
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms  149 ( 1129),  selected  149 , name T0317_D1.pdb
# PARAMETERS: T0317TS393_5-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          3.715
LGA    P      16      P      16          2.554
LGA    A      17      A      17          2.928
LGA    L      18      L      18          2.624
LGA    F      19      F      19          1.429
LGA    I      20      I      20          1.133
LGA    G      21      G      21          0.815
LGA    N      22      N      22          1.236
LGA    A      23      A      23           #
LGA    R      24      R      24          2.540
LGA    A      25      A      25          1.020
LGA    A      26      A      26          0.916
LGA    G      27      G      27          1.330
LGA    A      28      A      28          1.882
LGA    T      29      T      29          4.811
LGA    E      30      E      30          2.984
LGA    L      31      L      31          2.395
LGA    L      32      L      32          0.733
LGA    V      33      V      33          2.666
LGA    R      34      R      34          2.578
LGA    A      35      A      35          4.218
LGA    G      36      G      36          4.278
LGA    I      37      I      37          2.324
LGA    T      38      T      38          2.040
LGA    L      39      L      39          0.924
LGA    C      40      C      40          1.053
LGA    V      41      V      41          1.015
LGA    N      42      N      42          3.577
LGA    V      43      V      43          1.055
LGA    S      44      S      44          1.671
LGA    R      45      R      45          2.749
LGA    Q      46      Q      46          2.805
LGA    Q      47      Q      47          3.029
LGA    -       -      P      48           -
LGA    P      48      G      49           #
LGA    G      49      P      50           -
LGA    P      50      -       -           -
LGA    R      51      R      51          5.215
LGA    A      52      A      52          4.017
LGA    P      53      P      53          2.132
LGA    G      54      G      54          3.447
LGA    V      55      V      55          2.733
LGA    A      56      A      56          2.357
LGA    E      57      E      57          2.240
LGA    L      58      L      58          2.190
LGA    R      59      R      59          2.061
LGA    V      60      V      60          2.095
LGA    P      61      P      61          1.466
LGA    V      62      V      62          2.333
LGA    F      63      F      63          0.826
LGA    D      64      D      64           #
LGA    -       -      D      65           -
LGA    -       -      P      66           -
LGA    D      65      A      67           #
LGA    P      66      E      68          2.026
LGA    A      67      D      69          2.771
LGA    E      68      -       -           -
LGA    D      69      -       -           -
LGA    L      70      L      70          1.703
LGA    L      71      L      71          2.754
LGA    T      72      T      72          3.831
LGA    H      73      H      73          2.930
LGA    L      74      L      74          2.931
LGA    E      75      E      75          2.687
LGA    P      76      P      76          3.180
LGA    T      77      T      77          3.288
LGA    C      78      C      78          2.241
LGA    A      79      A      79          2.122
LGA    A      80      A      80          2.677
LGA    M      81      M      81          2.609
LGA    E      82      E      82          1.990
LGA    A      83      A      83          2.160
LGA    A      84      A      84          2.327
LGA    V      85      V      85          2.367
LGA    R      86      R      86          2.508
LGA    D      87      D      87          2.399
LGA    G      88      G      88          2.246
LGA    G      89      G      89          2.601
LGA    S      90      S      90          0.911
LGA    C      91      C      91          1.353
LGA    L      92      L      92          1.866
LGA    V      93      V      93          1.833
