
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  149 ( 1129),  selected  149 , name T0317_D1.pdb
# PARAMETERS: T0317TS393_2-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      R      13           -
LGA    V      14      V      14           -
LGA    A      15      A      15          3.675
LGA    P      16      P      16          2.515
LGA    A      17      A      17          3.655
LGA    L      18      L      18          3.320
LGA    F      19      F      19          1.377
LGA    I      20      I      20          2.185
LGA    G      21      G      21          3.101
LGA    N      22      N      22          1.775
LGA    A      23      A      23          5.422
LGA    R      24      R      24          2.590
LGA    A      25      A      25          2.909
LGA    A      26      A      26          2.459
LGA    G      27      G      27          0.761
LGA    -       -      A      28           -
LGA    A      28      T      29          1.138
LGA    T      29      E      30          4.536
LGA    E      30      L      31          1.276
LGA    L      31      -       -           -
LGA    L      32      L      32          1.741
LGA    V      33      V      33          1.086
LGA    R      34      R      34          1.448
LGA    A      35      A      35          3.239
LGA    G      36      G      36          3.104
LGA    I      37      I      37          2.317
LGA    T      38      T      38          1.823
LGA    L      39      L      39          1.891
LGA    C      40      C      40          1.660
LGA    V      41      V      41          1.519
LGA    N      42      N      42          2.179
LGA    V      43      V      43          1.851
LGA    S      44      S      44          1.887
LGA    R      45      R      45          2.120
LGA    Q      46      Q      46          3.412
LGA    Q      47      Q      47          3.567
LGA    P      48      P      48          3.056
LGA    G      49      G      49           #
LGA    P      50      P      50          4.222
LGA    R      51      R      51          1.374
LGA    A      52      A      52          0.614
LGA    P      53      P      53          1.630
LGA    G      54      G      54          1.749
LGA    V      55      V      55          1.295
LGA    A      56      A      56          1.285
LGA    E      57      E      57          2.961
LGA    L      58      L      58          1.916
LGA    R      59      R      59          2.091
LGA    V      60      V      60          1.072
LGA    P      61      P      61          2.242
LGA    V      62      V      62          0.581
LGA    F      63      F      63          1.555
LGA    -       -      D      64           -
LGA    -       -      D      65           -
LGA    -       -      P      66           -
LGA    D      64      A      67           #
LGA    D      65      E      68          3.046
LGA    P      66      D      69          2.367
LGA    A      67      -       -           -
LGA    E      68      -       -           -
LGA    D      69      -       -           -
LGA    L      70      L      70          1.335
LGA    L      71      L      71          1.606
LGA    T      72      T      72          2.412
LGA    H      73      H      73          1.590
LGA    L      74      L      74          2.346
LGA    E      75      E      75          1.992
LGA    P      76      P      76          1.861
LGA    T      77      T      77          1.879
LGA    C      78      C      78          1.186
LGA    A      79      A      79          0.920
LGA    A      80      A      80          1.019
LGA    M      81      M      81          1.235
LGA    E      82      E      82          1.156
LGA    A      83      A      83          1.200
LGA    A      84      A      84          0.935
LGA    V      85      V      85          1.641
LGA    R      86      R      86          2.348
LGA    D      87      D      87          1.720
LGA    G      88      G      88          1.670
LGA    G      89      G      89          1.612
LGA    S      90      S      90          1.323
LGA    C      91      C      91          1.009
