          3.084
LGA    P      68      Q      69          3.077
LGA    Q      69      L      70          5.393
LGA    L      70      I      71          1.425
LGA    I      71      -       -           -
LGA    D      72      D      72          1.272
LGA    Y      73      Y      73          0.626
LGA    L      74      L      74          2.363
LGA    Q      75      Q      75          3.048
LGA    Q      76      Q      76          2.112
LGA    K      77      K      77          0.957
LGA    K      78      K      78          3.235
LGA    T      79      T      79          3.861
LGA    E      80      E      80          2.938
LGA    G      81      G      81          2.875
LGA    Y      82      -       -           -
LGA    T      83      Y      82          3.812
LGA    I      84      T      83           #
LGA    I      85      I      84           #
LGA    G      86      I      85          3.236
LGA    V      87      G      86          1.202
LGA    E      88      V      87          3.438
LGA    Q      89      E      88          1.766
LGA    T      90      Q      89           #
LGA    A      91      T      90           -
LGA    K      92      A      91           -
LGA    -       -      K      92           -
LGA    S      93      S      93           #
LGA    L      94      L      94          3.417
LGA    D      95      D      95          2.185
LGA    L      96      L      96          2.037
LGA    T      97      T      97          2.852
LGA    Q      98      Q      98          2.811
LGA    Y      99      Y      99          2.612
LGA    C     100      C     100          2.556
LGA    F     101      F     101          2.028
LGA    P     102      P     102          3.956
LGA    E     103      E     103          3.165
LGA    K     104      K     104          1.514
LGA    S     105      S     105          1.204
LGA    L     106      L     106          2.094
LGA    L     107      L     107          2.533
LGA    L     108      L     108          3.036
LGA    L     109      L     109          1.885
LGA    G     110      G     110          1.672
LGA    N     111      N     111          2.702
LGA    E     112      E     112          1.677
LGA    R     113      R     113          2.018
LGA    E     114      E     114          2.764
LGA    G     115      G     115          0.843
LGA    I     116      I     116          0.982
LGA    P     117      P     117          0.445
LGA    A     118      A     118          1.335
LGA    N     119      N     119          2.168
LGA    L     120      L     120          2.225
LGA    I     121      I     121          1.848
LGA    Q     122      Q     122          1.883
LGA    Q     123      Q     123          1.603
LGA    L     124      L     124          1.566
LGA    D     125      D     125          1.486
LGA    V     126      V     126          1.092
LGA    C     127      C     127          1.053
LGA    V     128      V     128          1.231
LGA    E     129      E     129          0.823
LGA    I     130      I     130          5.449
LGA    P     131      P     131          4.671
LGA    Q     132      Q     132          2.805
LGA    Q     133      Q     133          1.797
LGA    G     134      G     134          2.071
LGA    I     135      I     135          1.954
LGA    I     136      I     136          0.681
LGA    R     137      R     137          0.746
LGA    S     138      S     138          1.576
LGA    L     139      L     139          0.337
LGA    N     140      N     140          1.484
LGA    V     141      V     141          1.738
LGA    H     142      H     142          0.586
LGA    V     143      V     143          2.143