LGA    Y      94      Y      94          1.305
LGA    C      95      C      95          1.104
LGA    K      96      K      96          0.721
LGA    N      97      N      97          1.220
LGA    G      98      G      98          2.334
LGA    R      99      R      99          2.819
LGA    S     100      S     100          1.797
LGA    R     101      R     101          1.095
LGA    S     102      S     102          1.169
LGA    A     103      A     103          1.177
LGA    A     104      A     104          0.914
LGA    V     105      V     105          0.953
LGA    C     106      C     106          1.194
LGA    T     107      T     107          1.324
LGA    A     108      A     108          1.072
LGA    Y     109      Y     109          0.839
LGA    L     110      L     110          1.288
LGA    M     111      M     111          1.565
LGA    R     112      R     112          1.261
LGA    H     113      H     113          1.644
LGA    R     114      R     114          1.741
LGA    G     115      G     115          2.172
LGA    H     116      H     116          3.024
LGA    S     117      S     117          0.669
LGA    L     118      L     118          1.102
LGA    D     119      D     119          1.277
LGA    R     120      R     120          0.847
LGA    A     121      A     121          0.613
LGA    F     122      F     122          1.191
LGA    Q     123      Q     123          1.661
LGA    M     124      M     124          1.631
LGA    V     125      V     125          1.530
LGA    K     126      K     126          1.855
LGA    S     127      S     127          2.073
LGA    A     128      A     128          1.908
LGA    R     129      R     129          1.722
LGA    P     130      P     130          1.735
LGA    V     131      V     131          2.857
LGA    A     132      A     132          1.861
LGA    E     133      E     133          2.469
LGA    P     134      -       -           -
LGA    N     135      P     134          4.857
LGA    L     136      N     135          3.753
LGA    G     137      L     136          2.386
LGA    -       -      G     137           -
LGA    F     138      F     138          3.075
LGA    W     139      W     139          1.609
LGA    A     140      A     140          1.976
LGA    Q     141      Q     141          2.135
LGA    L     142      L     142          0.821
LGA    Q     143      Q     143          1.785
LGA    K     144      K     144          2.950
LGA    Y     145      Y     145          2.280
LGA    E     146      E     146          3.137
LGA    Q     147      Q     147          4.554
LGA    T     148      -       -           -
LGA    L     149      T     148          1.135
LGA    Q     150      L     149           -
LGA    A     151      Q     150           -
LGA    Q     152      A     151           -
LGA    A     153      Q     152           -
LGA    I     154      A     153           -
LGA    L     155      I     154           -
LGA    P     156      L     155           -
LGA    R     157      P     156           -
LGA    E     158      R     157           -
LGA    -       -      E     158           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  149    5.0    125    2.32    95.20     59.026     5.157

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.974468 * X  +   0.218657 * Y  +  -0.051011 * Z  +  31.731619
  Y_new =  -0.166383 * X  +  -0.550676 * Y  +   0.817969 * Z  +  31.229544
  Z_new =   0.150764 * X  +   0.805571 * Y  +   0.572997 * Z  +   6.383490 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.952532   -2.189061  [ DEG:    54.5760   -125.4240 ]
  Theta =  -0.151341   -2.990252  [ DEG:    -8.6712   -171.3288 ]
  Phi   =  -2.972481    0.169111  [ DEG:  -170.3106      9.6894 ]
 
# 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_5-D1                               
REMARK     2: T0317_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0317TS393_5-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   2.32   95.20  59.026