LGA    L      92      L      92          1.391
LGA    V      93      V      93          1.684
LGA    Y      94      Y      94          1.442
LGA    C      95      C      95          3.506
LGA    K      96      K      96          1.907
LGA    N      97      N      97          2.021
LGA    G      98      G      98          1.570
LGA    R      99      R      99          0.692
LGA    S     100      S     100          1.784
LGA    R     101      R     101          0.874
LGA    S     102      S     102          1.231
LGA    A     103      A     103          1.255
LGA    A     104      A     104          0.711
LGA    V     105      V     105          0.721
LGA    C     106      C     106          0.784
LGA    T     107      T     107          0.582
LGA    A     108      A     108          0.502
LGA    Y     109      Y     109          0.708
LGA    L     110      L     110          0.515
LGA    M     111      M     111          0.366
LGA    R     112      R     112          0.803
LGA    H     113      H     113          1.835
LGA    R     114      R     114          4.885
LGA    G     115      G     115          2.949
LGA    H     116      H     116          1.110
LGA    S     117      S     117          0.951
LGA    L     118      L     118          0.560
LGA    D     119      D     119          0.653
LGA    R     120      R     120          0.556
LGA    A     121      A     121          0.705
LGA    F     122      F     122          0.926
LGA    Q     123      Q     123          1.093
LGA    M     124      M     124          1.203
LGA    V     125      V     125          1.247
LGA    K     126      K     126          1.281
LGA    S     127      S     127          1.237
LGA    A     128      A     128          1.177
LGA    R     129      R     129          0.430
LGA    P     130      P     130          1.783
LGA    V     131      V     131          2.276
LGA    A     132      A     132          2.180
LGA    E     133      E     133          2.992
LGA    P     134      P     134           -
LGA    N     135      -       -           -
LGA    L     136      -       -           -
LGA    G     137      N     135          1.090
LGA    F     138      -       -           -
LGA    W     139      L     136          5.156
LGA    A     140      G     137          4.573
LGA    Q     141      F     138          2.023
LGA    L     142      W     139          2.967
LGA    Q     143      A     140          3.274
LGA    K     144      Q     141          3.397
LGA    Y     145      L     142          3.324
LGA    E     146      Q     143          2.047
LGA    Q     147      K     144          3.628
LGA    T     148      Y     145           #
LGA    L     149      E     146          5.258
LGA    Q     150      Q     147          3.575
LGA    A     151      T     148           -
LGA    Q     152      L     149           -
LGA    A     153      Q     150           -
LGA    I     154      A     151           -
LGA    L     155      Q     152           -
LGA    P     156      A     153           -
LGA    R     157      I     154           -
LGA    E     158      L     155           -
LGA    -       -      P     156           -
LGA    -       -      R     157           -
LGA    -       -      E     158           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  149    5.0    125    2.23    87.20     65.903     5.357

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.897018 * X  +  -0.126274 * Y  +  -0.423573 * Z  +  31.077259
  Y_new =  -0.432655 * X  +   0.054889 * Y  +   0.899887 * Z  +  31.195709
  Z_new =  -0.090383 * X  +   0.990476 * Y  +  -0.103870 * Z  +   5.918545 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.675283   -1.466310  [ DEG:    95.9866    -84.0134 ]
  Theta =   0.090506    3.051086  [ DEG:     5.1856    174.8144 ]
  Phi   =  -2.692184    0.449409  [ DEG:  -154.2508     25.7492 ]
 
# 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_2-D1                               
REMARK     2: T0317_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0317TS393_2-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  125   2.23   87.20  65.903
