
#######################################################
#                                                     #
#                        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 T0354TS393_3
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS393_3.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    E       2      E       2          4.486
LGA    I       3      I       3          1.521
LGA    Q       4      Q       4          3.170
LGA    E       5      E       5          3.329
LGA    I       6      I       6          2.736
LGA    S       7      S       7          2.640
LGA    K       8      K       8          4.511
LGA    L       9      -       -           -
LGA    A      10      -       -           -
LGA    I      11      L       9           #
LGA    E      12      A      10           -
LGA    A      13      I      11          4.940
LGA    L      14      E      12          4.090
LGA    E      15      -       -           -
LGA    D      16      -       -           -
LGA    I      17      -       -           -
LGA    K      18      A      13          4.194
LGA    -       -      L      14           -
LGA    G      19      E      15          1.883
LGA    K      20      D      16          3.553
LGA    D      21      I      17          2.331
LGA    -       -      K      18           -
LGA    I      22      G      19          2.643
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    I      23      I      22           #
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      I      23          2.717
LGA    Q      35      E      24          3.440
LGA    R      36      L      25          5.062
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    M      37      I      38          2.755
LGA    I      38      V      39          2.416
LGA    V      39      A      40           #
LGA    A      40      T      41           #
LGA    T      41      -       -           -
LGA    G      42      -       -           -
LGA    D      43      G      42           #
LGA    S      44      D      43          2.237
LGA    N      45      S      44          2.742
LGA    R      46      N      45          2.669
LGA    -       -      R      46           -
LGA    Q      47      Q      47          1.386
LGA    V      48      V      48          0.790
LGA    K      49      K      49          0.987
LGA    A      50      A      50          0.891
LGA    L      51      L      51          0.755
LGA    A      52      A      52          1.147
LGA    N      53      N      53          1.349
LGA    S      54      S      54          1.092
LGA    V      55      V      55          1.911
LGA    Q      56      Q      56          2.469
LGA    V      57      V      57          1.494
LGA    K      58      K      58          2.302
LGA    L      59      L      59          3.841
LGA    K      60      K      60          3.428
LGA    E      61      E      61          2.037
LGA    A      62      A      62          2.569
LGA    G      63      G      63          1.606
LGA    V      64      V      64          2.728
LGA    D      65      D      65          4.717
LGA    I      66      I      66          3.905
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      80           -
LGA    V      67      D      81          3.333
LGA    -       -      A      82           -
LGA    -       -      G      83           -
LGA    -       -      D      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    G      68      V      87           #
LGA    S      69      H      88           #
LGA    E      70      V      89           -
LGA    G      71      M      90           -
LGA    -       -      L      91           -
LGA    -       -      P      92           -
LGA    -       -      A      93           -
LGA    -       -      V      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    -       -      Y      97           -
LGA    H      72      Y      98          3.865
LGA    E      73      D      99          3.264
LGA    S      74      I     100          2.949
LGA    G      75      E     101          2.575
LGA    E      76      A     102          4.424
LGA    -       -      L     103           -