LGA    S     144      S     144          2.596
LGA    G     145      G     145          1.345
LGA    A     146      A     146          0.843
LGA    L     147      L     147          2.341
LGA    L     148      L     148          2.490
LGA    I     149      I     149          1.418
LGA    W     150      W     150          1.165
LGA    E     151      E     151          2.454
LGA    Y     152      Y     152          2.621
LGA    T     153      T     153          1.696
LGA    R     154      R     154          1.779
LGA    Q     155      Q     155          2.888
LGA    Q     156      Q     156          2.943
LGA    -       -      L     157           -
LGA    L     157      L     158          1.119
LGA    L     158      S     159          4.717
LGA    S     159      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  159  159    5.0    142    2.38    83.10     58.503     5.729

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.595311 * X  +   0.687120 * Y  +   0.416499 * Z  +  27.450367
  Y_new =  -0.658903 * X  +   0.120819 * Y  +   0.742462 * Z  +  42.814762
  Z_new =   0.459839 * X  +  -0.716428 * Y  +   0.524670 * Z  +  31.062965 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.938693    2.202900  [ DEG:   -53.7831    126.2169 ]
  Theta =  -0.477814   -2.663779  [ DEG:   -27.3767   -152.6233 ]
  Phi   =  -0.836057    2.305536  [ DEG:   -47.9025    132.0975 ]
 
# 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: T0332TS393_2                                  
REMARK     2: T0332.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0332TS393_2.T0332.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  159  159   5.0  142   2.38   83.10  58.503
REMARK  ---------------------------------------------------------- 
MOLECULE T0332TS393_2
PFRMAT TS
TARGET T0332
MODEL 2
PARENT N/A
ATOM      1  CA  LEU     1       8.123  35.725  40.851  1.00 25.00           C
ATOM      2  CA  GLY     2       8.439  33.198  43.646  1.00 25.00           C
ATOM      3  CA  LYS     3      11.783  32.537  45.385  1.00 25.00           C
ATOM      4  CA  SER     4      15.001  33.442  43.705  1.00 25.00           C
ATOM      5  CA  ILE     5      18.553  34.244  42.792  1.00 25.00           C
ATOM      6  CA  SER     6      18.779  37.931  41.955  1.00 25.00           C
ATOM      7  CA  ARG     7      22.554  38.268  41.673  1.00 25.00           C
ATOM      8  CA  LEU     8      22.508  38.189  37.859  1.00 25.00           C
ATOM      9  CA  ILE     9      24.646  41.279  37.393  1.00 25.00           C
ATOM     10  CA  VAL    10      24.605  42.786  33.900  1.00 25.00           C
ATOM     11  CA  VAL    11      27.310  45.411  33.903  1.00 25.00           C
ATOM     12  CA  ALA    12      28.917  46.793  30.766  1.00 25.00           C
ATOM     13  CA  SER    13      32.201  48.568  30.203  1.00 25.00           C
ATOM     14  CA  LEU    14      32.664  51.251  27.496  1.00 25.00           C
ATOM     15  CA  ILE    15      29.172  51.012  25.870  1.00 25.00           C
ATOM     16  CA  ASP    16      29.429  53.395  22.866  1.00 25.00           C
ATOM     17  CA  LYS    17      27.098  55.649  20.821  1.00 25.00           C
ATOM     18  CA  PRO    18      23.824  55.051  22.619  1.00 25.00           C
ATOM     19  CA  THR    19      22.445  52.306  20.332  1.00 25.00           C
ATOM     20  CA  ASN    20      24.699  49.720  22.036  1.00 25.00           C
ATOM     21  CA  LEU    21      23.489  50.895  25.474  1.00 25.00           C
ATOM     22  CA  GLY    22      19.849  50.604  24.320  1.00 25.00           C
