
#######################################################
#                                                     #
#                        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 T0367TS393_3-D1
# Molecule2: number of CA atoms  123 (  996),  selected  123 , name T0367_D1.pdb
# PARAMETERS: T0367TS393_3-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      -       -           -
LGA    E       3      -       -           -
LGA    L       4      -       -           -
LGA    E       5      -       -           -
LGA    L       6      -       -           -
LGA    R       7      -       -           -
LGA    I       8      -       -           -
LGA    R       9      -       -           -
LGA    K      10      -       -           -
LGA    A      11      -       -           -
LGA    E      12      -       -           -
LGA    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    E      23      -       -           -
LGA    M      24      -       -           -
LGA    G      25      D       2          2.637
LGA    L      26      E       3          1.899
LGA    Y      27      L       4          2.543
LGA    E      28      E       5          2.128
LGA    R      29      L       6          1.849
LGA    C      30      R       7          1.799
LGA    C      31      I       8          1.477
LGA    S      32      R       9          1.514
LGA    T      33      K      10          1.585
LGA    A      34      A      11          1.381
LGA    Y      35      E      12          1.210
LGA    Y      36      K      13          1.493
LGA    A      37      L      14          1.384
LGA    M      38      V      15          0.886
LGA    F      39      Q      16          0.736
LGA    H      40      D      17          0.995
LGA    A      41      A      18          0.972
LGA    A      42      K      19          0.541
LGA    K      43      K      20          0.499
LGA    A      44      E      21          1.270
LGA    M      45      F      22          1.652
LGA    L      46      E      23          1.746
LGA    L      47      M      24          1.840
LGA    G      48      G      25          2.476
LGA    Y      49      L      26          2.369
LGA    G      50      Y      27          3.874
LGA    -       -      E      28           -
LGA    R      51      R      29          1.969
LGA    -       -      C      30           -
LGA    -       -      C      31           -
LGA    D      52      S      32           #
LGA    S      53      -       -           -
LGA    K      54      -       -           -
LGA    T      55      T      33           #
LGA    H      56      A      34           -
LGA    R      57      Y      35           -
LGA    G      58      Y      36          3.178
LGA    T      59      A      37           -
LGA    I      60      -       -           -
LGA    Y      61      -       -           -
LGA    L      62      M      38          3.108
LGA    I      63      F      39          3.689
LGA    W      64      H      40          3.638
LGA    E      65      A      41          0.783
LGA    C      66      A      42          2.405
LGA    -       -      K      43           -
LGA    R      67      A      44          3.765
LGA    E      68      M      45          3.369
LGA    E      69      L      46           -
LGA    L      70      L      47           -
LGA    G      71      G      48           -
LGA    L      72      Y      49           -
LGA    S      73      G      50           -
LGA    D      74      -       -           -
LGA    D      75      -       -           -
LGA    D      76      -       -           -
LGA    C      77      -       -           -
LGA    S      78      -       -           -
LGA    K      79      -       -           -
LGA    L      80      -       -           -
LGA    S      81      -       -           -
LGA    R      82      -       -           -
LGA    A      83      -       -           -
LGA    F      84      -       -           -
LGA    D      85      -       -           -
LGA    L      86      -       -           -
LGA    R      87      -       -           -
LGA    E      88      -       -           -
LGA    E      89      -       -           -
LGA    S      90      -       -           -
LGA    D      91      -       -           -
LGA    Y      92      -       -           -
LGA    G      93      -       -           -
LGA    I      94      -       -           -
LGA    Y      95      -       -           -
LGA    K      96      -       -           -
LGA    E      97      -       -           -
LGA    V      98      -       -           -
LGA    S      99      -       -           -
LGA    K     100      -       -           -
