
#######################################################
#                                                     #
#                        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  149 (  149),  selected  149 , name T0317TS393_1-D1
# Molecule2: number of CA atoms  149 ( 1129),  selected  149 , name T0317_D1.pdb
# PARAMETERS: T0317TS393_1-D1.T0317_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    P      10      P      10           -
LGA    F      11      F      11           -
LGA    A      12      A      12           -
LGA    R      13      -       -           -
LGA    V      14      -       -           -
LGA    A      15      R      13           #
LGA    -       -      V      14           -
LGA    -       -      A      15           -
LGA    P      16      P      16          1.944
LGA    A      17      A      17          3.121
LGA    L      18      L      18          3.177
LGA    F      19      F      19          1.755
LGA    I      20      I      20          0.332
LGA    G      21      G      21          1.634
LGA    N      22      N      22          2.013
LGA    A      23      A      23          5.515
LGA    R      24      R      24          4.062
LGA    A      25      A      25          3.099
LGA    A      26      A      26          2.990
LGA    G      27      G      27          2.194
LGA    A      28      A      28          3.152
LGA    T      29      T      29          2.419
LGA    E      30      E      30          1.222
LGA    L      31      L      31          2.284
LGA    L      32      L      32          1.460
LGA    V      33      V      33          1.682
LGA    R      34      R      34          2.591
LGA    A      35      A      35          2.993
LGA    G      36      G      36          1.901
LGA    I      37      I      37          1.030
LGA    T      38      T      38          1.782
LGA    L      39      L      39          1.668
LGA    C      40      C      40          1.246
LGA    V      41      V      41          0.849
LGA    N      42      N      42          1.535
LGA    V      43      V      43          2.001
LGA    S      44      S      44          1.993
LGA    R      45      R      45          2.371
LGA    Q      46      Q      46          1.949
LGA    Q      47      Q      47          2.709
LGA    P      48      P      48          3.731
LGA    G      49      G      49           #
LGA    P      50      P      50          4.794
LGA    R      51      R      51          3.121
LGA    A      52      A      52          3.259
LGA    P      53      P      53          2.072
LGA    G      54      G      54          2.451
LGA    V      55      V      55          2.436
LGA    A      56      A      56          2.461
LGA    E      57      E      57          1.963
LGA    L      58      L      58          1.898
LGA    R      59      R      59          2.728
LGA    V      60      V      60          1.254
LGA    P      61      P      61          0.849
LGA    V      62      V      62          1.475
LGA    F      63      F      63          0.552
LGA    -       -      D      64           -
LGA    D      64      D      65          4.009
LGA    -       -      P      66           -
LGA    D      65      A      67           #
LGA    P      66      E      68          2.489
LGA    A      67      D      69          3.606
LGA    E      68      -       -           -
LGA    D      69      -       -           -
LGA    L      70      L      70          1.370
LGA    L      71      L      71          2.171
LGA    T      72      T      72          2.902
LGA    H      73      H      73          1.845
LGA    L      74      L      74          2.163
LGA    E      75      E      75          2.018
LGA    P      76      P      76          2.395
LGA    T      77      T      77          2.286
LGA    C      78      C      78          1.498
LGA    A      79      A      79          1.668
LGA    A      80      A      80          1.793
LGA    M      81      M      81          1.612
LGA    E      82      E      82          1.821
LGA    A      83      A      83          2.122
LGA    A      84      A      84          1.491
