
#######################################################
#                                                     #
#                        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  123 (  123),  selected  123 , name T0367TS168_4-D1
# Molecule2: number of CA atoms  123 (  996),  selected  123 , name T0367_D1.pdb
# PARAMETERS: T0367TS168_4-D1.T0367_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    D       2      D       2           -
LGA    E       3      E       3           -
LGA    L       4      L       4           -
LGA    E       5      E       5           -
LGA    L       6      L       6           -
LGA    R       7      R       7           -
LGA    I       8      I       8           -
LGA    R       9      R       9           -
LGA    K      10      K      10           -
LGA    A      11      A      11           -
LGA    E      12      E      12           -
LGA    K      13      K      13           -
LGA    -       -      L      14           -
LGA    -       -      V      15           -
LGA    -       -      Q      16           -
LGA    -       -      D      17           -
LGA    -       -      A      18           -
LGA    -       -      K      19           -
LGA    -       -      K      20           -
LGA    -       -      E      21           -
LGA    -       -      F      22           -
LGA    L      14      E      23          4.942
LGA    V      15      M      24          3.373
LGA    Q      16      G      25          4.358
LGA    D      17      -       -           -
LGA    A      18      -       -           -
LGA    K      19      L      26          2.568
LGA    K      20      Y      27           -
LGA    E      21      E      28           -
LGA    -       -      R      29           -
LGA    F      22      C      30          2.112
LGA    E      23      C      31           #
LGA    -       -      S      32           -
LGA    M      24      T      33          4.165
LGA    G      25      A      34          2.962
LGA    L      26      Y      35          2.897
LGA    Y      27      Y      36          2.700
LGA    E      28      A      37          1.819
LGA    R      29      M      38          1.351
LGA    C      30      F      39          1.625
LGA    C      31      H      40          1.274
LGA    S      32      A      41          0.738
LGA    T      33      A      42          1.231
LGA    A      34      K      43          1.112
LGA    Y      35      A      44          0.936
LGA    Y      36      M      45          1.819
LGA    A      37      L      46          2.056
LGA    M      38      L      47          1.476
LGA    F      39      G      48          2.733
LGA    H      40      Y      49          3.500
LGA    A      41      G      50          2.574
LGA    A      42      R      51          5.086
LGA    K      43      -       -           -
LGA    A      44      -       -           -
LGA    M      45      -       -           -
LGA    L      46      -       -           -
LGA    L      47      -       -           -
LGA    G      48      -       -           -
LGA    Y      49      -       -           -
LGA    G      50      -       -           -
LGA    R      51      D      52           #
LGA    D      52      S      53           -
LGA    S      53      -       -           -
LGA    K      54      -       -           -
LGA    T      55      K      54          3.158
LGA    H      56      T      55          1.583
LGA    R      57      -       -           -
LGA    G      58      -       -           -
LGA    T      59      H      56          4.690
LGA    I      60      R      57          4.004
LGA    Y      61      G      58          2.685
LGA    L      62      T      59          2.108
LGA    I      63      I      60          1.184
LGA    W      64      Y      61          2.337
LGA    E      65      L      62          2.008
LGA    C      66      I      63          3.350
LGA    R      67      W      64          4.443
LGA    E      68      -       -           -
LGA    E      69      E      65          3.129
LGA    L      70      C      66           -
LGA    G      71      R      67           #
LGA    L      72      E      68          4.188
LGA    S      73      E      69          4.254
LGA    D      74      L      70          1.976
LGA    -       -      G      71           -
LGA    D      75      L      72          1.887
LGA    D      76      S      73           #
LGA    C      77      D      74           -