LGA    D     101      -       -           -
LGA    L     102      -       -           -
LGA    A     103      -       -           -
LGA    I     104      R      51           #
LGA    K     105      D      52          1.248
LGA    I     106      S      53          3.572
LGA    -       -      K      54           -
LGA    -       -      T      55           -
LGA    -       -      H      56           -
LGA    -       -      R      57           -
LGA    -       -      G      58           -
LGA    L     107      T      59          2.365
LGA    K     108      I      60           -
LGA    D     109      Y      61           -
LGA    -       -      L      62           -
LGA    A     110      I      63          2.894
LGA    E     111      W      64          4.126
LGA    I     112      E      65          5.337
LGA    F     113      C      66          4.126
LGA    V     114      R      67          1.190
LGA    Q     115      E      68          2.878
LGA    K     116      E      69          1.371
LGA    -       -      L      70           -
LGA    A     117      G      71          2.342
LGA    K     118      L      72           #
LGA    N     119      -       -           -
LGA    A     120      -       -           -
LGA    V     121      S      73           #
LGA    N     122      D      74           -
LGA    K     123      D      75           -
LGA    -       -      D      76           -
LGA    -       -      C      77           -
LGA    -       -      S      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      S      81           -
LGA    -       -      R      82           -
LGA    -       -      A      83           -
LGA    -       -      F      84           -
LGA    -       -      D      85           -
LGA    -       -      L      86           -
LGA    -       -      R      87           -
LGA    -       -      E      88           -
LGA    -       -      E      89           -
LGA    -       -      S      90           -
LGA    -       -      D      91           -
LGA    -       -      Y      92           -
LGA    -       -      G      93           -
LGA    -       -      I      94           -
LGA    -       -      Y      95           -
LGA    -       -      K      96           -
LGA    -       -      E      97           -
LGA    -       -      V      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      D     101           -
LGA    -       -      L     102           -
LGA    -       -      A     103           -
LGA    -       -      I     104           -
LGA    -       -      K     105           -
LGA    -       -      I     106           -
LGA    -       -      L     107           -
LGA    -       -      K     108           -
LGA    -       -      D     109           -
LGA    -       -      A     110           -
LGA    -       -      E     111           -
LGA    -       -      I     112           -
LGA    -       -      F     113           -
LGA    -       -      V     114           -
LGA    -       -      Q     115           -
LGA    -       -      K     116           -
LGA    -       -      A     117           -
LGA    -       -      K     118           -
LGA    -       -      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     46    2.44    13.04     27.273     1.810

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.879139 * X  +  -0.442991 * Y  +   0.175708 * Z  +  48.521832
  Y_new =   0.010151 * X  +   0.351207 * Y  +   0.936243 * Z  +  31.098087
  Z_new =  -0.476457 * X  +   0.824872 * Y  +  -0.304263 * Z  +  30.140869 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.924174   -1.217419  [ DEG:   110.2470    -69.7530 ]
  Theta =   0.496620    2.644973  [ DEG:    28.4542    151.5458 ]
  Phi   =   3.130046   -0.011546  [ DEG:   179.3385     -0.6615 ]
 
# 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: T0367TS393_3-D1                               
REMARK     2: T0367_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0367TS393_3-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   46   2.44   13.04  27.273
REMARK  ---------------------------------------------------------- 
MOLECULE T0367TS393_3-D1
PFRMAT TS
TARGET T0367
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      91.342  28.212  29.269  1.00 25.00           C
ATOM      2  CA  ASP     2      88.512  25.700  29.230  1.00 25.00           C
ATOM      3  CA  GLU     3      87.071  22.678  31.089  1.00 25.00           C
ATOM      4  CA  LEU     4      85.721  24.980  33.836  1.00 25.00           C
ATOM      5  CA  GLU     5      84.114  27.235  31.190  1.00 25.00           C
ATOM      6  CA  LEU     6      82.505  24.183  29.530  1.00 25.00           C