ATOM     23  CA  GLY    23      20.516  47.061  23.025  1.00 25.00           C
ATOM     24  CA  LEU    24      22.118  46.114  26.373  1.00 25.00           C
ATOM     25  CA  CYS    25      19.088  47.516  28.248  1.00 25.00           C
ATOM     26  CA  ARG    26      16.732  45.508  25.993  1.00 25.00           C
ATOM     27  CA  THR    27      18.774  42.334  26.644  1.00 25.00           C
ATOM     28  CA  CYS    28      18.615  42.976  30.416  1.00 25.00           C
ATOM     29  CA  GLU    29      14.821  43.458  30.198  1.00 25.00           C
ATOM     30  CA  VAL    30      14.493  40.181  28.245  1.00 25.00           C
ATOM     31  CA  PHE    31      16.251  38.111  30.917  1.00 25.00           C
ATOM     32  CA  GLY    32      16.013  40.153  34.147  1.00 25.00           C
ATOM     33  CA  ALA    33      19.806  40.343  34.218  1.00 25.00           C
ATOM     34  CA  SER    34      19.812  43.328  36.634  1.00 25.00           C
ATOM     35  CA  VAL    35      22.382  46.009  37.522  1.00 25.00           C
ATOM     36  CA  LEU    36      23.268  48.515  34.805  1.00 25.00           C
ATOM     37  CA  VAL    37      26.164  49.513  36.980  1.00 25.00           C
ATOM     38  CA  VAL    38      27.832  50.889  33.897  1.00 25.00           C
ATOM     39  CA  GLY    39      30.156  53.026  31.771  1.00 25.00           C
ATOM     40  CA  SER    40      31.436  56.603  31.571  1.00 25.00           C
ATOM     41  CA  LEU    41      31.649  56.205  27.841  1.00 25.00           C
ATOM     42  CA  GLN    42      29.014  57.865  25.584  1.00 25.00           C
ATOM     43  CA  CYS    43      27.137  58.108  28.914  1.00 25.00           C
ATOM     44  CA  ILE    44      23.802  59.693  29.994  1.00 25.00           C
ATOM     45  CA  SER    45      23.543  60.536  26.323  1.00 25.00           C
ATOM     46  CA  ASP    46      20.769  62.932  27.531  1.00 25.00           C
ATOM     47  CA  LYS    47      18.881  60.023  29.169  1.00 25.00           C
ATOM     48  CA  GLN    48      18.730  58.732  25.566  1.00 25.00           C
ATOM     49  CA  PHE    49      19.572  55.197  26.771  1.00 25.00           C
ATOM     50  CA  GLN    50      16.817  55.417  29.422  1.00 25.00           C
ATOM     51  CA  HIS    51      14.318  56.578  26.763  1.00 25.00           C
ATOM     52  CA  LEU    52      15.327  53.656  24.503  1.00 25.00           C
ATOM     53  CA  SER    53      14.863  51.212  27.413  1.00 25.00           C
ATOM     54  CA  VAL    54      11.502  52.262  28.695  1.00 25.00           C
ATOM     55  CA  SER    55      10.062  49.034  27.177  1.00 25.00           C
ATOM     56  CA  ALA    56      10.833  46.583  29.980  1.00 25.00           C
ATOM     57  CA  GLU    57      13.705  48.355  31.792  1.00 25.00           C
ATOM     58  CA  GLN    58      11.594  48.573  34.979  1.00 25.00           C
ATOM     59  CA  TRP    59      14.850  49.912  36.422  1.00 25.00           C
ATOM     60  CA  LEU    60      18.094  48.585  35.099  1.00 25.00           C
ATOM     61  CA  PRO    61      19.699  50.714  37.786  1.00 25.00           C
ATOM     62  CA  LEU    62      21.097  53.187  35.216  1.00 25.00           C
ATOM     63  CA  VAL    63      24.648  54.444  35.860  1.00 25.00           C
ATOM     64  CA  GLU    64      28.322  54.883  36.962  1.00 25.00           C
ATOM     65  CA  VAL    65      31.417  52.659  37.078  1.00 25.00           C
ATOM     66  CA  LYS    66      33.895  55.358  36.053  1.00 25.00           C
ATOM     67  CA  PRO    67      34.981  57.605  38.895  1.00 25.00           C
ATOM     68  CA  PRO    68      37.294  55.264  40.832  1.00 25.00           C