LGA    -       -      D      75           -
LGA    S      78      D      76          5.128
LGA    K      79      -       -           -
LGA    L      80      -       -           -
LGA    S      81      C      77          4.133
LGA    R      82      S      78          3.341
LGA    A      83      K      79          3.444
LGA    F      84      L      80          2.855
LGA    D      85      S      81          1.611
LGA    L      86      R      82          2.133
LGA    R      87      A      83          2.260
LGA    E      88      F      84          1.296
LGA    E      89      D      85          0.548
LGA    S      90      L      86           #
LGA    D      91      R      87           -
LGA    Y      92      E      88          3.429
LGA    G      93      E      89           #
LGA    -       -      S      90           -
LGA    -       -      D      91           -
LGA    I      94      Y      92          4.458
LGA    Y      95      G      93          3.718
LGA    K      96      I      94          5.305
LGA    E      97      Y      95          3.397
LGA    V      98      K      96          3.216
LGA    S      99      E      97          4.681
LGA    K     100      V      98          2.036
LGA    D     101      S      99          5.413
LGA    L     102      K     100           -
LGA    -       -      D     101           -
LGA    A     103      L     102           #
LGA    I     104      A     103          2.115
LGA    K     105      -       -           -
LGA    I     106      -       -           -
LGA    L     107      I     104          4.781
LGA    K     108      K     105          2.053
LGA    D     109      I     106          4.132
LGA    A     110      L     107          3.931
LGA    E     111      K     108          1.857
LGA    I     112      D     109          4.509
LGA    F     113      A     110           #
LGA    V     114      E     111          2.631
LGA    Q     115      I     112           #
LGA    K     116      F     113           -
LGA    -       -      V     114           -
LGA    A     117      Q     115          3.834
LGA    K     118      -       -           -
LGA    N     119      -       -           -
LGA    A     120      K     116           #
LGA    V     121      A     117           -
LGA    N     122      K     118           -
LGA    K     123      N     119           -
LGA    -       -      A     120           -
LGA    -       -      V     121           -
LGA    -       -      N     122           -
LGA    -       -      K     123           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  123  123    5.0     68    3.18     5.88     32.740     2.071

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.162384 * X  +   0.815504 * Y  +  -0.555504 * Z  +  37.948032
  Y_new =   0.139769 * X  +   0.576309 * Y  +   0.805191 * Z  +  33.480282
  Z_new =   0.976778 * X  +   0.053108 * Y  +  -0.207565 * Z  +  29.100187 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.891104   -0.250488  [ DEG:   165.6481    -14.3519 ]
  Theta =  -1.354870   -1.786722  [ DEG:   -77.6284   -102.3716 ]
  Phi   =   2.430903   -0.710690  [ DEG:   139.2805    -40.7195 ]
 
# 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: T0367TS168_4-D1                               
REMARK     2: T0367_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0367TS168_4-D1.T0367_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  123  123   5.0   68   3.18    5.88  32.740
REMARK  ---------------------------------------------------------- 
MOLECULE T0367TS168_4-D1
PFRMAT TS
TARGET T0367
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1       0.172  25.849  44.366  1.00 25.00           C
ATOM      2  CA  ASP     2       3.093  24.111  46.134  1.00 25.00           C
ATOM      3  CA  GLU     3       3.723  22.795  42.595  1.00 25.00           C
ATOM      4  CA  LEU     4       4.372  26.361  41.358  1.00 25.00           C
ATOM      5  CA  GLU     5       6.827  26.941  44.239  1.00 25.00           C
ATOM      6  CA  LEU     6       8.636  23.675  43.387  1.00 25.00           C
ATOM      7  CA  ARG     7       8.864  24.731  39.713  1.00 25.00           C
ATOM      8  CA  ILE     8      10.286  28.132  40.752  1.00 25.00           C
ATOM      9  CA  ARG     9      12.876  26.397  42.977  1.00 25.00           C
ATOM     10  CA  LYS    10      13.864  24.101  40.076  1.00 25.00           C
ATOM     11  CA  ALA    11      14.243  27.136  37.771  1.00 25.00           C
