
#######################################################
#                                                     #
#                        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  130 (  130),  selected  130 , name T0354TS168_4
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS168_4.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    E       2      -       -           -
LGA    I       3      -       -           -
LGA    Q       4      -       -           -
LGA    E       5      M       1          4.830
LGA    I       6      E       2          4.067
LGA    S       7      I       3          2.805
LGA    K       8      Q       4          2.420
LGA    L       9      E       5          2.150
LGA    A      10      I       6          1.987
LGA    -       -      S       7           -
LGA    I      11      K       8          1.157
LGA    E      12      L       9          4.298
LGA    A      13      A      10           #
LGA    L      14      I      11          3.799
LGA    E      15      E      12          4.704
LGA    D      16      -       -           -
LGA    I      17      -       -           -
LGA    K      18      A      13          5.007
LGA    G      19      L      14          4.738
LGA    -       -      E      15           -
LGA    K      20      D      16          1.743
LGA    D      21      I      17          1.060
LGA    I      22      K      18          3.720
LGA    I      23      G      19          4.228
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      I      22           -
LGA    -       -      I      23           -
LGA    -       -      E      24           -
LGA    -       -      L      25           -
LGA    -       -      D      26           -
LGA    -       -      T      27           -
LGA    -       -      S      28           -
LGA    -       -      K      29           -
LGA    -       -      L      30           -
LGA    -       -      T      31           -
LGA    -       -      S      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      Q      35           -
LGA    -       -      R      36           -
LGA    -       -      M      37           -
LGA    -       -      I      38           -
LGA    E      24      V      39           #
LGA    L      25      A      40          1.714
LGA    D      26      -       -           -
LGA    T      27      -       -           -
LGA    S      28      -       -           -
LGA    K      29      -       -           -
LGA    L      30      -       -           -
LGA    T      31      -       -           -
LGA    S      32      -       -           -
LGA    L      33      -       -           -
LGA    F      34      -       -           -
LGA    Q      35      -       -           -
LGA    R      36      -       -           -
LGA    M      37      -       -           -
LGA    I      38      -       -           -
LGA    V      39      -       -           -
LGA    A      40      T      41           #
LGA    T      41      G      42          4.494
LGA    G      42      -       -           -
LGA    D      43      D      43          4.158
LGA    S      44      S      44          0.917
LGA    N      45      N      45          1.069
LGA    R      46      R      46          0.741
LGA    Q      47      Q      47          1.026
LGA    V      48      V      48          0.761
LGA    K      49      K      49          0.787
LGA    A      50      A      50          0.769
LGA    L      51      L      51          0.683
LGA    A      52      A      52          0.684
LGA    N      53      N      53          0.659
LGA    S      54      S      54          0.877
LGA    V      55      V      55          1.148
LGA    Q      56      Q      56          0.925
LGA    V      57      V      57          1.341
LGA    K      58      K      58          1.973
LGA    L      59      L      59          1.749
LGA    K      60      K      60          0.979
LGA    E      61      E      61          2.896
