
#######################################################
#                                                     #
#                        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  163 (  163),  selected  163 , name T0317TS168_4
# Molecule2: number of CA atoms  158 ( 1185),  selected  158 , name T0317.pdb
# PARAMETERS: T0317TS168_4.T0317.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    G       2      G       2           -
LGA    T       3      T       3           -
LGA    S       4      S       4           -
LGA    E       5      E       5           -
LGA    A       6      A       6           -
LGA    A       7      A       7           -
LGA    P       8      P       8           -
LGA    P       9      P       9           -
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          3.067
LGA    A      17      A      17          3.375
LGA    L      18      L      18          3.066
LGA    F      19      F      19          2.493
LGA    I      20      I      20          1.606
LGA    G      21      G      21          2.009
LGA    N      22      N      22          2.214
LGA    A      23      A      23           #
LGA    R      24      R      24           #
LGA    A      25      A      25          4.015
LGA    A      26      A      26          3.723
LGA    G      27      G      27          2.066
LGA    A      28      A      28          1.346
LGA    T      29      T      29          1.174
LGA    E      30      E      30          1.072
LGA    L      31      L      31          1.077
LGA    L      32      L      32          1.063
LGA    V      33      V      33          1.083
LGA    R      34      R      34          1.076
LGA    A      35      A      35          1.739
LGA    G      36      G      36          0.540
LGA    I      37      I      37          1.201
LGA    T      38      T      38          1.036
LGA    L      39      L      39          1.108
LGA    C      40      C      40          1.395
LGA    V      41      V      41          1.157
LGA    N      42      N      42          1.766
LGA    V      43      V      43          1.885
LGA    S      44      S      44          2.118
LGA    R      45      R      45          2.392
LGA    Q      46      Q      46          1.238
LGA    Q      47      Q      47          3.467
LGA    P      48      P      48          3.536
LGA    G      49      G      49          4.968
LGA    P      50      P      50          5.966
LGA    R      51      R      51          3.288
LGA    A      52      A      52          3.218
LGA    P      53      P      53          2.806
LGA    G      54      G      54          2.480
LGA    V      55      V      55          1.835
LGA    A      56      A      56          1.667
LGA    E      57      E      57          1.605
LGA    L      58      L      58          1.506
LGA    R      59      R      59          2.281
LGA    V      60      V      60          1.290
LGA    P      61      P      61          1.404
LGA    V      62      V      62          1.513
LGA    F      63      F      63          2.359
LGA    D      64      D      64           -
LGA    -       -      D      65           -
LGA    D      65      P      66           #
LGA    P      66      A      67          4.806
LGA    A      67      E      68           #
LGA    E      68      -       -           -
LGA    D      69      D      69          3.495
LGA    L      70      L      70          1.454
LGA    L      71      L      71          2.205
LGA    T      72      T      72          2.698
LGA    H      73      H      73          1.869
LGA    L      74      L      74          1.263
LGA    E      75      E      75          1.554
LGA    P      76      P      76          2.584
LGA    T      77      T      77          2.215
LGA    C      78      C      78          1.162
LGA    A      79      A      79          1.535
LGA    A      80      A      80          1.696
LGA    M      81      M      81          1.627
LGA    E      82      E      82          1.918
LGA    A      83      A      83          1.715
LGA    A      84      A      84          1.078
LGA    V      85      V      85          2.259
LGA    R      86      R      86          3.047
LGA    D      87      D      87          1.805
LGA    G      88      G      88          1.176
LGA    G      89      G      89          2.010