ATOM     12  CA  GLU    12      16.432  28.879  40.384  1.00 25.00           C
ATOM     13  CA  LYS    13      18.605  25.741  40.693  1.00 25.00           C
ATOM     14  CA  LEU    14      18.971  25.589  36.884  1.00 25.00           C
ATOM     15  CA  VAL    15      19.982  29.281  36.810  1.00 25.00           C
ATOM     16  CA  GLN    16      22.576  28.653  39.557  1.00 25.00           C
ATOM     17  CA  ASP    17      23.974  25.680  37.588  1.00 25.00           C
ATOM     18  CA  ALA    18      24.206  27.843  34.438  1.00 25.00           C
ATOM     19  CA  LYS    19      26.037  30.567  36.411  1.00 25.00           C
ATOM     20  CA  LYS    20      28.481  27.959  37.789  1.00 25.00           C
ATOM     21  CA  GLU    21      29.112  26.643  34.248  1.00 25.00           C
ATOM     22  CA  PHE    22      29.760  30.209  33.012  1.00 25.00           C
ATOM     23  CA  GLU    23      32.215  30.789  35.893  1.00 25.00           C
ATOM     24  CA  MET    24      34.025  27.523  35.041  1.00 25.00           C
ATOM     25  CA  GLY    25      34.252  28.580  31.367  1.00 25.00           C
ATOM     26  CA  LEU    26      35.673  31.981  32.407  1.00 25.00           C
ATOM     27  CA  TYR    27      38.263  30.245  34.631  1.00 25.00           C
ATOM     28  CA  GLU    28      39.253  27.949  31.730  1.00 25.00           C
ATOM     29  CA  ARG    29      39.630  30.984  29.425  1.00 25.00           C
ATOM     30  CA  CYS    30      41.820  32.728  32.038  1.00 25.00           C
ATOM     31  CA  CYS    31      43.992  29.589  32.347  1.00 25.00           C
ATOM     32  CA  SER    32      44.359  29.437  28.538  1.00 25.00           C
ATOM     33  CA  THR    33      45.370  33.131  28.463  1.00 25.00           C
ATOM     34  CA  ALA    34      47.963  32.501  31.210  1.00 25.00           C
ATOM     35  CA  TYR    35      49.362  29.528  29.242  1.00 25.00           C
ATOM     36  CA  TYR    36      49.593  31.692  26.091  1.00 25.00           C
ATOM     37  CA  ALA    37      51.425  34.415  28.065  1.00 25.00           C
ATOM     38  CA  MET    38      53.868  31.807  29.443  1.00 25.00           C
ATOM     39  CA  PHE    39      54.499  30.491  25.902  1.00 25.00           C
ATOM     40  CA  HIS    40      55.147  34.059  24.665  1.00 25.00           C
ATOM     41  CA  ALA    41      57.602  34.637  27.548  1.00 25.00           C
ATOM     42  CA  ALA    42      59.412  31.372  26.694  1.00 25.00           C
ATOM     43  CA  LYS    43      59.639  32.429  23.020  1.00 25.00           C
ATOM     44  CA  ALA    44      61.061  35.829  24.061  1.00 25.00           C
ATOM     45  CA  MET    45      63.651  34.092  26.285  1.00 25.00           C
ATOM     46  CA  LEU    46      64.640  31.797  23.384  1.00 25.00           C
ATOM     47  CA  LEU    47      65.018  34.832  21.079  1.00 25.00           C
ATOM     48  CA  GLY    48      67.208  36.576  23.692  1.00 25.00           C
ATOM     49  CA  TYR    49      65.029  38.995  25.637  1.00 25.00           C
ATOM     50  CA  GLY    50      63.029  40.526  28.559  1.00 25.00           C
ATOM     51  CA  ARG    51      60.240  42.033  30.713  1.00 25.00           C
ATOM     52  CA  ASP    52      58.861  44.086  33.555  1.00 25.00           C
ATOM     53  CA  SER    53      57.061  46.164  36.200  1.00 25.00           C
ATOM     54  CA  LYS    54      54.199  44.780  38.276  1.00 25.00           C
ATOM     55  CA  THR    55      50.953  43.308  36.883  1.00 25.00           C
ATOM     56  CA  HIS    56      47.311  42.823  36.175  1.00 25.00           C
ATOM     57  CA  ARG    57      46.893  39.143  36.782  1.00 25.00           C
ATOM     58  CA  GLY    58      48.447  36.714  34.262  1.00 25.00           C
ATOM     59  CA  THR    59      45.119  36.496  32.381  1.00 25.00           C
ATOM     60  CA  ILE    60      44.890  40.319  32.293  1.00 25.00           C
ATOM     61  CA  TYR    61      48.468  40.525  30.944  1.00 25.00           C
ATOM     62  CA  LEU    62      47.624  37.949  28.239  1.00 25.00           C
ATOM     63  CA  ILE    63      44.508  39.953  27.267  1.00 25.00           C
ATOM     64  CA  TRP    64      46.605  43.151  27.049  1.00 25.00           C
ATOM     65  CA  GLU    65      49.161  41.353  24.836  1.00 25.00           C
ATOM     66  CA  CYS    66      46.347  40.097  22.562  1.00 25.00           C
ATOM     67  CA  ARG    67      44.937  43.649  22.304  1.00 25.00           C