REMARK  ---------------------------------------------------------- 
MOLECULE T0317TS393_2-D1
PFRMAT TS
TARGET T0317
MODEL 2
PARENT N/A
ATOM     10  CA  PRO    10      39.569  36.155 -13.980  1.00 25.00           C
ATOM     11  CA  PHE    11      39.507  36.819 -10.239  1.00 25.00           C
ATOM     12  CA  ALA    12      43.230  36.343 -10.386  1.00 25.00           C
ATOM     13  CA  ARG    13      45.493  35.428  -7.516  1.00 25.00           C
ATOM     14  CA  VAL    14      43.569  33.467  -4.883  1.00 25.00           C
ATOM     15  CA  ALA    15      40.074  32.056  -4.365  1.00 25.00           C
ATOM     16  CA  PRO    16      38.228  30.230  -1.651  1.00 25.00           C
ATOM     17  CA  ALA    17      37.834  28.428   1.724  1.00 25.00           C
ATOM     18  CA  LEU    18      34.262  28.050   3.054  1.00 25.00           C
ATOM     19  CA  PHE    19      32.049  27.615  -0.063  1.00 25.00           C
ATOM     20  CA  ILE    20      28.670  25.932  -0.092  1.00 25.00           C
ATOM     21  CA  GLY    21      27.136  22.419  -0.549  1.00 25.00           C
ATOM     22  CA  ASN    22      23.452  23.467  -0.338  1.00 25.00           C
ATOM     23  CA  ALA    23      20.772  21.422  -1.973  1.00 25.00           C
ATOM     24  CA  ARG    24      21.338  17.775  -3.056  1.00 25.00           C
ATOM     25  CA  ALA    25      24.861  19.062  -3.681  1.00 25.00           C
ATOM     26  CA  ALA    26      25.877  16.844  -0.761  1.00 25.00           C
ATOM     27  CA  GLY    27      26.196  13.233  -1.705  1.00 25.00           C
ATOM     28  CA  ALA    28      29.487  12.172  -3.245  1.00 25.00           C
ATOM     29  CA  THR    29      29.563  15.813  -4.432  1.00 25.00           C
ATOM     30  CA  GLU    30      31.473  15.976  -7.747  1.00 25.00           C
ATOM     31  CA  LEU    31      32.450  19.609  -7.034  1.00 25.00           C
ATOM     32  CA  LEU    32      33.669  18.622  -3.540  1.00 25.00           C
ATOM     33  CA  VAL    33      35.736  15.768  -5.040  1.00 25.00           C
ATOM     34  CA  ARG    34      37.267  18.184  -7.587  1.00 25.00           C
ATOM     35  CA  ALA    35      39.458  19.123  -4.600  1.00 25.00           C
ATOM     36  CA  GLY    36      41.092  16.392  -2.415  1.00 25.00           C
ATOM     37  CA  ILE    37      38.021  17.065  -0.257  1.00 25.00           C
ATOM     38  CA  THR    38      37.900  18.848   3.103  1.00 25.00           C
ATOM     39  CA  LEU    39      36.467  20.413   6.235  1.00 25.00           C
ATOM     40  CA  CYS    40      32.763  19.780   6.912  1.00 25.00           C
ATOM     41  CA  VAL    41      31.996  22.819   9.043  1.00 25.00           C
ATOM     42  CA  ASN    42      28.297  22.364   9.886  1.00 25.00           C
ATOM     43  CA  VAL    43      24.588  23.272  10.390  1.00 25.00           C
ATOM     44  CA  SER    44      22.002  20.457  10.742  1.00 25.00           C
ATOM     45  CA  ARG    45      22.050  17.340  12.939  1.00 25.00           C
ATOM     46  CA  GLN    46      22.061  13.678  11.774  1.00 25.00           C
ATOM     47  CA  GLN    47      23.856  14.589   8.546  1.00 25.00           C
ATOM     48  CA  PRO    48      23.794  11.252   6.707  1.00 25.00           C
ATOM     49  CA  GLY    49      26.591   9.462   8.504  1.00 25.00           C
ATOM     50  CA  PRO    50      29.341   9.852   5.965  1.00 25.00           C
ATOM     51  CA  ARG    51      30.274   8.114   2.729  1.00 25.00           C
ATOM     52  CA  ALA    52      32.887  10.073   0.843  1.00 25.00           C
ATOM     53  CA  PRO    53      36.312   9.724  -0.865  1.00 25.00           C
ATOM     54  CA  GLY    54      37.497  10.938   2.577  1.00 25.00           C
ATOM     55  CA  VAL    55      35.288  13.847   3.639  1.00 25.00           C
ATOM     56  CA  ALA    56      35.613  15.503   7.080  1.00 25.00           C
ATOM     57  CA  GLU    57      34.854  16.842  10.566  1.00 25.00           C