LGA    A      62      A      62          1.676
LGA    G      63      G      63          1.237
LGA    V      64      V      64          1.023
LGA    D      65      D      65          1.947
LGA    I      66      I      66          1.665
LGA    -       -      V      67           -
LGA    -       -      G      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      H      72           -
LGA    -       -      E      73           -
LGA    -       -      S      74           -
LGA    -       -      G      75           -
LGA    -       -      E      76           -
LGA    -       -      W      77           -
LGA    -       -      V      78           -
LGA    -       -      L      79           -
LGA    V      67      V      80          2.220
LGA    G      68      D      81          2.929
LGA    -       -      A      82           -
LGA    -       -      G      83           -
LGA    -       -      D      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      V      87           -
LGA    S      69      H      88           #
LGA    E      70      V      89           #
LGA    G      71      M      90           -
LGA    H      72      L      91           -
LGA    -       -      P      92           -
LGA    -       -      A      93           -
LGA    -       -      V      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    -       -      Y      97           -
LGA    E      73      Y      98          1.855
LGA    S      74      D      99          0.946
LGA    -       -      I     100           -
LGA    G      75      E     101          2.688
LGA    E      76      A     102           #
LGA    -       -      L     103           -
LGA    -       -      W     104           -
LGA    -       -      G     105           -
LGA    -       -      G     106           -
LGA    -       -      Q     107           -
LGA    W      77      K     108          1.255
LGA    V      78      P     109          2.169
LGA    L      79      S     110           #
LGA    V      80      -       -           -
LGA    D      81      -       -           -
LGA    A      82      -       -           -
LGA    G      83      -       -           -
LGA    D      84      -       -           -
LGA    V      85      -       -           -
LGA    V      86      -       -           -
LGA    V      87      -       -           -
LGA    H      88      F     111           #
LGA    V      89      A     112           -
LGA    -       -      V     113           -
LGA    -       -      G     114           -
LGA    M      90      A     115           #
LGA    -       -      A     116           -
LGA    -       -      K     117           -
LGA    L      91      P     118          4.429
LGA    -       -      W     119           -
LGA    -       -      S     120           -
LGA    P      92      A     121           #
LGA    A      93      V     122           -
LGA    V      94      -       -           -
LGA    R      95      -       -           -
LGA    D      96      -       -           -
LGA    Y      97      -       -           -
LGA    Y      98      -       -           -
LGA    D      99      -       -           -
LGA    I     100      -       -           -
LGA    E     101      -       -           -
LGA    A     102      -       -           -
LGA    L     103      -       -           -
LGA    W     104      -       -           -
LGA    G     105      -       -           -
LGA    G     106      -       -           -
LGA    Q     107      -       -           -
LGA    K     108      -       -           -
LGA    P     109      -       -           -
LGA    S     110      -       -           -
LGA    F     111      -       -           -
LGA    A     112      -       -           -
LGA    V     113      -       -           -
LGA    G     114      -       -           -
LGA    A     115      -       -           -
LGA    A     116      -       -           -
LGA    K     117      -       -           -
LGA    P     118      -       -           -