LGA    S      90      S      90          1.745
LGA    C      91      C      91          0.529
LGA    L      92      L      92          0.889
LGA    V      93      V      93          0.813
LGA    Y      94      Y      94          0.871
LGA    C      95      C      95          2.514
LGA    K      96      K      96          1.052
LGA    N      97      N      97          0.857
LGA    G      98      G      98          1.438
LGA    R      99      R      99          2.669
LGA    S     100      S     100          2.487
LGA    R     101      R     101          0.978
LGA    S     102      S     102          1.343
LGA    A     103      A     103          1.388
LGA    A     104      A     104          0.836
LGA    V     105      V     105          0.720
LGA    C     106      C     106          0.702
LGA    T     107      T     107          0.530
LGA    A     108      A     108          0.470
LGA    Y     109      Y     109          0.592
LGA    L     110      L     110          0.543
LGA    M     111      M     111          0.716
LGA    R     112      R     112          0.435
LGA    H     113      H     113          1.451
LGA    R     114      R     114          3.553
LGA    G     115      G     115          3.366
LGA    H     116      H     116          2.534
LGA    S     117      S     117          1.452
LGA    L     118      L     118          1.232
LGA    D     119      D     119          1.207
LGA    R     120      R     120          0.504
LGA    A     121      A     121          0.763
LGA    F     122      F     122          1.433
LGA    Q     123      Q     123          1.324
LGA    M     124      M     124          1.473
LGA    V     125      V     125          2.099
LGA    K     126      K     126          2.151
LGA    S     127      S     127          1.941
LGA    A     128      A     128          2.488
LGA    R     129      R     129          1.844
LGA    P     130      P     130          3.734
LGA    V     131      -       -           -
LGA    A     132      V     131          1.524
LGA    E     133      A     132          3.566
LGA    P     134      E     133          4.734
LGA    N     135      -       -           -
LGA    L     136      -       -           -
LGA    G     137      P     134           #
LGA    F     138      N     135          1.897
LGA    W     139      L     136          4.562
LGA    A     140      G     137          4.792
LGA    Q     141      F     138          2.118
LGA    L     142      W     139          1.968
LGA    Q     143      A     140          4.150
LGA    K     144      Q     141          4.484
LGA    Y     145      L     142          2.595
LGA    E     146      Q     143          1.462
LGA    Q     147      K     144          4.948
LGA    T     148      Y     145           #
LGA    L     149      E     146          3.227
LGA    Q     150      Q     147          3.189
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     159      P     156           -
LGA    I     160      R     157           -
LGA    D     161      E     158           -
LGA    P     162      -       -           -
LGA    E     163      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  163  158    5.0    124    2.34    87.90     55.381     5.083

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.358154 * X  +  -0.026975 * Y  +  -0.933273 * Z  +  30.565973
  Y_new =  -0.886782 * X  +   0.322590 * Y  +   0.330988 * Z  +  31.288200
  Z_new =   0.292136 * X  +   0.946154 * Y  +  -0.139458 * Z  +   5.554209 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.717137   -1.424456  [ DEG:    98.3847    -81.6153 ]
  Theta =  -0.296459   -2.845133  [ DEG:   -16.9859   -163.0141 ]
  Phi   =  -1.954643    1.186949  [ DEG:  -111.9928     68.0072 ]
 
# 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: T0317TS168_4                                  
REMARK     2: T0317.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0317TS168_4.T0317.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  163  158   5.0  124   2.34   87.90  55.381
REMARK  ---------------------------------------------------------- 
MOLECULE T0317TS168_4
PFRMAT TS
TARGET T0317
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      25.889  51.220 -11.159  1.00 25.00           C