ATOM     68  CA  GLU    68      48.412  44.989  21.406  1.00 25.00           C
ATOM     69  CA  GLU    69      48.784  42.289  18.715  1.00 25.00           C
ATOM     70  CA  LEU    70      45.515  42.228  16.805  1.00 25.00           C
ATOM     71  CA  GLY    71      47.479  40.976  13.801  1.00 25.00           C
ATOM     72  CA  LEU    72      47.455  37.693  15.745  1.00 25.00           C
ATOM     73  CA  SER    73      50.019  35.073  14.797  1.00 25.00           C
ATOM     74  CA  ASP    74      49.953  32.037  17.086  1.00 25.00           C
ATOM     75  CA  ASP    75      46.258  31.849  16.093  1.00 25.00           C
ATOM     76  CA  ASP    76      45.486  29.829  19.254  1.00 25.00           C
ATOM     77  CA  CYS    77      47.329  32.419  21.390  1.00 25.00           C
ATOM     78  CA  SER    78      45.343  35.240  19.726  1.00 25.00           C
ATOM     79  CA  LYS    79      42.071  33.372  20.408  1.00 25.00           C
ATOM     80  CA  LEU    80      43.074  32.900  24.074  1.00 25.00           C
ATOM     81  CA  SER    81      43.880  36.634  24.359  1.00 25.00           C
ATOM     82  CA  ARG    82      40.477  37.510  22.833  1.00 25.00           C
ATOM     83  CA  ALA    83      38.735  35.173  25.318  1.00 25.00           C
ATOM     84  CA  PHE    84      40.624  36.810  28.220  1.00 25.00           C
ATOM     85  CA  ASP    85      39.592  40.278  26.967  1.00 25.00           C
ATOM     86  CA  LEU    86      35.943  39.138  26.740  1.00 25.00           C
ATOM     87  CA  ARG    87      36.123  37.766  30.311  1.00 25.00           C
ATOM     88  CA  GLU    88      37.591  41.084  31.537  1.00 25.00           C
ATOM     89  CA  GLU    89      34.782  43.004  29.780  1.00 25.00           C
ATOM     90  CA  SER    90      36.054  45.944  31.766  1.00 25.00           C
ATOM     91  CA  ASP    91      36.816  48.407  34.541  1.00 25.00           C
ATOM     92  CA  TYR    92      34.777  46.060  36.682  1.00 25.00           C
ATOM     93  CA  GLY    93      34.967  48.412  39.711  1.00 25.00           C
ATOM     94  CA  ILE    94      31.155  48.859  40.101  1.00 25.00           C
ATOM     95  CA  TYR    95      27.358  48.994  39.518  1.00 25.00           C
ATOM     96  CA  LYS    96      26.233  50.362  36.119  1.00 25.00           C
ATOM     97  CA  GLU    97      23.424  48.750  34.164  1.00 25.00           C
ATOM     98  CA  VAL    98      26.196  46.405  33.009  1.00 25.00           C
ATOM     99  CA  SER    99      27.024  43.068  34.693  1.00 25.00           C
ATOM    100  CA  LYS   100      25.568  40.614  32.184  1.00 25.00           C
ATOM    101  CA  ASP   101      25.496  40.788  28.360  1.00 25.00           C
ATOM    102  CA  LEU   102      29.321  40.962  28.270  1.00 25.00           C
ATOM    103  CA  ALA   103      29.538  37.923  30.590  1.00 25.00           C
ATOM    104  CA  ILE   104      27.110  35.999  28.338  1.00 25.00           C
ATOM    105  CA  LYS   105      29.209  36.902  25.264  1.00 25.00           C
ATOM    106  CA  ILE   106      32.380  35.707  27.048  1.00 25.00           C
ATOM    107  CA  LEU   107      30.653  32.415  27.965  1.00 25.00           C
ATOM    108  CA  LYS   108      29.555  31.948  24.327  1.00 25.00           C
ATOM    109  CA  ASP   109      33.138  32.598  23.136  1.00 25.00           C
ATOM    110  CA  ALA   110      34.465  30.034  25.652  1.00 25.00           C
ATOM    111  CA  GLU   111      31.895  27.470  24.432  1.00 25.00           C
ATOM    112  CA  ILE   112      32.933  28.120  20.803  1.00 25.00           C
ATOM    113  CA  PHE   113      36.615  27.653  21.747  1.00 25.00           C
ATOM    114  CA  VAL   114      35.771  24.360  23.513  1.00 25.00           C
ATOM    115  CA  GLN   115      33.856  23.166  20.419  1.00 25.00           C
ATOM    116  CA  LYS   116      36.837  24.069  18.192  1.00 25.00           C
ATOM    117  CA  ALA   117      39.190  22.145  20.523  1.00 25.00           C
ATOM    118  CA  LYS   118      36.864  19.106  20.403  1.00 25.00           C
ATOM    119  CA  ASN   119      36.792  19.279  16.578  1.00 25.00           C
ATOM    120  CA  ALA   120      40.617  19.454  16.490  1.00 25.00           C
ATOM    121  CA  VAL   121      40.833  16.414  18.809  1.00 25.00           C
ATOM    122  CA  ASN   122      38.406  14.491  16.556  1.00 25.00           C
ATOM    123  CA  LYS   123      39.376  10.929  15.497  1.00 25.00           C
TER
END