REMARK  ---------------------------------------------------------- 
MOLECULE T0317TS393_5-D1
PFRMAT TS
TARGET T0317
MODEL 5
PARENT N/A
ATOM     10  CA  PRO    10      43.329  39.314 -12.308  1.00 25.00           C
ATOM     11  CA  PHE    11      39.661  38.940 -11.159  1.00 25.00           C
ATOM     12  CA  ALA    12      39.836  35.331 -12.373  1.00 25.00           C
ATOM     13  CA  ARG    13      43.058  33.956 -10.884  1.00 25.00           C
ATOM     14  CA  VAL    14      42.214  33.927  -7.197  1.00 25.00           C
ATOM     15  CA  ALA    15      40.480  33.145  -3.886  1.00 25.00           C
ATOM     16  CA  PRO    16      39.464  31.602  -0.577  1.00 25.00           C
ATOM     17  CA  ALA    17      37.589  28.278  -0.735  1.00 25.00           C
ATOM     18  CA  LEU    18      35.463  29.774   2.106  1.00 25.00           C
ATOM     19  CA  PHE    19      32.977  27.054   1.030  1.00 25.00           C
ATOM     20  CA  ILE    20      29.247  26.989   1.823  1.00 25.00           C
ATOM     21  CA  GLY    21      26.876  24.680  -0.131  1.00 25.00           C
ATOM     22  CA  ASN    22      23.475  23.027   0.269  1.00 25.00           C
ATOM     23  CA  ALA    23      22.904  22.557  -3.469  1.00 25.00           C
ATOM     24  CA  ARG    24      21.931  18.917  -3.225  1.00 25.00           C
ATOM     25  CA  ALA    25      25.323  18.410  -1.676  1.00 25.00           C
ATOM     26  CA  ALA    26      27.053  16.196   0.867  1.00 25.00           C
ATOM     27  CA  GLY    27      25.962  12.728  -0.131  1.00 25.00           C
ATOM     28  CA  ALA    28      28.095  13.301  -3.277  1.00 25.00           C
ATOM     29  CA  THR    29      28.411  16.604  -5.205  1.00 25.00           C
ATOM     30  CA  GLU    30      31.051  15.884  -7.884  1.00 25.00           C
ATOM     31  CA  LEU    31      33.255  18.694  -6.503  1.00 25.00           C
ATOM     32  CA  LEU    32      32.892  17.275  -2.965  1.00 25.00           C
ATOM     33  CA  VAL    33      33.856  13.793  -4.237  1.00 25.00           C
ATOM     34  CA  ARG    34      36.927  15.258  -5.994  1.00 25.00           C
ATOM     35  CA  ALA    35      39.541  17.490  -4.366  1.00 25.00           C
ATOM     36  CA  GLY    36      40.045  15.025  -1.477  1.00 25.00           C
ATOM     37  CA  ILE    37      38.510  17.758   0.689  1.00 25.00           C
ATOM     38  CA  THR    38      39.394  17.364   4.339  1.00 25.00           C
ATOM     39  CA  LEU    39      36.492  19.272   6.009  1.00 25.00           C
ATOM     40  CA  CYS    40      32.708  19.281   6.328  1.00 25.00           C
ATOM     41  CA  VAL    41      32.180  21.987   8.954  1.00 25.00           C
ATOM     42  CA  ASN    42      29.301  22.375  11.488  1.00 25.00           C
ATOM     43  CA  VAL    43      25.575  22.759  10.789  1.00 25.00           C
ATOM     44  CA  SER    44      22.106  21.277  10.462  1.00 25.00           C
ATOM     45  CA  ARG    45      21.496  17.767  11.757  1.00 25.00           C
ATOM     46  CA  GLN    46      19.743  15.599   9.187  1.00 25.00           C
ATOM     47  CA  GLN    47      23.271  14.777   8.104  1.00 25.00           C
ATOM     48  CA  PRO    48      22.988  11.031   8.758  1.00 25.00           C
ATOM     49  CA  GLY    49      26.167  10.111  10.578  1.00 25.00           C
ATOM     50  CA  PRO    50      28.052   9.587   7.260  1.00 25.00           C
ATOM     51  CA  ARG    51      31.468   7.965   7.509  1.00 25.00           C
ATOM     52  CA  ALA    52      32.359   9.741   4.221  1.00 25.00           C
ATOM     53  CA  PRO    53      35.674   8.992   2.423  1.00 25.00           C
ATOM     54  CA  GLY    54      37.949  10.370   5.096  1.00 25.00           C
ATOM     55  CA  VAL    55      35.822  13.488   5.759  1.00 25.00           C
ATOM     56  CA  ALA    56      36.635  15.160   9.039  1.00 25.00           C
ATOM     57  CA  GLU    57      33.430  16.498  10.546  1.00 25.00           C