ATOM      2  CA  GLY     2      28.684  53.177  -9.402  1.00 25.00           C
ATOM      3  CA  THR     3      30.993  55.689 -11.017  1.00 25.00           C
ATOM      4  CA  SER     4      32.006  53.523 -14.021  1.00 25.00           C
ATOM      5  CA  GLU     5      35.663  54.587 -13.395  1.00 25.00           C
ATOM      6  CA  ALA     6      37.904  51.732 -14.661  1.00 25.00           C
ATOM      7  CA  ALA     7      37.676  47.979 -15.405  1.00 25.00           C
ATOM      8  CA  PRO     8      37.704  44.658 -17.216  1.00 25.00           C
ATOM      9  CA  PRO     9      39.629  41.529 -16.205  1.00 25.00           C
ATOM     10  CA  PRO    10      36.889  38.895 -16.661  1.00 25.00           C
ATOM     11  CA  PHE    11      35.631  36.454 -14.036  1.00 25.00           C
ATOM     12  CA  ALA    12      39.177  35.805 -12.711  1.00 25.00           C
ATOM     13  CA  ARG    13      42.621  34.589 -11.600  1.00 25.00           C
ATOM     14  CA  VAL    14      41.723  33.681  -8.019  1.00 25.00           C
ATOM     15  CA  ALA    15      39.955  33.808  -4.708  1.00 25.00           C
ATOM     16  CA  PRO    16      39.117  32.556  -1.256  1.00 25.00           C
ATOM     17  CA  ALA    17      38.159  29.288   0.442  1.00 25.00           C
ATOM     18  CA  LEU    18      35.132  29.676   2.715  1.00 25.00           C
ATOM     19  CA  PHE    19      32.022  27.892   1.594  1.00 25.00           C
ATOM     20  CA  ILE    20      28.206  27.419   1.554  1.00 25.00           C
ATOM     21  CA  GLY    21      28.120  24.246  -0.588  1.00 25.00           C
ATOM     22  CA  ASN    22      24.662  22.569  -0.385  1.00 25.00           C
ATOM     23  CA  ALA    23      21.705  22.697  -2.728  1.00 25.00           C
ATOM     24  CA  ARG    24      23.063  20.713  -5.748  1.00 25.00           C
ATOM     25  CA  ALA    25      26.571  19.331  -5.040  1.00 25.00           C
ATOM     26  CA  ALA    26      26.952  17.970  -1.568  1.00 25.00           C
ATOM     27  CA  GLY    27      24.962  14.792  -2.427  1.00 25.00           C
ATOM     28  CA  ALA    28      27.364  14.097  -5.292  1.00 25.00           C
ATOM     29  CA  THR    29      30.876  13.584  -3.923  1.00 25.00           C
ATOM     30  CA  GLU    30      32.013  14.155  -7.536  1.00 25.00           C
ATOM     31  CA  LEU    31      32.107  17.936  -6.934  1.00 25.00           C
ATOM     32  CA  LEU    32      34.182  17.405  -3.759  1.00 25.00           C
ATOM     33  CA  VAL    33      36.609  15.160  -5.691  1.00 25.00           C
ATOM     34  CA  ARG    34      36.935  17.823  -8.424  1.00 25.00           C
ATOM     35  CA  ALA    35      38.314  20.631  -6.361  1.00 25.00           C
ATOM     36  CA  GLY    36      39.758  18.869  -3.337  1.00 25.00           C
ATOM     37  CA  ILE    37      38.136  18.988   0.132  1.00 25.00           C
ATOM     38  CA  THR    38      38.342  16.732   3.209  1.00 25.00           C
ATOM     39  CA  LEU    39      37.231  19.182   5.978  1.00 25.00           C
ATOM     40  CA  CYS    40      33.474  19.581   6.495  1.00 25.00           C
ATOM     41  CA  VAL    41      31.004  21.131   8.940  1.00 25.00           C
ATOM     42  CA  ASN    42      27.557  20.452  10.342  1.00 25.00           C
ATOM     43  CA  VAL    43      24.608  22.872  10.494  1.00 25.00           C
ATOM     44  CA  SER    44      21.232  21.256  11.085  1.00 25.00           C
ATOM     45  CA  ARG    45      22.859  17.999  12.244  1.00 25.00           C
ATOM     46  CA  GLN    46      20.148  15.406  11.375  1.00 25.00           C
ATOM     47  CA  GLN    47      21.574  13.738   8.225  1.00 25.00           C
ATOM     48  CA  PRO    48      22.348  11.000   5.685  1.00 25.00           C
ATOM     49  CA  GLY    49      25.773   9.472   6.525  1.00 25.00           C
ATOM     50  CA  PRO    50      29.177   9.731   8.203  1.00 25.00           C
ATOM     51  CA  ARG    51      31.195   8.025   5.456  1.00 25.00           C
ATOM     52  CA  ALA    52      30.857  10.571   2.690  1.00 25.00           C
ATOM     53  CA  PRO    53      33.729   8.978   0.852  1.00 25.00           C
ATOM     54  CA  GLY    54      36.799  11.190   1.062  1.00 25.00           C
ATOM     55  CA  VAL    55      35.387  12.681   4.224  1.00 25.00           C