LGA    W     119      -       -           -
LGA    S     120      -       -           -
LGA    A     121      -       -           -
LGA    V     122      -       -           -
LGA    L     123      -       -           -
LGA    E     124      -       -           -
LGA    H     125      -       -           -
LGA    H     126      -       -           -
LGA    H     127      -       -           -
LGA    H     128      -       -           -
LGA    H     129      -       -           -
LGA    H     130      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  130  122    5.0     50    2.58    52.00     28.963     1.865

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.357829 * X  +  -0.932122 * Y  +   0.055735 * Z  +  42.615852
  Y_new =  -0.933485 * X  +  -0.358594 * Y  +  -0.004036 * Z  +  29.859699
  Z_new =   0.023748 * X  +  -0.050584 * Y  +  -0.998437 * Z  +  21.734125 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.090973    0.050620  [ DEG:  -177.0997      2.9003 ]
  Theta =  -0.023750   -3.117842  [ DEG:    -1.3608   -178.6392 ]
  Phi   =  -1.204746    1.936846  [ DEG:   -69.0269    110.9731 ]
 
# 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: T0354TS168_4                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS168_4.T0354.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  130  122   5.0   50   2.58   52.00  28.963
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS168_4
PFRMAT TS
TARGET T0354
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      50.982  20.960   7.988  1.00 25.00           C
ATOM      2  CA  GLU     2      52.532  22.287  11.226  1.00 25.00           C
ATOM      3  CA  ILE     3      49.403  21.920  13.358  1.00 25.00           C
ATOM      4  CA  GLN     4      50.642  18.778  15.162  1.00 25.00           C
ATOM      5  CA  GLU     5      53.762  20.657  16.346  1.00 25.00           C
ATOM      6  CA  ILE     6      51.575  23.527  17.630  1.00 25.00           C
ATOM      7  CA  SER     7      49.351  21.030  19.497  1.00 25.00           C
ATOM      8  CA  LYS     8      52.447  19.407  21.063  1.00 25.00           C
ATOM      9  CA  LEU     9      53.732  22.848  22.149  1.00 25.00           C
ATOM     10  CA  ALA    10      50.327  23.657  23.704  1.00 25.00           C
ATOM     11  CA  ILE    11      50.361  20.315  25.575  1.00 25.00           C
ATOM     12  CA  GLU    12      53.890  21.048  26.868  1.00 25.00           C
ATOM     13  CA  ALA    13      52.766  24.514  28.045  1.00 25.00           C
ATOM     14  CA  LEU    14      49.764  22.959  29.841  1.00 25.00           C
ATOM     15  CA  GLU    15      52.066  20.412  31.538  1.00 25.00           C
ATOM     16  CA  ASP    16      54.407  23.232  32.650  1.00 25.00           C
ATOM     17  CA  ILE    17      55.052  26.913  32.919  1.00 25.00           C
ATOM     18  CA  LYS    18      52.135  28.954  34.206  1.00 25.00           C
ATOM     19  CA  GLY    19      48.715  27.228  34.245  1.00 25.00           C
ATOM     20  CA  LYS    20      48.259  27.719  38.008  1.00 25.00           C
ATOM     21  CA  ASP    21      45.329  30.131  37.298  1.00 25.00           C
ATOM     22  CA  ILE    22      43.703  27.589  34.969  1.00 25.00           C
ATOM     23  CA  ILE    23      43.887  24.698  32.501  1.00 25.00           C
ATOM     24  CA  GLU    24      41.825  26.800  30.127  1.00 25.00           C
ATOM     25  CA  LEU    25      38.231  26.449  28.887  1.00 25.00           C
ATOM     26  CA  ASP    26      35.447  25.534  26.482  1.00 25.00           C
ATOM     27  CA  THR    27      34.322  26.927  23.107  1.00 25.00           C
ATOM     28  CA  SER    28      34.511  27.287  19.277  1.00 25.00           C
ATOM     29  CA  LYS    29      35.658  26.927  15.632  1.00 25.00           C
ATOM     30  CA  LEU    30      36.655  23.352  16.510  1.00 25.00           C
ATOM     31  CA  THR    31      35.180  21.970  19.778  1.00 25.00           C