ATOM     69  CA  GLN    69      39.439  53.312  38.393  1.00 25.00           C
ATOM     70  CA  LEU    70      36.809  50.607  39.002  1.00 25.00           C
ATOM     71  CA  ILE    71      38.449  49.954  42.401  1.00 25.00           C
ATOM     72  CA  ASP    72      35.475  51.587  44.178  1.00 25.00           C
ATOM     73  CA  TYR    73      33.048  49.417  42.161  1.00 25.00           C
ATOM     74  CA  LEU    74      35.044  46.282  43.083  1.00 25.00           C
ATOM     75  CA  GLN    75      34.958  47.285  46.778  1.00 25.00           C
ATOM     76  CA  GLN    76      31.171  47.816  46.572  1.00 25.00           C
ATOM     77  CA  LYS    77      30.752  44.373  44.947  1.00 25.00           C
ATOM     78  CA  LYS    78      32.864  42.783  47.717  1.00 25.00           C
ATOM     79  CA  THR    79      30.729  44.522  50.378  1.00 25.00           C
ATOM     80  CA  GLU    80      27.460  42.677  49.516  1.00 25.00           C
ATOM     81  CA  GLY    81      28.888  39.291  48.405  1.00 25.00           C
ATOM     82  CA  TYR    82      28.741  39.189  44.595  1.00 25.00           C
ATOM     83  CA  THR    83      28.689  41.653  41.647  1.00 25.00           C
ATOM     84  CA  ILE    84      29.757  43.180  38.331  1.00 25.00           C
ATOM     85  CA  ILE    85      32.131  44.585  35.702  1.00 25.00           C
ATOM     86  CA  GLY    86      33.780  41.209  35.340  1.00 25.00           C
ATOM     87  CA  VAL    87      34.629  40.979  31.681  1.00 25.00           C
ATOM     88  CA  GLU    88      36.764  40.691  28.563  1.00 25.00           C
ATOM     89  CA  GLN    89      34.793  39.424  25.608  1.00 25.00           C
ATOM     90  CA  THR    90      33.249  37.494  22.664  1.00 25.00           C
ATOM     91  CA  ALA    91      32.591  34.458  20.410  1.00 25.00           C
ATOM     92  CA  LYS    92      33.705  30.841  20.790  1.00 25.00           C
ATOM     93  CA  SER    93      36.994  30.147  22.628  1.00 25.00           C
ATOM     94  CA  LEU    94      37.255  28.880  26.213  1.00 25.00           C
ATOM     95  CA  ASP    95      33.489  29.081  26.046  1.00 25.00           C
ATOM     96  CA  LEU    96      30.543  29.921  28.385  1.00 25.00           C
ATOM     97  CA  THR    97      30.306  26.106  28.613  1.00 25.00           C
ATOM     98  CA  GLN    98      32.825  26.097  31.497  1.00 25.00           C
ATOM     99  CA  TYR    99      32.083  29.107  33.691  1.00 25.00           C
ATOM    100  CA  CYS   100      29.702  28.499  36.600  1.00 25.00           C
ATOM    101  CA  PHE   101      26.661  30.853  36.320  1.00 25.00           C
ATOM    102  CA  PRO   102      24.549  30.537  39.476  1.00 25.00           C
ATOM    103  CA  GLU   103      27.884  30.924  41.227  1.00 25.00           C
ATOM    104  CA  LYS   104      26.521  34.359  42.066  1.00 25.00           C
ATOM    105  CA  SER   105      27.160  36.520  39.016  1.00 25.00           C
ATOM    106  CA  LEU   106      29.877  38.316  37.096  1.00 25.00           C
ATOM    107  CA  LEU   107      27.921  38.704  33.845  1.00 25.00           C
ATOM    108  CA  LEU   108      29.602  41.443  31.860  1.00 25.00           C
ATOM    109  CA  LEU   109      30.528  42.612  28.308  1.00 25.00           C
ATOM    110  CA  GLY   110      32.845  45.074  26.595  1.00 25.00           C
ATOM    111  CA  ASN   111      32.382  47.534  23.679  1.00 25.00           C
ATOM    112  CA  GLU   112      32.411  47.993  19.863  1.00 25.00           C
ATOM    113  CA  ARG   113      36.168  48.268  20.052  1.00 25.00           C
ATOM    114  CA  GLU   114      39.450  47.116  21.659  1.00 25.00           C