ATOM     56  CA  ALA    56      34.935  14.004   7.805  1.00 25.00           C
ATOM     57  CA  GLU    57      32.410  15.993   9.903  1.00 25.00           C
ATOM     58  CA  LEU    58      33.055  18.185  12.944  1.00 25.00           C
ATOM     59  CA  ARG    59      29.887  19.154  14.870  1.00 25.00           C
ATOM     60  CA  VAL    60      28.301  22.539  15.612  1.00 25.00           C
ATOM     61  CA  PRO    61      24.854  22.066  17.076  1.00 25.00           C
ATOM     62  CA  VAL    62      22.354  24.386  15.283  1.00 25.00           C
ATOM     63  CA  PHE    63      20.349  26.626  17.602  1.00 25.00           C
ATOM     64  CA  ASP    64      22.568  26.017  20.636  1.00 25.00           C
ATOM     65  CA  ASP    65      20.984  29.239  22.036  1.00 25.00           C
ATOM     66  CA  PRO    66      23.838  31.500  20.912  1.00 25.00           C
ATOM     67  CA  ALA    67      26.764  33.686  21.912  1.00 25.00           C
ATOM     68  CA  GLU    68      29.282  31.430  23.626  1.00 25.00           C
ATOM     69  CA  ASP    69      28.091  28.411  21.593  1.00 25.00           C
ATOM     70  CA  LEU    70      28.331  30.458  18.365  1.00 25.00           C
ATOM     71  CA  LEU    71      31.882  31.551  19.294  1.00 25.00           C
ATOM     72  CA  THR    72      32.851  27.909  19.974  1.00 25.00           C
ATOM     73  CA  HIS    73      31.407  26.866  16.585  1.00 25.00           C
ATOM     74  CA  LEU    74      33.383  29.654  14.856  1.00 25.00           C
ATOM     75  CA  GLU    75      36.584  28.514  16.621  1.00 25.00           C
ATOM     76  CA  PRO    76      35.939  24.905  15.511  1.00 25.00           C
ATOM     77  CA  THR    77      35.405  26.084  11.907  1.00 25.00           C
ATOM     78  CA  CYS    78      38.678  28.067  12.044  1.00 25.00           C
ATOM     79  CA  ALA    79      40.519  24.985  13.375  1.00 25.00           C
ATOM     80  CA  ALA    80      39.050  22.856  10.551  1.00 25.00           C
ATOM     81  CA  MET    81      40.162  25.462   7.975  1.00 25.00           C
ATOM     82  CA  GLU    82      43.689  25.469   9.470  1.00 25.00           C
ATOM     83  CA  ALA    83      43.794  21.645   9.302  1.00 25.00           C
ATOM     84  CA  ALA    84      42.675  21.750   5.641  1.00 25.00           C
ATOM     85  CA  VAL    85      45.401  24.323   4.855  1.00 25.00           C
ATOM     86  CA  ARG    86      48.017  22.109   6.564  1.00 25.00           C
ATOM     87  CA  ASP    87      47.893  20.123   3.336  1.00 25.00           C
ATOM     88  CA  GLY    88      45.330  20.813   0.642  1.00 25.00           C
ATOM     89  CA  GLY    89      41.880  22.436   0.611  1.00 25.00           C
ATOM     90  CA  SER    90      38.602  24.237   0.089  1.00 25.00           C
ATOM     91  CA  CYS    91      36.248  23.081   2.911  1.00 25.00           C
ATOM     92  CA  LEU    92      32.677  22.826   1.666  1.00 25.00           C
ATOM     93  CA  VAL    93      30.633  24.157   4.634  1.00 25.00           C
ATOM     94  CA  TYR    94      26.949  23.078   4.416  1.00 25.00           C
ATOM     95  CA  CYS    95      23.593  21.742   5.499  1.00 25.00           C
ATOM     96  CA  LYS    96      19.785  21.940   5.117  1.00 25.00           C
ATOM     97  CA  ASN    97      18.788  25.113   3.339  1.00 25.00           C
ATOM     98  CA  GLY    98      22.377  25.987   2.504  1.00 25.00           C
ATOM     99  CA  ARG    99      23.765  29.432   3.396  1.00 25.00           C
ATOM    100  CA  SER   100      22.409  29.353   6.983  1.00 25.00           C
ATOM    101  CA  ARG   101      24.945  28.428   9.699  1.00 25.00           C
ATOM    102  CA  SER   102      27.589  27.366   7.140  1.00 25.00           C
ATOM    103  CA  ALA   103      27.714  30.933   5.751  1.00 25.00           C
ATOM    104  CA  ALA   104      28.139  32.323   9.294  1.00 25.00           C
ATOM    105  CA  VAL   105      30.980  29.840   9.953  1.00 25.00           C
ATOM    106  CA  CYS   106      32.680  30.880   6.684  1.00 25.00           C
ATOM    107  CA  THR   107      32.362  34.569   7.662  1.00 25.00           C
ATOM    108  CA  ALA   108      33.885  33.815  11.094  1.00 25.00           C
ATOM    109  CA  TYR   109      36.787  31.955   9.425  1.00 25.00           C