ATOM     58  CA  LEU    58      33.154  19.421  12.737  1.00 25.00           C
ATOM     59  CA  ARG    59      30.069  17.799  14.381  1.00 25.00           C
ATOM     60  CA  VAL    60      28.636  21.237  15.122  1.00 25.00           C
ATOM     61  CA  PRO    61      26.060  22.485  17.633  1.00 25.00           C
ATOM     62  CA  VAL    62      23.654  24.973  15.936  1.00 25.00           C
ATOM     63  CA  PHE    63      19.944  24.530  16.690  1.00 25.00           C
ATOM     64  CA  ASP    64      20.929  25.735  20.141  1.00 25.00           C
ATOM     65  CA  ASP    65      21.731  28.591  22.500  1.00 25.00           C
ATOM     66  CA  PRO    66      23.200  31.423  20.451  1.00 25.00           C
ATOM     67  CA  ALA    67      25.183  32.042  23.610  1.00 25.00           C
ATOM     68  CA  GLU    68      28.900  32.316  22.805  1.00 25.00           C
ATOM     69  CA  ASP    69      28.492  28.576  22.086  1.00 25.00           C
ATOM     70  CA  LEU    70      27.773  29.338  18.402  1.00 25.00           C
ATOM     71  CA  LEU    71      30.894  31.551  18.224  1.00 25.00           C
ATOM     72  CA  THR    72      32.993  28.758  19.793  1.00 25.00           C
ATOM     73  CA  HIS    73      31.606  26.254  17.249  1.00 25.00           C
ATOM     74  CA  LEU    74      32.451  28.654  14.387  1.00 25.00           C
ATOM     75  CA  GLU    75      36.007  29.063  15.749  1.00 25.00           C
ATOM     76  CA  PRO    76      36.390  25.259  15.961  1.00 25.00           C
ATOM     77  CA  THR    77      35.164  24.908  12.350  1.00 25.00           C
ATOM     78  CA  CYS    78      37.670  27.573  11.214  1.00 25.00           C
ATOM     79  CA  ALA    79      40.489  25.736  13.044  1.00 25.00           C
ATOM     80  CA  ALA    80      39.467  22.447  11.367  1.00 25.00           C
ATOM     81  CA  MET    81      39.466  24.165   7.944  1.00 25.00           C
ATOM     82  CA  GLU    82      42.952  25.595   8.633  1.00 25.00           C
ATOM     83  CA  ALA    83      44.205  22.118   9.640  1.00 25.00           C
ATOM     84  CA  ALA    84      42.748  20.634   6.425  1.00 25.00           C
ATOM     85  CA  VAL    85      44.463  23.364   4.358  1.00 25.00           C
ATOM     86  CA  ARG    86      47.788  22.638   6.114  1.00 25.00           C
ATOM     87  CA  ASP    87      47.806  19.689   3.755  1.00 25.00           C
ATOM     88  CA  GLY    88      45.677  20.041   0.564  1.00 25.00           C
ATOM     89  CA  GLY    89      42.306  21.687   0.015  1.00 25.00           C
ATOM     90  CA  SER    90      38.908  23.384  -0.561  1.00 25.00           C
ATOM     91  CA  CYS    91      36.214  23.522   2.179  1.00 25.00           C
ATOM     92  CA  LEU    92      32.758  22.108   1.651  1.00 25.00           C
ATOM     93  CA  VAL    93      30.235  23.494   4.178  1.00 25.00           C
ATOM     94  CA  TYR    94      26.635  22.544   4.776  1.00 25.00           C
ATOM     95  CA  CYS    95      23.112  21.166   4.617  1.00 25.00           C
ATOM     96  CA  LYS    96      19.620  21.078   6.163  1.00 25.00           C
ATOM     97  CA  ASN    97      19.522  24.699   4.904  1.00 25.00           C
ATOM     98  CA  GLY    98      22.403  27.121   4.198  1.00 25.00           C
ATOM     99  CA  ARG    99      20.926  30.603   4.631  1.00 25.00           C
ATOM    100  CA  SER   100      21.727  29.946   8.307  1.00 25.00           C
ATOM    101  CA  ARG   101      25.171  29.045   9.804  1.00 25.00           C
ATOM    102  CA  SER   102      27.780  27.819   7.284  1.00 25.00           C
ATOM    103  CA  ALA   103      27.951  31.312   5.723  1.00 25.00           C
ATOM    104  CA  ALA   104      28.421  32.866   9.191  1.00 25.00           C
ATOM    105  CA  VAL   105      31.228  30.374   9.953  1.00 25.00           C
ATOM    106  CA  CYS   106      32.922  31.227   6.627  1.00 25.00           C
ATOM    107  CA  THR   107      32.667  34.963   7.425  1.00 25.00           C