ATOM      7  CA  ARG     7      81.154  23.020  32.919  1.00 25.00           C
ATOM      8  CA  ILE     8      79.715  26.509  33.571  1.00 25.00           C
ATOM      9  CA  ARG     9      78.049  26.492  30.121  1.00 25.00           C
ATOM     10  CA  LYS    10      76.550  23.041  30.835  1.00 25.00           C
ATOM     11  CA  ALA    11      75.220  24.289  34.204  1.00 25.00           C
ATOM     12  CA  GLU    12      73.665  27.338  32.487  1.00 25.00           C
ATOM     13  CA  LYS    13      72.017  25.065  29.883  1.00 25.00           C
ATOM     14  CA  LEU    14      70.628  22.837  32.670  1.00 25.00           C
ATOM     15  CA  VAL    15      69.240  25.917  34.475  1.00 25.00           C
ATOM     16  CA  GLN    16      67.595  27.108  31.227  1.00 25.00           C
ATOM     17  CA  ASP    17      66.037  23.646  30.718  1.00 25.00           C
ATOM     18  CA  ALA    18      64.707  23.690  34.309  1.00 25.00           C
ATOM     19  CA  LYS    19      63.210  27.168  33.739  1.00 25.00           C
ATOM     20  CA  LYS    20      61.543  25.949  30.513  1.00 25.00           C
ATOM     21  CA  GLU    21      60.103  22.926  32.372  1.00 25.00           C
ATOM     22  CA  PHE    22      58.752  25.228  35.119  1.00 25.00           C
ATOM     23  CA  GLU    23      57.145  27.484  32.474  1.00 25.00           C
ATOM     24  CA  MET    24      55.537  24.431  30.813  1.00 25.00           C
ATOM     25  CA  GLY    25      54.185  23.268  34.202  1.00 25.00           C
ATOM     26  CA  LEU    26      52.747  26.758  34.853  1.00 25.00           C
ATOM     27  CA  TYR    27      51.081  26.741  31.405  1.00 25.00           C
ATOM     28  CA  GLU    28      49.581  23.290  32.119  1.00 25.00           C
ATOM     29  CA  ARG    29      48.252  24.537  35.487  1.00 25.00           C
ATOM     30  CA  CYS    30      46.696  27.587  33.771  1.00 25.00           C
ATOM     31  CA  CYS    31      45.049  25.313  31.166  1.00 25.00           C
ATOM     32  CA  SER    32      43.659  23.086  33.954  1.00 25.00           C
ATOM     33  CA  THR    33      42.272  26.166  35.757  1.00 25.00           C
ATOM     34  CA  ALA    34      40.627  27.356  32.511  1.00 25.00           C
ATOM     35  CA  TYR    35      39.069  23.895  32.002  1.00 25.00           C
ATOM     36  CA  TYR    36      37.738  23.939  35.593  1.00 25.00           C
ATOM     37  CA  ALA    37      36.242  27.417  35.022  1.00 25.00           C
ATOM     38  CA  MET    38      34.575  26.198  31.796  1.00 25.00           C
ATOM     39  CA  PHE    39      33.134  23.175  33.655  1.00 25.00           C
ATOM     40  CA  HIS    40      31.784  25.477  36.402  1.00 25.00           C
ATOM     41  CA  ALA    41      30.177  27.732  33.757  1.00 25.00           C
ATOM     42  CA  ALA    42      28.568  24.679  32.095  1.00 25.00           C
ATOM     43  CA  LYS    43      27.217  23.517  35.485  1.00 25.00           C
ATOM     44  CA  ALA    44      25.778  27.005  36.136  1.00 25.00           C
ATOM     45  CA  MET    45      24.112  26.989  32.688  1.00 25.00           C
ATOM     46  CA  LEU    46      22.613  23.539  33.402  1.00 25.00           C
ATOM     47  CA  LEU    47      21.282  24.786  36.770  1.00 25.00           C
ATOM     48  CA  GLY    48      19.727  27.836  35.053  1.00 25.00           C
ATOM     49  CA  TYR    49      22.205  30.529  36.178  1.00 25.00           C
ATOM     50  CA  GLY    50      24.892  32.542  37.957  1.00 25.00           C
ATOM     51  CA  ARG    51      28.119  33.972  39.468  1.00 25.00           C
ATOM     52  CA  ASP    52      28.591  35.481  42.943  1.00 25.00           C
ATOM     53  CA  SER    53      31.709  35.672  45.108  1.00 25.00           C
ATOM     54  CA  LYS    54      35.175  34.323  45.637  1.00 25.00           C
ATOM     55  CA  THR    55      37.109  32.858  42.755  1.00 25.00           C
ATOM     56  CA  HIS    56      40.788  32.545  41.832  1.00 25.00           C
ATOM     57  CA  ARG    57      43.331  34.408  39.700  1.00 25.00           C
ATOM     58  CA  GLY    58      40.782  33.842  36.898  1.00 25.00           C
ATOM     59  CA  THR    59      42.653  36.326  34.661  1.00 25.00           C
ATOM     60  CA  ILE    60      45.955  34.525  35.382  1.00 25.00           C
ATOM     61  CA  TYR    61      44.341  31.163  34.510  1.00 25.00           C
ATOM     62  CA  LEU    62      43.002  32.628  31.235  1.00 25.00           C
ATOM     63  CA  ILE    63      46.485  33.978  30.386  1.00 25.00           C
ATOM     64  CA  TRP    64      48.017  30.541  31.099  1.00 25.00           C
ATOM     65  CA  GLU    65      45.406  28.882  28.841  1.00 25.00           C