ATOM    110  CA  LEU   110      37.369  34.921   7.075  1.00 25.00           C
ATOM    111  CA  MET   111      37.378  37.319  10.061  1.00 25.00           C
ATOM    112  CA  ARG   112      39.906  35.086  11.876  1.00 25.00           C
ATOM    113  CA  HIS   113      42.132  35.031   8.760  1.00 25.00           C
ATOM    114  CA  ARG   114      43.763  38.282   7.635  1.00 25.00           C
ATOM    115  CA  GLY   115      43.526  41.502   9.677  1.00 25.00           C
ATOM    116  CA  HIS   116      40.909  42.159   6.916  1.00 25.00           C
ATOM    117  CA  SER   117      37.886  42.693   9.189  1.00 25.00           C
ATOM    118  CA  LEU   118      34.290  41.439   9.515  1.00 25.00           C
ATOM    119  CA  ASP   119      32.418  43.890   7.244  1.00 25.00           C
ATOM    120  CA  ARG   120      34.309  42.548   4.196  1.00 25.00           C
ATOM    121  CA  ALA   121      33.425  38.958   5.198  1.00 25.00           C
ATOM    122  CA  PHE   122      29.743  39.944   5.570  1.00 25.00           C
ATOM    123  CA  GLN   123      29.807  41.586   2.111  1.00 25.00           C
ATOM    124  CA  MET   124      31.369  38.427   0.612  1.00 25.00           C
ATOM    125  CA  VAL   125      28.663  36.277   2.263  1.00 25.00           C
ATOM    126  CA  LYS   126      25.943  38.578   0.861  1.00 25.00           C
ATOM    127  CA  SER   127      27.494  38.326  -2.632  1.00 25.00           C
ATOM    128  CA  ALA   128      27.578  34.508  -2.344  1.00 25.00           C
ATOM    129  CA  ARG   129      24.861  32.563  -4.164  1.00 25.00           C
ATOM    130  CA  PRO   130      22.323  34.617  -6.113  1.00 25.00           C
ATOM    131  CA  VAL   131      20.891  36.260  -3.032  1.00 25.00           C
ATOM    132  CA  ALA   132      22.082  34.787   0.216  1.00 25.00           C
ATOM    133  CA  GLU   133      21.399  36.622   3.535  1.00 25.00           C
ATOM    134  CA  PRO   134      17.740  35.768   3.359  1.00 25.00           C
ATOM    135  CA  ASN   135      15.706  35.413   6.548  1.00 25.00           C
ATOM    136  CA  LEU   136      17.966  37.814   8.473  1.00 25.00           C
ATOM    137  CA  GLY   137      18.429  36.472  12.030  1.00 25.00           C
ATOM    138  CA  PHE   138      21.804  34.956  11.045  1.00 25.00           C
ATOM    139  CA  TRP   139      22.888  38.297   9.519  1.00 25.00           C
ATOM    140  CA  ALA   140      21.853  40.124  12.721  1.00 25.00           C
ATOM    141  CA  GLN   141      23.847  37.620  14.824  1.00 25.00           C
ATOM    142  CA  LEU   142      26.906  38.134  12.578  1.00 25.00           C
ATOM    143  CA  GLN   143      26.566  41.931  12.943  1.00 25.00           C
ATOM    144  CA  LYS   144      26.342  41.571  16.749  1.00 25.00           C
ATOM    145  CA  TYR   145      29.477  39.370  16.750  1.00 25.00           C
ATOM    146  CA  GLU   146      31.329  41.966  14.631  1.00 25.00           C
ATOM    147  CA  GLN   147      30.269  44.737  17.054  1.00 25.00           C
ATOM    148  CA  THR   148      31.501  42.649  20.019  1.00 25.00           C
ATOM    149  CA  LEU   149      34.851  42.076  18.255  1.00 25.00           C
ATOM    150  CA  GLN   150      35.172  45.834  17.589  1.00 25.00           C
ATOM    151  CA  ALA   151      34.100  49.302  18.475  1.00 25.00           C
ATOM    152  CA  GLN   152      31.700  51.332  20.574  1.00 25.00           C
ATOM    153  CA  ALA   153      28.440  53.205  20.177  1.00 25.00           C
ATOM    154  CA  ILE   154      26.756  55.450  17.564  1.00 25.00           C
ATOM    155  CA  LEU   155      23.060  56.191  17.974  1.00 25.00           C
ATOM    156  CA  PRO   156      20.536  57.603  15.502  1.00 25.00           C
ATOM    157  CA  ARG   157      21.125  55.984  12.171  1.00 25.00           C
ATOM    158  CA  GLU   158      22.350  58.093   9.314  1.00 25.00           C
ATOM    159  CA  PRO   159      20.265  56.794   6.413  1.00 25.00           C
ATOM    160  CA  ILE   160      19.341  54.717   3.367  1.00 25.00           C
ATOM    161  CA  ASP   161      16.045  54.665   1.447  1.00 25.00           C
ATOM    162  CA  PRO   162      16.379  52.528  -1.612  1.00 25.00           C
ATOM    163  CA  GLU   163      16.536  49.051  -3.116  1.00 25.00           C
TER
END
