
#######################################################
#                                                     #
#                        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  153 (  153),  selected  153 , name T0332TS393_2-D1
# Molecule2: number of CA atoms  153 ( 1194),  selected  153 , name T0332_D1.pdb
# PARAMETERS: T0332TS393_2-D1.T0332_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R       7      R       7          1.378
LGA    L       8      L       8          0.719
LGA    I       9      I       9          0.728
LGA    V      10      V      10          1.068
LGA    V      11      V      11          1.097
LGA    A      12      A      12          1.940
LGA    S      13      S      13          4.023
LGA    L      14      L      14          1.636
LGA    I      15      I      15          0.906
LGA    D      16      D      16          1.762
LGA    K      17      K      17          1.938
LGA    P      18      P      18          0.717
LGA    T      19      T      19          0.475
LGA    N      20      N      20          0.675
LGA    L      21      L      21          0.580
LGA    G      22      G      22          0.512
LGA    G      23      G      23          1.071
LGA    L      24      L      24          1.099
LGA    C      25      C      25          0.482
LGA    R      26      R      26          0.977
LGA    T      27      T      27          1.094
LGA    C      28      C      28          0.479
LGA    E      29      E      29          0.797
LGA    V      30      V      30          1.127
LGA    F      31      F      31          0.339
LGA    G      32      G      32          0.964
LGA    A      33      A      33          1.305
LGA    S      34      S      34          2.307
LGA    V      35      V      35          1.909
LGA    L      36      L      36          1.865
LGA    V      37      V      37          2.124
LGA    V      38      V      38          2.724
LGA    G      39      G      39          2.652
LGA    S      40      -       -           -
LGA    L      41      -       -           -
LGA    Q      42      S      40           #
LGA    C      43      L      41           #
LGA    I      44      Q      42          1.754
LGA    S      45      C      43          3.745
LGA    D      46      I      44           #
LGA    K      47      S      45          2.091
LGA    Q      48      D      46          1.778
LGA    F      49      K      47           -
LGA    Q      50      Q      48           -
LGA    H      51      F      49          5.854
LGA    L      52      Q      50          1.538
LGA    -       -      H      51           -
LGA    -       -      L      52           -
LGA    S      53      S      53          3.099
LGA    V      54      V      54          5.269
LGA    S      55      S      55          2.261
LGA    A      56      A      56          2.711
LGA    E      57      E      57          2.971
LGA    -       -      Q      58           -
LGA    Q      58      W      59          0.882
LGA    W      59      L      60          3.242
LGA    L      60      P      61          2.674
LGA    P      61      L      62          1.762
LGA    L      62      V      63          3.362
LGA    V      63      E      64          1.415
LGA    E      64      V      65          1.430
LGA    V      65      K      66          3.724
LGA    K      66      P      67          1.891
LGA    P      67      P      68          2.906
LGA    P      68      Q      69          3.074
LGA    Q      69      L      70          5.513
LGA    L      70      I      71          1.670
LGA    I      71      -       -           -
LGA    D      72      D      72          1.320
LGA    Y      73      Y      73          0.787
LGA    L      74      L      74          2.340
LGA    Q      75      Q      75          3.075
LGA    Q      76      Q      76          2.264
LGA    K      77      K      77          1.154
LGA    K      78      K      78          3.344
LGA    T      79      T      79          4.023
LGA    E      80      E      80          3.068
LGA    G      81      -       -           -
LGA    Y      82      G      81          3.195
LGA    T      83      Y      82          3.967
LGA    I      84      T      83           #
LGA    I      85      I      84           #
LGA    G      86      I      85          3.342
LGA    V      87      G      86          1.211
LGA    E      88      V      87          3.484
LGA    Q      89      E      88          1.729
LGA    T      90      Q      89           #
LGA    A      91      T      90           -
LGA    K      92      A      91           -
LGA    -       -      K      92           -
LGA    S      93      S      93           #
LGA    L      94      L      94          3.280
LGA    D      95      D      95          2.105
LGA    L      96      L      96          2.128
LGA    T      97      T      97          3.077
LGA    Q      98      Q      98          3.045
LGA    Y      99      Y      99          2.813
LGA    C     100      C     100          2.796
LGA    F     101      F     101          2.015
LGA    P     102      P     102          3.815
LGA    E     103      E     103          3.233
LGA    K     104      K     104          1.372
LGA    S     105      S     105          1.190
LGA    L     106      L     106          2.025
LGA    L     107      L     107          2.435
LGA    L     108      L     108          2.964
LGA    L     109      L     109          1.888
LGA    G     110      G     110          1.678
LGA    N     111      N     111          2.819
LGA    E     112      E     112          1.885
LGA    R     113      R     113          2.168
LGA    E     114      E     114          2.950