ATOM     58  CA  LEU    58      32.710  18.802  13.507  1.00 25.00           C
ATOM     59  CA  ARG    59      29.080  18.493  14.707  1.00 25.00           C
ATOM     60  CA  VAL    60      29.078  21.894  16.465  1.00 25.00           C
ATOM     61  CA  PRO    61      25.344  22.620  16.311  1.00 25.00           C
ATOM     62  CA  VAL    62      24.360  25.899  14.617  1.00 25.00           C
ATOM     63  CA  PHE    63      20.538  25.624  15.098  1.00 25.00           C
ATOM     64  CA  ASP    64      20.518  26.061  18.892  1.00 25.00           C
ATOM     65  CA  ASP    65      22.195  26.896  22.225  1.00 25.00           C
ATOM     66  CA  PRO    66      23.177  30.395  21.103  1.00 25.00           C
ATOM     67  CA  ALA    67      26.127  31.028  23.419  1.00 25.00           C
ATOM     68  CA  GLU    68      29.713  31.255  22.265  1.00 25.00           C
ATOM     69  CA  ASP    69      28.982  27.752  20.903  1.00 25.00           C
ATOM     70  CA  LEU    70      28.479  29.195  17.391  1.00 25.00           C
ATOM     71  CA  LEU    71      31.799  31.084  17.665  1.00 25.00           C
ATOM     72  CA  THR    72      33.564  27.871  18.773  1.00 25.00           C
ATOM     73  CA  HIS    73      32.045  25.984  15.807  1.00 25.00           C
ATOM     74  CA  LEU    74      33.223  28.739  13.421  1.00 25.00           C
ATOM     75  CA  GLU    75      36.747  28.555  14.908  1.00 25.00           C
ATOM     76  CA  PRO    76      36.760  24.750  14.470  1.00 25.00           C
ATOM     77  CA  THR    77      35.646  25.142  10.827  1.00 25.00           C
ATOM     78  CA  CYS    78      38.434  27.696  10.223  1.00 25.00           C
ATOM     79  CA  ALA    79      40.995  25.304  11.768  1.00 25.00           C
ATOM     80  CA  ALA    80      39.732  22.467   9.528  1.00 25.00           C
ATOM     81  CA  MET    81      40.025  24.731   6.453  1.00 25.00           C
ATOM     82  CA  GLU    82      43.601  25.668   7.454  1.00 25.00           C
ATOM     83  CA  ALA    83      44.481  21.965   7.873  1.00 25.00           C
ATOM     84  CA  ALA    84      43.014  21.199   4.419  1.00 25.00           C
ATOM     85  CA  VAL    85      45.058  24.056   2.891  1.00 25.00           C
ATOM     86  CA  ARG    86      48.230  22.714   4.568  1.00 25.00           C
ATOM     87  CA  ASP    87      47.481  19.393   2.974  1.00 25.00           C
ATOM     88  CA  GLY    88      45.482  19.943  -0.272  1.00 25.00           C
ATOM     89  CA  GLY    89      42.062  21.086  -1.344  1.00 25.00           C
ATOM     90  CA  SER    90      39.713  23.561   0.327  1.00 25.00           C
ATOM     91  CA  CYS    91      36.300  22.801   1.864  1.00 25.00           C
ATOM     92  CA  LEU    92      32.754  21.782   1.279  1.00 25.00           C
ATOM     93  CA  VAL    93      30.863  23.221   4.218  1.00 25.00           C
ATOM     94  CA  TYR    94      27.177  22.615   4.807  1.00 25.00           C
ATOM     95  CA  CYS    95      23.546  23.129   5.933  1.00 25.00           C
ATOM     96  CA  LYS    96      19.763  22.877   5.947  1.00 25.00           C
ATOM     97  CA  ASN    97      19.657  26.180   4.064  1.00 25.00           C
ATOM     98  CA  GLY    98      21.246  27.675   1.014  1.00 25.00           C
ATOM     99  CA  ARG    99      23.820  29.425   3.118  1.00 25.00           C
ATOM    100  CA  SER   100      22.922  30.842   6.530  1.00 25.00           C
ATOM    101  CA  ARG   101      25.263  29.498   9.205  1.00 25.00           C
ATOM    102  CA  SER   102      27.674  28.949   6.281  1.00 25.00           C
ATOM    103  CA  ALA   103      28.005  32.735   5.811  1.00 25.00           C
ATOM    104  CA  ALA   104      28.728  33.161   9.548  1.00 25.00           C
ATOM    105  CA  VAL   105      31.395  30.418   9.369  1.00 25.00           C
ATOM    106  CA  CYS   106      32.995  32.136   6.343  1.00 25.00           C
ATOM    107  CA  THR   107      33.022  35.473   8.222  1.00 25.00           C
ATOM    108  CA  ALA   108      34.661  33.788  11.244  1.00 25.00           C