LGA    -       -      W     104           -
LGA    -       -      G     105           -
LGA    -       -      G     106           -
LGA    -       -      Q     107           -
LGA    W      77      K     108          1.838
LGA    V      78      P     109          1.076
LGA    -       -      S     110           -
LGA    L      79      F     111          3.309
LGA    V      80      A     112          4.098
LGA    D      81      V     113          5.553
LGA    A      82      G     114           -
LGA    G      83      -       -           -
LGA    D      84      -       -           -
LGA    V      85      -       -           -
LGA    V      86      -       -           -
LGA    V      87      -       -           -
LGA    H      88      -       -           -
LGA    V      89      A     115           #
LGA    -       -      A     116           -
LGA    -       -      K     117           -
LGA    M      90      P     118           #
LGA    L      91      -       -           -
LGA    P      92      W     119           #
LGA    A      93      S     120           -
LGA    V      94      A     121           -
LGA    R      95      V     122           -
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     53    3.04    50.94     26.427     1.688

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.269246 * X  +  -0.806863 * Y  +   0.525812 * Z  +  41.813099
  Y_new =  -0.795858 * X  +   0.493859 * Y  +   0.350305 * Z  +  32.327427
  Z_new =  -0.542325 * X  +  -0.324153 * Y  +  -0.775118 * Z  +  23.450773 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.745497    0.396095  [ DEG:  -157.3054     22.6946 ]
  Theta =   0.573202    2.568390  [ DEG:    32.8421    147.1579 ]
  Phi   =  -1.897019    1.244574  [ DEG:  -108.6912     71.3088 ]
 
# 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: T0354TS393_3                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS393_3.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   53   3.04   50.94  26.427
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS393_3
PFRMAT TS
TARGET T0354
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      53.056  15.862  13.385  1.00 25.00           C
ATOM      2  CA  GLU     2      52.630  19.674  12.997  1.00 25.00           C
ATOM      3  CA  ILE     3      51.043  21.643  15.913  1.00 25.00           C
ATOM      4  CA  GLN     4      50.487  18.091  17.233  1.00 25.00           C
ATOM      5  CA  GLU     5      53.447  18.491  19.631  1.00 25.00           C
ATOM      6  CA  ILE     6      52.025  21.825  20.868  1.00 25.00           C
ATOM      7  CA  SER     7      48.609  20.186  21.429  1.00 25.00           C
ATOM      8  CA  LYS     8      50.266  17.342  23.387  1.00 25.00           C
ATOM      9  CA  LEU     9      52.156  19.888  25.534  1.00 25.00           C
ATOM     10  CA  ALA    10      48.891  21.769  26.221  1.00 25.00           C
ATOM     11  CA  ILE    11      47.185  18.490  27.224  1.00 25.00           C
ATOM     12  CA  GLU    12      50.091  17.669  29.579  1.00 25.00           C
ATOM     13  CA  ALA    13      49.838  21.154  31.147  1.00 25.00           C
ATOM     14  CA  LEU    14      46.068  20.686  31.637  1.00 25.00           C
ATOM     15  CA  GLU    15      46.680  17.284  33.287  1.00 25.00           C
ATOM     16  CA  ASP    16      49.286  18.855  35.614  1.00 25.00           C
ATOM     17  CA  ILE    17      50.207  22.547  36.092  1.00 25.00           C
ATOM     18  CA  LYS    18      47.640  24.615  34.308  1.00 25.00           C
ATOM     19  CA  GLY    19      44.278  24.173  36.124  1.00 25.00           C
ATOM     20  CA  LYS    20      44.820  27.300  38.217  1.00 25.00           C
ATOM     21  CA  ASP    21      44.859  29.104  34.867  1.00 25.00           C
ATOM     22  CA  ILE    22      41.548  27.792  33.703  1.00 25.00           C
ATOM     23  CA  ILE    23      43.382  26.495  30.656  1.00 25.00           C
ATOM     24  CA  GLU    24      43.208  28.979  27.745  1.00 25.00           C
ATOM     25  CA  LEU    25      40.173  30.365  25.882  1.00 25.00           C
ATOM     26  CA  ASP    26      39.041  28.084  22.980  1.00 25.00           C