LGA    V      85      V      85          1.955
LGA    R      86      R      86          3.163
LGA    D      87      D      87          2.805
LGA    G      88      G      88          2.174
LGA    G      89      G      89          2.205
LGA    S      90      S      90          1.585
LGA    C      91      C      91          0.533
LGA    L      92      L      92          1.050
LGA    V      93      V      93          1.190
LGA    Y      94      Y      94          1.483
LGA    C      95      C      95          2.852
LGA    K      96      K      96          1.029
LGA    N      97      N      97          1.844
LGA    G      98      G      98          1.395
LGA    R      99      R      99          1.451
LGA    S     100      S     100          1.838
LGA    R     101      R     101          1.528
LGA    S     102      S     102          0.674
LGA    A     103      A     103          0.765
LGA    A     104      A     104          1.612
LGA    V     105      V     105          1.221
LGA    C     106      C     106          0.563
LGA    T     107      T     107          1.697
LGA    A     108      A     108          1.764
LGA    Y     109      Y     109          0.457
LGA    L     110      L     110          1.484
LGA    M     111      M     111          2.343
LGA    R     112      R     112          1.362
LGA    H     113      H     113          1.629
LGA    R     114      R     114          2.654
LGA    G     115      G     115          2.192
LGA    H     116      H     116          1.440
LGA    S     117      S     117          1.602
LGA    L     118      L     118          1.284
LGA    D     119      D     119          0.943
LGA    R     120      R     120          0.639
LGA    A     121      A     121          0.979
LGA    F     122      F     122          0.781
LGA    Q     123      Q     123          0.935
LGA    M     124      M     124          1.203
LGA    V     125      V     125          1.377
LGA    K     126      K     126          1.429
LGA    S     127      S     127          1.469
LGA    A     128      A     128          1.592
LGA    R     129      R     129          1.375
LGA    P     130      P     130          2.007
LGA    V     131      V     131          3.886
LGA    A     132      A     132          3.380
LGA    E     133      E     133          4.629
LGA    P     134      P     134           #
LGA    N     135      N     135          2.792
LGA    L     136      L     136          1.646
LGA    G     137      G     137          2.172
LGA    F     138      F     138          3.091
LGA    W     139      W     139          2.072
LGA    A     140      A     140          0.891
LGA    Q     141      Q     141          1.950
LGA    L     142      L     142          1.959
LGA    Q     143      Q     143          0.935
LGA    K     144      K     144          0.704
LGA    Y     145      Y     145          1.148
LGA    E     146      E     146          1.427
LGA    Q     147      Q     147          1.275
LGA    T     148      T     148          0.727
LGA    L     149      L     149          1.526
LGA    Q     150      Q     150          2.285
LGA    A     151      A     151          4.300
LGA    Q     152      Q     152           -
LGA    A     153      A     153           -
LGA    I     154      I     154           -
LGA    L     155      L     155           -
LGA    P     156      P     156           -
LGA    R     157      R     157           -
LGA    E     158      E     158           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  149    5.0    131    2.18    98.47     64.006     5.749

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.237445 * X  +  -0.903055 * Y  +  -0.357928 * Z  +  31.473560
  Y_new =  -0.065307 * X  +  -0.352791 * Y  +   0.933420 * Z  +  31.179750
  Z_new =  -0.969203 * X  +   0.245011 * Y  +   0.024793 * Z  +   5.804590 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.469950   -1.671643  [ DEG:    84.2219    -95.7781 ]
  Theta =   1.321974    1.819618  [ DEG:    75.7435    104.2565 ]
  Phi   =  -2.873188    0.268404  [ DEG:  -164.6216     15.3784 ]
 