ATOM    108  CA  ALA   108      34.201  34.354  10.881  1.00 25.00           C
ATOM    109  CA  TYR   109      37.063  32.370   9.288  1.00 25.00           C
ATOM    110  CA  LEU   110      37.675  35.209   6.792  1.00 25.00           C
ATOM    111  CA  MET   111      37.740  37.748   9.657  1.00 25.00           C
ATOM    112  CA  ARG   112      40.245  35.568  11.565  1.00 25.00           C
ATOM    113  CA  HIS   113      42.450  35.327   8.442  1.00 25.00           C
ATOM    114  CA  ARG   114      43.656  38.862   9.240  1.00 25.00           C
ATOM    115  CA  GLY   115      41.112  41.664   8.698  1.00 25.00           C
ATOM    116  CA  HIS   116      38.291  41.521   6.151  1.00 25.00           C
ATOM    117  CA  SER   117      36.423  43.862   8.494  1.00 25.00           C
ATOM    118  CA  LEU   118      33.635  41.405   9.147  1.00 25.00           C
ATOM    119  CA  ASP   119      31.569  43.769   6.953  1.00 25.00           C
ATOM    120  CA  ARG   120      33.796  42.961   3.943  1.00 25.00           C
ATOM    121  CA  ALA   121      33.364  39.212   4.602  1.00 25.00           C
ATOM    122  CA  PHE   122      29.566  39.658   4.803  1.00 25.00           C
ATOM    123  CA  GLN   123      29.594  41.587   1.494  1.00 25.00           C
ATOM    124  CA  MET   124      31.660  38.806  -0.138  1.00 25.00           C
ATOM    125  CA  VAL   125      29.193  36.179   1.156  1.00 25.00           C
ATOM    126  CA  LYS   126      26.261  38.208  -0.242  1.00 25.00           C
ATOM    127  CA  SER   127      28.025  38.466  -3.632  1.00 25.00           C
ATOM    128  CA  ALA   128      28.622  34.682  -3.637  1.00 25.00           C
ATOM    129  CA  ARG   129      25.537  32.739  -2.719  1.00 25.00           C
ATOM    130  CA  PRO   130      23.668  35.631  -4.448  1.00 25.00           C
ATOM    131  CA  VAL   131      20.557  34.972  -2.438  1.00 25.00           C
ATOM    132  CA  ALA   132      22.017  33.668   0.819  1.00 25.00           C
ATOM    133  CA  GLU   133      22.001  37.055   2.585  1.00 25.00           C
ATOM    134  CA  PRO   134      18.445  38.128   2.989  1.00 25.00           C
ATOM    135  CA  ASN   135      17.995  36.533   6.385  1.00 25.00           C
ATOM    136  CA  LEU   136      19.593  39.286   8.426  1.00 25.00           C
ATOM    137  CA  GLY   137      19.963  36.875  11.378  1.00 25.00           C
ATOM    138  CA  PHE   138      23.530  36.028  10.271  1.00 25.00           C
ATOM    139  CA  TRP   139      24.365  39.758  10.023  1.00 25.00           C
ATOM    140  CA  ALA   140      22.951  40.332  13.535  1.00 25.00           C
ATOM    141  CA  GLN   141      25.051  37.427  14.883  1.00 25.00           C
ATOM    142  CA  LEU   142      28.179  38.885  13.222  1.00 25.00           C
ATOM    143  CA  GLN   143      27.435  42.308  14.771  1.00 25.00           C
ATOM    144  CA  LYS   144      27.010  40.685  18.213  1.00 25.00           C
ATOM    145  CA  TYR   145      30.343  38.850  17.788  1.00 25.00           C
ATOM    146  CA  GLU   146      32.055  42.134  16.812  1.00 25.00           C
ATOM    147  CA  GLN   147      30.570  43.853  19.896  1.00 25.00           C
ATOM    148  CA  THR   148      31.817  40.995  22.119  1.00 25.00           C
ATOM    149  CA  LEU   149      35.313  41.293  20.583  1.00 25.00           C
ATOM    150  CA  GLN   150      35.294  45.071  21.212  1.00 25.00           C
ATOM    151  CA  ALA   151      33.249  48.108  22.353  1.00 25.00           C
ATOM    152  CA  GLN   152      33.285  51.696  23.579  1.00 25.00           C
ATOM    153  CA  ALA   153      32.020  54.233  21.043  1.00 25.00           C
ATOM    154  CA  ILE   154      28.396  55.048  21.555  1.00 25.00           C
ATOM    155  CA  LEU   155      27.754  57.697  18.971  1.00 25.00           C
ATOM    156  CA  PRO   156      25.320  59.174  16.452  1.00 25.00           C
ATOM    157  CA  ARG   157      22.130  57.255  15.686  1.00 25.00           C
ATOM    158  CA  GLU   158      22.327  57.107  11.880  1.00 25.00           C
TER
END