ATOM     66  CA  CYS    66      46.183  31.392  26.055  1.00 25.00           C
ATOM     67  CA  ARG    67      49.927  30.676  26.422  1.00 25.00           C
ATOM     68  CA  GLU    68      49.252  26.912  26.223  1.00 25.00           C
ATOM     69  CA  GLU    69      47.145  27.431  23.067  1.00 25.00           C
ATOM     70  CA  LEU    70      46.110  23.839  23.434  1.00 25.00           C
ATOM     71  CA  GLY    71      44.715  20.714  21.681  1.00 25.00           C
ATOM     72  CA  LEU    72      41.207  19.602  22.742  1.00 25.00           C
ATOM     73  CA  SER    73      40.238  21.607  19.605  1.00 25.00           C
ATOM     74  CA  ASP    74      36.553  22.378  19.880  1.00 25.00           C
ATOM     75  CA  ASP    75      35.057  22.690  23.392  1.00 25.00           C
ATOM     76  CA  ASP    76      38.555  23.207  24.863  1.00 25.00           C
ATOM     77  CA  CYS    77      39.281  25.911  22.250  1.00 25.00           C
ATOM     78  CA  SER    78      35.975  27.651  23.097  1.00 25.00           C
ATOM     79  CA  LYS    79      36.842  27.538  26.825  1.00 25.00           C
ATOM     80  CA  LEU    80      40.291  29.033  26.094  1.00 25.00           C
ATOM     81  CA  SER    81      38.671  31.823  24.029  1.00 25.00           C
ATOM     82  CA  ARG    82      36.229  32.554  26.887  1.00 25.00           C
ATOM     83  CA  ALA    83      39.142  32.706  29.370  1.00 25.00           C
ATOM     84  CA  PHE    84      41.017  35.117  27.059  1.00 25.00           C
ATOM     85  CA  ASP    85      37.898  37.323  26.789  1.00 25.00           C
ATOM     86  CA  LEU    86      37.551  37.341  30.603  1.00 25.00           C
ATOM     87  CA  ARG    87      41.235  38.325  30.959  1.00 25.00           C
ATOM     88  CA  GLU    88      40.747  41.161  28.431  1.00 25.00           C
ATOM     89  CA  GLU    89      37.677  42.388  30.363  1.00 25.00           C
ATOM     90  CA  SER    90      36.648  43.548  33.899  1.00 25.00           C
ATOM     91  CA  ASP    91      39.547  46.004  33.381  1.00 25.00           C
ATOM     92  CA  TYR    92      42.699  46.521  35.341  1.00 25.00           C
ATOM     93  CA  GLY    93      42.067  50.184  36.332  1.00 25.00           C
ATOM     94  CA  ILE    94      44.751  50.062  39.022  1.00 25.00           C
ATOM     95  CA  TYR    95      46.274  50.655  42.458  1.00 25.00           C
ATOM     96  CA  LYS    96      49.859  49.596  42.195  1.00 25.00           C
ATOM     97  CA  GLU    97      51.736  47.211  44.457  1.00 25.00           C
ATOM     98  CA  VAL    98      52.974  43.705  43.534  1.00 25.00           C
ATOM     99  CA  SER    99      54.392  40.440  42.144  1.00 25.00           C
ATOM    100  CA  LYS   100      52.675  41.710  38.927  1.00 25.00           C
ATOM    101  CA  ASP   101      55.834  40.578  37.081  1.00 25.00           C
ATOM    102  CA  LEU   102      54.324  37.094  36.581  1.00 25.00           C
ATOM    103  CA  ALA   103      51.105  38.659  35.217  1.00 25.00           C
ATOM    104  CA  ILE   104      53.149  40.822  32.806  1.00 25.00           C
ATOM    105  CA  LYS   105      55.073  37.729  31.624  1.00 25.00           C
ATOM    106  CA  ILE   106      51.776  35.863  31.061  1.00 25.00           C
ATOM    107  CA  LEU   107      50.412  38.827  29.055  1.00 25.00           C
ATOM    108  CA  LYS   108      53.598  38.887  26.930  1.00 25.00           C
ATOM    109  CA  ASP   109      53.271  35.125  26.290  1.00 25.00           C
ATOM    110  CA  ALA   110      49.615  35.594  25.253  1.00 25.00           C
ATOM    111  CA  GLU   111      50.627  38.415  22.869  1.00 25.00           C
ATOM    112  CA  ILE   112      53.348  36.189  21.350  1.00 25.00           C
ATOM    113  CA  PHE   113      50.805  33.364  20.877  1.00 25.00           C
ATOM    114  CA  VAL   114      48.384  35.795  19.177  1.00 25.00           C
ATOM    115  CA  GLN   115      51.182  36.998  16.857  1.00 25.00           C
ATOM    116  CA  LYS   116      52.048  33.373  15.979  1.00 25.00           C
ATOM    117  CA  ALA   117      48.364  32.651  15.221  1.00 25.00           C
ATOM    118  CA  LYS   118      48.193  35.750  12.977  1.00 25.00           C
ATOM    119  CA  ASN   119      51.352  34.618  11.131  1.00 25.00           C
ATOM    120  CA  ALA   120      49.841  31.134  10.631  1.00 25.00           C
ATOM    121  CA  VAL   121      46.623  32.699   9.267  1.00 25.00           C
ATOM    122  CA  ASN   122      48.668  34.862   6.857  1.00 25.00           C
ATOM    123  CA  LYS   123      50.632  32.315   4.810  1.00 25.00           C
TER
END