# 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: T0317TS393_1-D1                               
REMARK     2: T0317_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0317TS393_1-D1.T0317_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  149  149   5.0  131   2.18   98.47  64.006
REMARK  ---------------------------------------------------------- 
MOLECULE T0317TS393_1-D1
PFRMAT TS
TARGET T0317
MODEL 1
PARENT N/A
ATOM     10  CA  PRO    10      36.553  41.347 -14.591  1.00 25.00           C
ATOM     11  CA  PHE    11      37.808  39.624 -11.439  1.00 25.00           C
ATOM     12  CA  ALA    12      39.818  37.481 -13.858  1.00 25.00           C
ATOM     13  CA  ARG    13      41.883  35.228 -11.675  1.00 25.00           C
ATOM     14  CA  VAL    14      40.489  32.460  -9.397  1.00 25.00           C
ATOM     15  CA  ALA    15      39.483  32.843  -5.722  1.00 25.00           C
ATOM     16  CA  PRO    16      39.110  31.273  -2.229  1.00 25.00           C
ATOM     17  CA  ALA    17      38.521  29.046   0.763  1.00 25.00           C
ATOM     18  CA  LEU    18      35.734  29.397   3.411  1.00 25.00           C
ATOM     19  CA  PHE    19      33.132  28.092   0.912  1.00 25.00           C
ATOM     20  CA  ILE    20      29.415  27.660   1.114  1.00 25.00           C
ATOM     21  CA  GLY    21      27.867  24.264   0.180  1.00 25.00           C
ATOM     22  CA  ASN    22      24.095  24.573  -0.182  1.00 25.00           C
ATOM     23  CA  ALA    23      22.209  22.035  -2.298  1.00 25.00           C
ATOM     24  CA  ARG    24      23.501  19.334  -4.551  1.00 25.00           C
ATOM     25  CA  ALA    25      27.235  19.133  -3.967  1.00 25.00           C
ATOM     26  CA  ALA    26      27.167  18.115  -0.275  1.00 25.00           C
ATOM     27  CA  GLY    27      24.993  15.254  -1.577  1.00 25.00           C
ATOM     28  CA  ALA    28      28.358  13.361  -1.527  1.00 25.00           C
ATOM     29  CA  THR    29      30.061  14.705  -4.661  1.00 25.00           C
ATOM     30  CA  GLU    30      32.089  14.152  -7.862  1.00 25.00           C
ATOM     31  CA  LEU    31      33.851  17.514  -7.356  1.00 25.00           C
ATOM     32  CA  LEU    32      34.665  16.570  -3.735  1.00 25.00           C
ATOM     33  CA  VAL    33      36.075  13.206  -4.904  1.00 25.00           C
ATOM     34  CA  ARG    34      38.225  14.990  -7.524  1.00 25.00           C
ATOM     35  CA  ALA    35      39.120  18.519  -6.414  1.00 25.00           C
ATOM     36  CA  GLY    36      40.204  17.041  -3.104  1.00 25.00           C
ATOM     37  CA  ILE    37      38.028  18.652  -0.411  1.00 25.00           C
ATOM     38  CA  THR    38      37.531  18.370   3.335  1.00 25.00           C
ATOM     39  CA  LEU    39      35.635  18.948   6.602  1.00 25.00           C
ATOM     40  CA  CYS    40      31.835  19.301   6.082  1.00 25.00           C
ATOM     41  CA  VAL    41      31.235  21.944   8.801  1.00 25.00           C
ATOM     42  CA  ASN    42      27.841  20.845  10.150  1.00 25.00           C
ATOM     43  CA  VAL    43      24.636  22.943   9.846  1.00 25.00           C
ATOM     44  CA  SER    44      22.950  19.708  10.924  1.00 25.00           C
ATOM     45  CA  ARG    45      21.880  16.882  13.246  1.00 25.00           C
ATOM     46  CA  GLN    46      19.818  15.000  10.705  1.00 25.00           C
ATOM     47  CA  GLN    47      21.455  14.625   7.337  1.00 25.00           C
ATOM     48  CA  PRO    48      21.402  11.199   5.717  1.00 25.00           C
ATOM     49  CA  GLY    49      24.503   9.166   5.028  1.00 25.00           C
ATOM     50  CA  PRO    50      27.704   8.577   2.984  1.00 25.00           C
ATOM     51  CA  ARG    51      30.491   8.459   5.620  1.00 25.00           C
ATOM     52  CA  ALA    52      32.312  10.972   3.421  1.00 25.00           C
ATOM     53  CA  PRO    53      34.892   8.676   1.762  1.00 25.00           C
ATOM     54  CA  GLY    54      37.607  10.462   3.751  1.00 25.00           C
ATOM     55  CA  VAL    55      36.782  13.694   5.520  1.00 25.00           C