ATOM    115  CA  GLY   115      37.395  47.158  24.821  1.00 25.00           C
ATOM    116  CA  ILE   116      37.621  46.658  28.567  1.00 25.00           C
ATOM    117  CA  PRO   117      41.141  48.047  29.084  1.00 25.00           C
ATOM    118  CA  ALA   118      43.637  45.785  30.919  1.00 25.00           C
ATOM    119  CA  ASN   119      42.204  46.898  34.293  1.00 25.00           C
ATOM    120  CA  LEU   120      38.835  45.302  33.414  1.00 25.00           C
ATOM    121  CA  ILE   121      40.602  42.045  32.447  1.00 25.00           C
ATOM    122  CA  GLN   122      42.520  42.073  35.762  1.00 25.00           C
ATOM    123  CA  GLN   123      39.251  42.622  37.678  1.00 25.00           C
ATOM    124  CA  LEU   124      38.179  39.054  36.789  1.00 25.00           C
ATOM    125  CA  ASP   125      38.391  35.628  38.438  1.00 25.00           C
ATOM    126  CA  VAL   126      38.057  34.290  34.875  1.00 25.00           C
ATOM    127  CA  CYS   127      36.781  36.283  31.824  1.00 25.00           C
ATOM    128  CA  VAL   128      34.346  35.360  29.029  1.00 25.00           C
ATOM    129  CA  GLU   129      35.887  34.225  25.720  1.00 25.00           C
ATOM    130  CA  ILE   130      37.700  35.215  22.526  1.00 25.00           C
ATOM    131  CA  PRO   131      37.684  33.881  18.964  1.00 25.00           C
ATOM    132  CA  GLN   132      35.721  34.275  15.765  1.00 25.00           C
ATOM    133  CA  GLN   133      35.270  31.803  12.967  1.00 25.00           C
ATOM    134  CA  GLY   134      36.239  33.358   9.579  1.00 25.00           C
ATOM    135  CA  ILE   135      38.009  36.541  10.520  1.00 25.00           C
ATOM    136  CA  ILE   136      34.769  38.301  11.438  1.00 25.00           C
ATOM    137  CA  ARG   137      37.013  40.046  13.987  1.00 25.00           C
ATOM    138  CA  SER   138      33.808  40.852  15.729  1.00 25.00           C
ATOM    139  CA  LEU   139      30.533  40.223  17.507  1.00 25.00           C
ATOM    140  CA  ASN   140      28.366  43.250  16.844  1.00 25.00           C
ATOM    141  CA  VAL   141      28.061  43.798  20.627  1.00 25.00           C
ATOM    142  CA  HIS   142      24.852  44.175  22.684  1.00 25.00           C
ATOM    143  CA  VAL   143      23.175  41.422  20.617  1.00 25.00           C
ATOM    144  CA  SER   144      26.194  39.132  21.169  1.00 25.00           C
ATOM    145  CA  GLY   145      26.052  39.813  24.936  1.00 25.00           C
ATOM    146  CA  ALA   146      22.309  38.998  24.966  1.00 25.00           C
ATOM    147  CA  LEU   147      22.980  35.732  23.081  1.00 25.00           C
ATOM    148  CA  LEU   148      25.718  34.814  25.597  1.00 25.00           C
ATOM    149  CA  ILE   149      23.324  35.531  28.500  1.00 25.00           C
ATOM    150  CA  TRP   150      20.646  33.333  26.868  1.00 25.00           C
ATOM    151  CA  GLU   151      23.198  30.512  26.423  1.00 25.00           C
ATOM    152  CA  TYR   152      24.218  30.821  30.101  1.00 25.00           C
ATOM    153  CA  THR   153      20.541  30.668  31.159  1.00 25.00           C
ATOM    154  CA  ARG   154      20.026  27.543  29.005  1.00 25.00           C
ATOM    155  CA  GLN   155      23.111  25.914  30.586  1.00 25.00           C
ATOM    156  CA  GLN   156      21.782  26.737  34.083  1.00 25.00           C
ATOM    157  CA  LEU   157      19.920  23.449  34.413  1.00 25.00           C
ATOM    158  CA  LEU   158      22.395  20.812  35.591  1.00 25.00           C
ATOM    159  CA  SER   159      22.367  22.377  38.989  1.00 25.00           C
TER
END