ATOM     32  CA  SER    32      37.906  20.543  22.016  1.00 25.00           C
ATOM     33  CA  LEU    33      38.571  19.788  25.692  1.00 25.00           C
ATOM     34  CA  PHE    34      41.488  17.851  27.104  1.00 25.00           C
ATOM     35  CA  GLN    35      43.989  20.519  27.986  1.00 25.00           C
ATOM     36  CA  ARG    36      45.060  23.501  25.906  1.00 25.00           C
ATOM     37  CA  MET    37      41.421  24.318  25.342  1.00 25.00           C
ATOM     38  CA  ILE    38      39.467  27.372  24.064  1.00 25.00           C
ATOM     39  CA  VAL    39      37.559  30.326  25.601  1.00 25.00           C
ATOM     40  CA  ALA    40      34.994  30.731  28.381  1.00 25.00           C
ATOM     41  CA  THR    41      32.819  30.697  31.536  1.00 25.00           C
ATOM     42  CA  GLY    42      29.877  32.910  32.521  1.00 25.00           C
ATOM     43  CA  ASP    43      30.127  31.696  36.087  1.00 25.00           C
ATOM     44  CA  SER    44      32.744  34.021  37.697  1.00 25.00           C
ATOM     45  CA  ASN    45      33.655  36.939  35.444  1.00 25.00           C
ATOM     46  CA  ARG    46      36.959  37.739  37.208  1.00 25.00           C
ATOM     47  CA  GLN    47      37.889  34.024  37.202  1.00 25.00           C
ATOM     48  CA  VAL    48      37.089  33.804  33.463  1.00 25.00           C
ATOM     49  CA  LYS    49      39.262  36.884  32.792  1.00 25.00           C
ATOM     50  CA  ALA    50      42.134  35.324  34.788  1.00 25.00           C
ATOM     51  CA  LEU    51      41.789  32.075  32.790  1.00 25.00           C
ATOM     52  CA  ALA    52      41.864  34.053  29.512  1.00 25.00           C
ATOM     53  CA  ASN    53      45.008  35.905  30.672  1.00 25.00           C
ATOM     54  CA  SER    54      46.668  32.573  31.571  1.00 25.00           C
ATOM     55  CA  VAL    55      45.773  31.168  28.124  1.00 25.00           C
ATOM     56  CA  GLN    56      47.251  34.278  26.446  1.00 25.00           C
ATOM     57  CA  VAL    57      50.459  33.892  28.501  1.00 25.00           C
ATOM     58  CA  LYS    58      50.694  30.206  27.489  1.00 25.00           C
ATOM     59  CA  LEU    59      50.230  31.161  23.809  1.00 25.00           C
ATOM     60  CA  LYS    60      52.983  33.805  24.124  1.00 25.00           C
ATOM     61  CA  GLU    61      55.317  31.221  25.718  1.00 25.00           C
ATOM     62  CA  ALA    62      58.379  30.707  23.514  1.00 25.00           C
ATOM     63  CA  GLY    63      57.498  33.434  20.936  1.00 25.00           C
ATOM     64  CA  VAL    64      54.149  32.514  19.369  1.00 25.00           C
ATOM     65  CA  ASP    65      50.539  33.445  18.706  1.00 25.00           C
ATOM     66  CA  ILE    66      46.934  34.157  19.636  1.00 25.00           C
ATOM     67  CA  VAL    67      43.530  34.045  21.302  1.00 25.00           C
ATOM     68  CA  GLY    68      40.275  32.444  20.230  1.00 25.00           C
ATOM     69  CA  SER    69      36.897  34.211  20.138  1.00 25.00           C
ATOM     70  CA  GLU    70      34.393  32.144  22.066  1.00 25.00           C
ATOM     71  CA  GLY    71      30.910  30.659  21.355  1.00 25.00           C
ATOM     72  CA  HIS    72      27.425  29.542  20.365  1.00 25.00           C
ATOM     73  CA  GLU    73      24.793  27.260  21.986  1.00 25.00           C
ATOM     74  CA  SER    74      27.263  24.726  23.491  1.00 25.00           C
ATOM     75  CA  GLY    75      30.371  22.698  24.161  1.00 25.00           C
ATOM     76  CA  GLU    76      28.441  21.432  27.220  1.00 25.00           C
ATOM     77  CA  TRP    77      29.898  18.042  26.445  1.00 25.00           C
ATOM     78  CA  VAL    78      31.704  18.124  29.774  1.00 25.00           C
ATOM     79  CA  LEU    79      33.274  17.802  33.241  1.00 25.00           C
ATOM     80  CA  VAL    80      36.114  17.557  35.808  1.00 25.00           C