ATOM     56  CA  ALA    56      36.682  14.657   9.250  1.00 25.00           C
ATOM     57  CA  GLU    57      33.446  16.346  10.298  1.00 25.00           C
ATOM     58  CA  LEU    58      33.533  19.412  12.554  1.00 25.00           C
ATOM     59  CA  ARG    59      30.682  18.759  15.064  1.00 25.00           C
ATOM     60  CA  VAL    60      29.020  22.145  15.605  1.00 25.00           C
ATOM     61  CA  PRO    61      25.388  21.777  16.606  1.00 25.00           C
ATOM     62  CA  VAL    62      23.179  24.329  14.881  1.00 25.00           C
ATOM     63  CA  PHE    63      19.879  25.770  16.066  1.00 25.00           C
ATOM     64  CA  ASP    64      19.849  28.452  18.731  1.00 25.00           C
ATOM     65  CA  ASP    65      21.958  27.452  21.746  1.00 25.00           C
ATOM     66  CA  PRO    66      23.030  31.071  21.651  1.00 25.00           C
ATOM     67  CA  ALA    67      25.995  32.966  23.218  1.00 25.00           C
ATOM     68  CA  GLU    68      29.692  32.188  22.910  1.00 25.00           C
ATOM     69  CA  ASP    69      28.783  28.640  21.793  1.00 25.00           C
ATOM     70  CA  LEU    70      28.312  29.867  18.196  1.00 25.00           C
ATOM     71  CA  LEU    71      31.720  31.609  18.317  1.00 25.00           C
ATOM     72  CA  THR    72      33.343  28.397  19.627  1.00 25.00           C
ATOM     73  CA  HIS    73      31.707  26.389  16.806  1.00 25.00           C
ATOM     74  CA  LEU    74      32.987  28.919  14.231  1.00 25.00           C
ATOM     75  CA  GLU    75      36.515  28.667  15.702  1.00 25.00           C
ATOM     76  CA  PRO    76      36.344  24.845  15.522  1.00 25.00           C
ATOM     77  CA  THR    77      35.211  25.044  11.869  1.00 25.00           C
ATOM     78  CA  CYS    78      38.111  27.416  11.073  1.00 25.00           C
ATOM     79  CA  ALA    79      40.571  25.014  12.758  1.00 25.00           C
ATOM     80  CA  ALA    80      39.153  22.096  10.724  1.00 25.00           C
ATOM     81  CA  MET    81      39.520  24.131   7.501  1.00 25.00           C
ATOM     82  CA  GLU    82      43.146  24.962   8.410  1.00 25.00           C
ATOM     83  CA  ALA    83      43.855  21.258   9.072  1.00 25.00           C
ATOM     84  CA  ALA    84      42.318  20.333   5.688  1.00 25.00           C
ATOM     85  CA  VAL    85      44.479  22.978   3.956  1.00 25.00           C
ATOM     86  CA  ARG    86      47.601  21.604   5.697  1.00 25.00           C
ATOM     87  CA  ASP    87      47.946  19.507   2.497  1.00 25.00           C
ATOM     88  CA  GLY    88      45.322  20.098  -0.249  1.00 25.00           C
ATOM     89  CA  GLY    89      42.064  21.984  -0.483  1.00 25.00           C
ATOM     90  CA  SER    90      38.643  23.709  -0.515  1.00 25.00           C
ATOM     91  CA  CYS    91      37.027  23.717   2.893  1.00 25.00           C
ATOM     92  CA  LEU    92      33.568  22.643   1.790  1.00 25.00           C
ATOM     93  CA  VAL    93      31.798  24.683   4.493  1.00 25.00           C
ATOM     94  CA  TYR    94      28.243  23.701   5.549  1.00 25.00           C
ATOM     95  CA  CYS    95      24.849  22.206   4.593  1.00 25.00           C
ATOM     96  CA  LYS    96      21.112  22.090   5.310  1.00 25.00           C
ATOM     97  CA  ASN    97      19.512  25.535   4.898  1.00 25.00           C
ATOM     98  CA  GLY    98      22.596  27.692   4.032  1.00 25.00           C
ATOM     99  CA  ARG    99      21.728  31.060   5.609  1.00 25.00           C
ATOM    100  CA  SER   100      22.532  30.660   9.325  1.00 25.00           C
ATOM    101  CA  ARG   101      25.108  27.873   9.570  1.00 25.00           C
ATOM    102  CA  SER   102      27.235  28.136   6.396  1.00 25.00           C
ATOM    103  CA  ALA   103      27.191  31.958   6.656  1.00 25.00           C
ATOM    104  CA  ALA   104      28.266  31.745  10.326  1.00 25.00           C
ATOM    105  CA  VAL   105      31.123  29.378   9.378  1.00 25.00           C
ATOM    106  CA  CYS   106      32.242  31.790   6.622  1.00 25.00           C
ATOM    107  CA  THR   107      32.183  34.699   9.113  1.00 25.00           C