ATOM     27  CA  THR    27      40.637  27.580  19.554  1.00 25.00           C
ATOM     28  CA  SER    28      39.880  28.167  15.871  1.00 25.00           C
ATOM     29  CA  LYS    29      37.606  26.638  13.263  1.00 25.00           C
ATOM     30  CA  LEU    30      35.587  24.738  15.891  1.00 25.00           C
ATOM     31  CA  THR    31      34.661  24.099  19.508  1.00 25.00           C
ATOM     32  CA  SER    32      36.700  21.514  21.447  1.00 25.00           C
ATOM     33  CA  LEU    33      36.337  18.235  23.434  1.00 25.00           C
ATOM     34  CA  PHE    34      36.494  18.718  27.239  1.00 25.00           C
ATOM     35  CA  GLN    35      40.295  18.817  27.526  1.00 25.00           C
ATOM     36  CA  ARG    36      41.037  21.009  24.458  1.00 25.00           C
ATOM     37  CA  MET    37      38.707  23.477  26.175  1.00 25.00           C
ATOM     38  CA  ILE    38      35.452  25.175  25.153  1.00 25.00           C
ATOM     39  CA  VAL    39      34.418  28.805  25.218  1.00 25.00           C
ATOM     40  CA  ALA    40      34.666  31.545  27.786  1.00 25.00           C
ATOM     41  CA  THR    41      32.039  32.166  30.447  1.00 25.00           C
ATOM     42  CA  GLY    42      29.253  34.161  32.021  1.00 25.00           C
ATOM     43  CA  ASP    43      29.293  31.608  34.894  1.00 25.00           C
ATOM     44  CA  SER    44      32.961  31.463  36.018  1.00 25.00           C
ATOM     45  CA  ASN    45      33.131  35.067  34.814  1.00 25.00           C
ATOM     46  CA  ARG    46      36.172  36.140  36.881  1.00 25.00           C
ATOM     47  CA  GLN    47      37.803  32.724  36.302  1.00 25.00           C
ATOM     48  CA  VAL    48      37.156  33.026  32.539  1.00 25.00           C
ATOM     49  CA  LYS    49      38.710  36.526  32.528  1.00 25.00           C
ATOM     50  CA  ALA    50      41.777  35.197  34.398  1.00 25.00           C
ATOM     51  CA  LEU    51      42.118  32.348  31.862  1.00 25.00           C
ATOM     52  CA  ALA    52      41.893  34.856  28.976  1.00 25.00           C
ATOM     53  CA  ASN    53      44.590  37.023  30.616  1.00 25.00           C
ATOM     54  CA  SER    54      46.839  33.951  31.036  1.00 25.00           C
ATOM     55  CA  VAL    55      46.321  33.040  27.352  1.00 25.00           C
ATOM     56  CA  GLN    56      47.212  36.617  26.315  1.00 25.00           C
ATOM     57  CA  VAL    57      50.381  36.476  28.462  1.00 25.00           C
ATOM     58  CA  LYS    58      51.349  33.136  26.856  1.00 25.00           C
ATOM     59  CA  LEU    59      50.804  34.626  23.371  1.00 25.00           C
ATOM     60  CA  LYS    60      52.985  37.637  24.290  1.00 25.00           C
ATOM     61  CA  GLU    61      55.734  35.291  25.560  1.00 25.00           C
ATOM     62  CA  ALA    62      57.940  32.200  26.073  1.00 25.00           C
ATOM     63  CA  GLY    63      58.351  32.354  22.287  1.00 25.00           C
ATOM     64  CA  VAL    64      54.843  30.963  22.157  1.00 25.00           C
ATOM     65  CA  ASP    65      51.309  30.625  20.659  1.00 25.00           C
ATOM     66  CA  ILE    66      47.631  31.538  20.893  1.00 25.00           C
ATOM     67  CA  VAL    67      44.077  32.584  21.776  1.00 25.00           C
ATOM     68  CA  GLY    68      40.335  32.480  20.857  1.00 25.00           C
ATOM     69  CA  SER    69      36.541  32.319  20.535  1.00 25.00           C
ATOM     70  CA  GLU    70      34.648  30.050  18.167  1.00 25.00           C
ATOM     71  CA  GLY    71      31.720  28.707  20.163  1.00 25.00           C
ATOM     72  CA  HIS    72      27.958  28.251  20.304  1.00 25.00           C
ATOM     73  CA  GLU    73      26.069  25.073  21.095  1.00 25.00           C
ATOM     74  CA  SER    74      28.290  22.033  20.490  1.00 25.00           C
ATOM     75  CA  GLY    75      30.691  23.503  23.008  1.00 25.00           C
ATOM     76  CA  GLU    76      29.952  20.272  24.971  1.00 25.00           C
ATOM     77  CA  TRP    77      31.413  17.873  27.516  1.00 25.00           C
ATOM     78  CA  VAL    78      30.258  19.685  30.701  1.00 25.00           C