ATOM     81  CA  ASP    81      39.136  19.684  34.803  1.00 25.00           C
ATOM     82  CA  ALA    82      39.735  20.649  38.436  1.00 25.00           C
ATOM     83  CA  GLY    83      40.601  24.277  39.264  1.00 25.00           C
ATOM     84  CA  ASP    84      37.897  26.863  40.214  1.00 25.00           C
ATOM     85  CA  VAL    85      35.035  24.397  39.651  1.00 25.00           C
ATOM     86  CA  VAL    86      34.981  25.059  35.886  1.00 25.00           C
ATOM     87  CA  VAL    87      34.823  23.983  32.241  1.00 25.00           C
ATOM     88  CA  HIS    88      31.735  24.114  30.023  1.00 25.00           C
ATOM     89  CA  VAL    89      29.846  26.669  27.987  1.00 25.00           C
ATOM     90  CA  MET    90      27.545  29.456  29.020  1.00 25.00           C
ATOM     91  CA  LEU    91      26.538  33.144  28.549  1.00 25.00           C
ATOM     92  CA  PRO    92      29.223  35.778  28.590  1.00 25.00           C
ATOM     93  CA  ALA    93      31.264  34.202  25.758  1.00 25.00           C
ATOM     94  CA  VAL    94      31.643  37.629  24.091  1.00 25.00           C
ATOM     95  CA  ARG    95      32.805  39.142  27.412  1.00 25.00           C
ATOM     96  CA  ASP    96      35.356  36.317  27.834  1.00 25.00           C
ATOM     97  CA  TYR    97      36.642  36.912  24.277  1.00 25.00           C
ATOM     98  CA  TYR    98      36.979  40.658  24.998  1.00 25.00           C
ATOM     99  CA  ASP    99      38.909  39.891  28.214  1.00 25.00           C
ATOM    100  CA  ILE   100      41.237  37.539  26.285  1.00 25.00           C
ATOM    101  CA  GLU   101      41.831  40.252  23.647  1.00 25.00           C
ATOM    102  CA  ALA   102      42.632  42.789  26.402  1.00 25.00           C
ATOM    103  CA  LEU   103      45.093  40.323  27.992  1.00 25.00           C
ATOM    104  CA  TRP   104      46.772  39.770  24.594  1.00 25.00           C
ATOM    105  CA  GLY   105      46.187  42.842  22.436  1.00 25.00           C
ATOM    106  CA  GLY   106      48.345  41.287  19.697  1.00 25.00           C
ATOM    107  CA  GLN   107      46.002  41.670  16.812  1.00 25.00           C
ATOM    108  CA  LYS   108      44.303  43.686  14.104  1.00 25.00           C
ATOM    109  CA  PRO   109      44.744  40.884  11.603  1.00 25.00           C
ATOM    110  CA  SER   110      42.424  38.411   9.812  1.00 25.00           C
ATOM    111  CA  PHE   111      40.404  35.322   8.940  1.00 25.00           C
ATOM    112  CA  ALA   112      37.348  35.280   6.675  1.00 25.00           C
ATOM    113  CA  VAL   113      36.755  32.230   4.577  1.00 25.00           C
ATOM    114  CA  GLY   114      37.945  31.132   1.188  1.00 25.00           C
ATOM    115  CA  ALA   115      37.555  31.534  -2.573  1.00 25.00           C
ATOM    116  CA  ALA   116      40.417  33.932  -3.289  1.00 25.00           C
ATOM    117  CA  LYS   117      42.899  36.328  -4.917  1.00 25.00           C
ATOM    118  CA  PRO   118      43.130  35.118  -8.456  1.00 25.00           C
ATOM    119  CA  TRP   119      45.384  32.083  -8.776  1.00 25.00           C
ATOM    120  CA  SER   120      47.542  30.218 -11.349  1.00 25.00           C
ATOM    121  CA  ALA   121      50.762  32.321 -11.457  1.00 25.00           C
ATOM    122  CA  VAL   122      53.509  33.414 -13.847  1.00 25.00           C
ATOM    123  CA  LEU   123      55.568  36.187 -12.260  1.00 25.00           C
ATOM    124  CA  GLU   124      57.914  35.205  -9.396  1.00 25.00           C
ATOM    125  CA  HIS   125      55.965  31.948  -8.884  1.00 25.00           C
ATOM    126  CA  HIS   126      56.351  31.081  -5.231  1.00 25.00           C
ATOM    127  CA  HIS   127      60.083  31.766  -5.341  1.00 25.00           C
ATOM    128  CA  HIS   128      62.635  33.254  -2.946  1.00 25.00           C
ATOM    129  CA  HIS   129      61.659  34.670   0.432  1.00 25.00           C
ATOM    130  CA  HIS   130      59.693  32.659   3.038  1.00 25.00           C
TER
END