ATOM    108  CA  ALA   108      34.270  32.655  11.588  1.00 25.00           C
ATOM    109  CA  TYR   109      36.791  31.835   8.824  1.00 25.00           C
ATOM    110  CA  LEU   110      37.015  35.543   7.894  1.00 25.00           C
ATOM    111  CA  MET   111      37.603  36.454  11.567  1.00 25.00           C
ATOM    112  CA  ARG   112      40.361  33.808  11.808  1.00 25.00           C
ATOM    113  CA  HIS   113      42.002  35.195   8.637  1.00 25.00           C
ATOM    114  CA  ARG   114      43.517  37.887   6.419  1.00 25.00           C
ATOM    115  CA  GLY   115      42.447  41.428   7.161  1.00 25.00           C
ATOM    116  CA  HIS   116      39.049  41.856   5.611  1.00 25.00           C
ATOM    117  CA  SER   117      37.520  41.801   9.146  1.00 25.00           C
ATOM    118  CA  LEU   118      33.933  40.674   9.044  1.00 25.00           C
ATOM    119  CA  ASP   119      31.911  43.164   6.951  1.00 25.00           C
ATOM    120  CA  ARG   120      33.935  42.227   3.838  1.00 25.00           C
ATOM    121  CA  ALA   121      33.311  38.510   4.520  1.00 25.00           C
ATOM    122  CA  PHE   122      29.561  39.187   4.904  1.00 25.00           C
ATOM    123  CA  GLN   123      29.544  41.116   1.596  1.00 25.00           C
ATOM    124  CA  MET   124      31.356  38.219  -0.132  1.00 25.00           C
ATOM    125  CA  VAL   125      28.800  35.743   1.284  1.00 25.00           C
ATOM    126  CA  LYS   126      25.932  37.949   0.028  1.00 25.00           C
ATOM    127  CA  SER   127      27.541  38.107  -3.444  1.00 25.00           C
ATOM    128  CA  ALA   128      27.906  34.294  -3.475  1.00 25.00           C
ATOM    129  CA  ARG   129      24.539  33.089  -2.192  1.00 25.00           C
ATOM    130  CA  PRO   130      21.584  35.461  -1.719  1.00 25.00           C
ATOM    131  CA  VAL   131      19.561  37.713   0.470  1.00 25.00           C
ATOM    132  CA  ALA   132      21.998  36.894   3.240  1.00 25.00           C
ATOM    133  CA  GLU   133      20.993  40.309   4.514  1.00 25.00           C
ATOM    134  CA  PRO   134      17.920  39.950   6.781  1.00 25.00           C
ATOM    135  CA  ASN   135      19.114  37.824   9.686  1.00 25.00           C
ATOM    136  CA  LEU   136      20.461  40.306  12.235  1.00 25.00           C
ATOM    137  CA  GLY   137      21.838  37.447  14.377  1.00 25.00           C
ATOM    138  CA  PHE   138      24.697  36.921  11.883  1.00 25.00           C
ATOM    139  CA  TRP   139      25.495  40.665  11.972  1.00 25.00           C
ATOM    140  CA  ALA   140      25.528  40.594  15.800  1.00 25.00           C
ATOM    141  CA  GLN   141      27.886  37.576  15.748  1.00 25.00           C
ATOM    142  CA  LEU   142      30.203  39.398  13.302  1.00 25.00           C
ATOM    143  CA  GLN   143      30.208  42.485  15.570  1.00 25.00           C
ATOM    144  CA  LYS   144      31.058  40.294  18.593  1.00 25.00           C
ATOM    145  CA  TYR   145      33.926  38.670  16.641  1.00 25.00           C
ATOM    146  CA  GLU   146      35.249  42.129  15.661  1.00 25.00           C
ATOM    147  CA  GLN   147      35.090  43.253  19.319  1.00 25.00           C
ATOM    148  CA  THR   148      36.992  40.106  20.394  1.00 25.00           C
ATOM    149  CA  LEU   149      39.658  40.778  17.728  1.00 25.00           C
ATOM    150  CA  GLN   150      40.000  44.393  18.944  1.00 25.00           C
ATOM    151  CA  ALA   151      39.565  46.452  22.047  1.00 25.00           C
ATOM    152  CA  GLN   152      37.158  49.313  22.411  1.00 25.00           C
ATOM    153  CA  ALA   153      36.604  52.847  23.696  1.00 25.00           C
ATOM    154  CA  ILE   154      35.347  55.536  21.321  1.00 25.00           C
ATOM    155  CA  LEU   155      35.737  56.532  17.660  1.00 25.00           C
ATOM    156  CA  PRO   156      32.863  58.659  16.537  1.00 25.00           C
ATOM    157  CA  ARG   157      29.154  58.894  15.773  1.00 25.00           C
ATOM    158  CA  GLU   158      28.700  58.706  11.964  1.00 25.00           C
TER
END