ATOM     79  CA  LEU    79      29.179  21.069  34.121  1.00 25.00           C
ATOM     80  CA  VAL    80      26.748  22.040  36.837  1.00 25.00           C
ATOM     81  CA  ASP    81      28.299  25.542  36.728  1.00 25.00           C
ATOM     82  CA  ALA    82      31.567  23.967  37.757  1.00 25.00           C
ATOM     83  CA  GLY    83      33.002  27.058  39.408  1.00 25.00           C
ATOM     84  CA  ASP    84      36.548  27.338  38.013  1.00 25.00           C
ATOM     85  CA  VAL    85      37.068  24.097  36.028  1.00 25.00           C
ATOM     86  CA  VAL    86      34.286  25.089  33.590  1.00 25.00           C
ATOM     87  CA  VAL    87      31.480  25.299  31.026  1.00 25.00           C
ATOM     88  CA  HIS    88      30.479  26.006  27.407  1.00 25.00           C
ATOM     89  CA  VAL    89      28.348  28.840  28.938  1.00 25.00           C
ATOM     90  CA  MET    90      27.318  30.720  25.777  1.00 25.00           C
ATOM     91  CA  LEU    91      25.839  33.684  27.686  1.00 25.00           C
ATOM     92  CA  PRO    92      29.326  35.076  27.080  1.00 25.00           C
ATOM     93  CA  ALA    93      31.080  33.927  23.875  1.00 25.00           C
ATOM     94  CA  VAL    94      31.056  37.519  22.545  1.00 25.00           C
ATOM     95  CA  ARG    95      32.541  38.775  25.844  1.00 25.00           C
ATOM     96  CA  ASP    96      35.277  36.102  25.659  1.00 25.00           C
ATOM     97  CA  TYR    97      36.070  37.129  22.055  1.00 25.00           C
ATOM     98  CA  TYR    98      36.287  40.800  23.124  1.00 25.00           C
ATOM     99  CA  ASP    99      38.647  39.854  25.987  1.00 25.00           C
ATOM    100  CA  ILE   100      40.839  37.866  23.557  1.00 25.00           C
ATOM    101  CA  GLU   101      40.947  40.858  21.168  1.00 25.00           C
ATOM    102  CA  ALA   102      41.946  43.162  24.060  1.00 25.00           C
ATOM    103  CA  LEU   103      44.720  40.725  25.075  1.00 25.00           C
ATOM    104  CA  TRP   104      45.987  40.623  21.462  1.00 25.00           C
ATOM    105  CA  GLY   105      47.416  38.660  18.535  1.00 25.00           C
ATOM    106  CA  GLY   106      48.786  36.076  16.149  1.00 25.00           C
ATOM    107  CA  GLN   107      47.297  34.889  12.907  1.00 25.00           C
ATOM    108  CA  LYS   108      46.620  35.392   9.149  1.00 25.00           C
ATOM    109  CA  PRO   109      44.530  34.558   6.135  1.00 25.00           C
ATOM    110  CA  SER   110      41.358  35.201   8.127  1.00 25.00           C
ATOM    111  CA  PHE   111      38.273  37.152   7.009  1.00 25.00           C
ATOM    112  CA  ALA   112      36.376  40.369   6.880  1.00 25.00           C
ATOM    113  CA  VAL   113      35.144  43.891   7.481  1.00 25.00           C
ATOM    114  CA  GLY   114      35.970  47.262   5.979  1.00 25.00           C
ATOM    115  CA  ALA   115      37.228  50.828   5.341  1.00 25.00           C
ATOM    116  CA  ALA   116      40.723  52.301   5.295  1.00 25.00           C
ATOM    117  CA  LYS   117      43.321  53.182   2.661  1.00 25.00           C
ATOM    118  CA  PRO   118      45.825  55.658   3.946  1.00 25.00           C
ATOM    119  CA  TRP   119      46.334  55.306   7.651  1.00 25.00           C
ATOM    120  CA  SER   120      45.016  56.354  11.060  1.00 25.00           C
ATOM    121  CA  ALA   121      48.246  57.452  12.735  1.00 25.00           C
ATOM    122  CA  VAL   122      51.317  58.863  10.965  1.00 25.00           C
ATOM    123  CA  LEU   123      54.073  58.270  13.434  1.00 25.00           C
ATOM    124  CA  GLU   124      54.430  55.405  15.949  1.00 25.00           C
ATOM    125  CA  HIS   125      54.007  52.845  13.131  1.00 25.00           C
ATOM    126  CA  HIS   126      56.828  54.230  11.004  1.00 25.00           C
ATOM    127  CA  HIS   127      59.380  54.223  13.874  1.00 25.00           C
ATOM    128  CA  HIS   128      60.031  50.466  13.364  1.00 25.00           C
ATOM    129  CA  HIS   129      62.911  48.089  14.083  1.00 25.00           C
ATOM    130  CA  HIS   130      60.766  45.092  15.209  1.00 25.00           C
TER
END