ATOM    109  CA  TYR   109      37.314  32.228   8.965  1.00 25.00           C
ATOM    110  CA  LEU   110      38.002  35.647   7.383  1.00 25.00           C
ATOM    111  CA  MET   111      38.359  37.211  10.861  1.00 25.00           C
ATOM    112  CA  ARG   112      40.796  34.440  11.884  1.00 25.00           C
ATOM    113  CA  HIS   113      42.841  35.029   8.700  1.00 25.00           C
ATOM    114  CA  ARG   114      42.561  37.463   5.776  1.00 25.00           C
ATOM    115  CA  GLY   115      43.700  40.842   6.926  1.00 25.00           C
ATOM    116  CA  HIS   116      40.495  41.301   8.906  1.00 25.00           C
ATOM    117  CA  SER   117      37.190  43.014   7.956  1.00 25.00           C
ATOM    118  CA  LEU   118      34.109  41.274   9.465  1.00 25.00           C
ATOM    119  CA  ASP   119      31.774  43.644   7.569  1.00 25.00           C
ATOM    120  CA  ARG   120      33.712  43.000   4.329  1.00 25.00           C
ATOM    121  CA  ALA   121      33.450  39.221   4.895  1.00 25.00           C
ATOM    122  CA  PHE   122      29.680  39.546   5.481  1.00 25.00           C
ATOM    123  CA  GLN   123      29.328  41.580   2.256  1.00 25.00           C
ATOM    124  CA  MET   124      31.297  38.917   0.332  1.00 25.00           C
ATOM    125  CA  VAL   125      29.042  36.176   1.771  1.00 25.00           C
ATOM    126  CA  LYS   126      25.932  38.159   0.738  1.00 25.00           C
ATOM    127  CA  SER   127      27.344  38.579  -2.797  1.00 25.00           C
ATOM    128  CA  ALA   128      28.040  34.818  -2.993  1.00 25.00           C
ATOM    129  CA  ARG   129      24.366  33.952  -2.527  1.00 25.00           C
ATOM    130  CA  PRO   130      22.469  36.963  -3.859  1.00 25.00           C
ATOM    131  CA  VAL   131      20.700  36.977  -0.526  1.00 25.00           C
ATOM    132  CA  ALA   132      21.866  34.856   2.396  1.00 25.00           C
ATOM    133  CA  GLU   133      22.070  38.127   4.324  1.00 25.00           C
ATOM    134  CA  PRO   134      18.821  39.523   5.692  1.00 25.00           C
ATOM    135  CA  ASN   135      18.528  36.848   8.366  1.00 25.00           C
ATOM    136  CA  LEU   136      20.288  39.471  10.563  1.00 25.00           C
ATOM    137  CA  GLY   137      20.916  36.715  13.147  1.00 25.00           C
ATOM    138  CA  PHE   138      24.340  36.000  11.589  1.00 25.00           C
ATOM    139  CA  TRP   139      25.202  39.730  11.712  1.00 25.00           C
ATOM    140  CA  ALA   140      24.157  39.874  15.394  1.00 25.00           C
ATOM    141  CA  GLN   141      26.337  36.819  16.158  1.00 25.00           C
ATOM    142  CA  LEU   142      29.305  38.461  14.377  1.00 25.00           C
ATOM    143  CA  GLN   143      28.774  41.670  16.398  1.00 25.00           C
ATOM    144  CA  LYS   144      28.670  39.640  19.643  1.00 25.00           C
ATOM    145  CA  TYR   145      31.916  37.860  18.661  1.00 25.00           C
ATOM    146  CA  GLU   146      33.572  41.233  17.923  1.00 25.00           C
ATOM    147  CA  GLN   147      32.430  42.566  21.327  1.00 25.00           C
ATOM    148  CA  THR   148      33.851  39.454  23.050  1.00 25.00           C
ATOM    149  CA  LEU   149      37.178  39.927  21.213  1.00 25.00           C
ATOM    150  CA  GLN   150      37.281  43.600  22.296  1.00 25.00           C
ATOM    151  CA  ALA   151      37.322  46.685  24.519  1.00 25.00           C
ATOM    152  CA  GLN   152      34.552  48.105  26.723  1.00 25.00           C
ATOM    153  CA  ALA   153      32.421  51.184  26.175  1.00 25.00           C
ATOM    154  CA  ILE   154      33.830  53.662  23.616  1.00 25.00           C
ATOM    155  CA  LEU   155      34.618  54.716  20.047  1.00 25.00           C
ATOM    156  CA  PRO   156      33.639  58.304  19.298  1.00 25.00           C
ATOM    157  CA  ARG   157      29.936  58.077  18.813  1.00 25.00           C
ATOM    158  CA  GLU   158      27.600  58.272  15.836  1.00 25.00           C
TER
END