LGA    G     115      G     115          0.712
LGA    I     116      I     116          0.900
LGA    P     117      P     117          0.528
LGA    A     118      A     118          1.281
LGA    N     119      N     119          2.052
LGA    L     120      L     120          2.197
LGA    I     121      I     121          1.789
LGA    Q     122      Q     122          1.769
LGA    Q     123      Q     123          1.497
LGA    L     124      L     124          1.388
LGA    D     125      D     125          1.313
LGA    V     126      V     126          0.973
LGA    C     127      C     127          1.010
LGA    V     128      V     128          1.184
LGA    E     129      E     129          0.923
LGA    I     130      I     130          5.442
LGA    P     131      P     131          4.554
LGA    Q     132      Q     132          2.598
LGA    Q     133      Q     133          1.519
LGA    G     134      G     134          1.951
LGA    I     135      I     135          1.828
LGA    I     136      I     136          0.902
LGA    R     137      R     137          0.545
LGA    S     138      S     138          1.476
LGA    L     139      L     139          0.287
LGA    N     140      N     140          1.544
LGA    V     141      V     141          1.808
LGA    H     142      H     142          0.509
LGA    V     143      V     143          2.057
LGA    S     144      S     144          2.569
LGA    G     145      G     145          1.356
LGA    A     146      A     146          0.770
LGA    L     147      L     147          2.227
LGA    L     148      L     148          2.385
LGA    I     149      I     149          1.371
LGA    W     150      W     150          1.025
LGA    E     151      E     151          2.257
LGA    Y     152      Y     152          2.469
LGA    T     153      T     153          1.596
LGA    R     154      R     154          1.569
LGA    Q     155      Q     155          2.657
LGA    Q     156      Q     156          2.770
LGA    -       -      L     157           -
LGA    L     157      L     158          1.300
LGA    L     158      S     159          4.545
LGA    S     159      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  153  153    5.0    137    2.32    81.75     59.363     5.654

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.598988 * X  +   0.683571 * Y  +   0.417065 * Z  +  27.508848
  Y_new =  -0.648882 * X  +   0.109156 * Y  +   0.753018 * Z  +  42.835011
  Z_new =   0.469217 * X  +  -0.721675 * Y  +   0.508940 * Z  +  31.023939 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.956575    2.185018  [ DEG:   -54.8077    125.1923 ]
  Theta =  -0.488404   -2.653189  [ DEG:   -27.9835   -152.0165 ]
  Phi   =  -0.825360    2.316232  [ DEG:   -47.2897    132.7103 ]
 
# 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: T0332TS393_2-D1                               
REMARK     2: T0332_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0332TS393_2-D1.T0332_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  153  153   5.0  137   2.32   81.75  59.363
REMARK  ---------------------------------------------------------- 
MOLECULE T0332TS393_2-D1
PFRMAT TS
TARGET T0332
MODEL 2
PARENT N/A
ATOM      7  CA  ARG     7      22.672  38.474  41.739  1.00 25.00           C
ATOM      8  CA  LEU     8      22.609  38.324  37.927  1.00 25.00           C
ATOM      9  CA  ILE     9      24.737  41.410  37.394  1.00 25.00           C
ATOM     10  CA  VAL    10      24.677  42.852  33.874  1.00 25.00           C
ATOM     11  CA  VAL    11      27.375  45.483  33.816  1.00 25.00           C
ATOM     12  CA  ALA    12      28.964  46.811  30.647  1.00 25.00           C
ATOM     13  CA  SER    13      32.242  48.582  30.036  1.00 25.00           C
ATOM     14  CA  LEU    14      32.686  51.216  27.278  1.00 25.00           C
ATOM     15  CA  ILE    15      29.187  50.939  25.673  1.00 25.00           C
ATOM     16  CA  ASP    16      29.425  53.267  22.623  1.00 25.00           C
ATOM     17  CA  LYS    17      27.079  55.476  20.548  1.00 25.00           C
ATOM     18  CA  PRO    18      23.814  54.904  22.372  1.00 25.00           C
ATOM     19  CA  THR    19      22.432  52.114  20.143  1.00 25.00           C
ATOM     20  CA  ASN    20      24.700  49.566  21.883  1.00 25.00           C
ATOM     21  CA  LEU    21      23.503  50.801  25.305  1.00 25.00           C
ATOM     22  CA  GLY    22      19.858  50.480  24.173  1.00 25.00           C
ATOM     23  CA  GLY    23      20.528  46.916  22.941  1.00 25.00           C
ATOM     24  CA  LEU    24      22.147  46.035  26.298  1.00 25.00           C
ATOM     25  CA  CYS    25      19.123  47.464  28.161  1.00 25.00           C
ATOM     26  CA  ARG    26      16.761  45.409  25.954  1.00 25.00           C
ATOM     27  CA  THR    27      18.814  42.252  26.655  1.00 25.00           C
ATOM     28  CA  CYS    28      18.670  42.964  30.414  1.00 25.00           C
ATOM     29  CA  GLU    29      14.875  43.433  30.205  1.00 25.00           C
ATOM     30  CA  VAL    30      14.545  40.119  28.315  1.00 25.00           C
ATOM     31  CA  PHE    31      16.321  38.103  31.016  1.00 25.00           C
ATOM     32  CA  GLY    32      16.092  40.204  34.209  1.00 25.00           C
ATOM     33  CA  ALA    33      19.885  40.404  34.259  1.00 25.00           C
ATOM     34  CA  SER    34      19.894  43.434  36.620  1.00 25.00           C
ATOM     35  CA  VAL    35      22.462  46.136  37.446  1.00 25.00           C
ATOM     36  CA  LEU    36      23.330  48.594  34.679  1.00 25.00           C
ATOM     37  CA  VAL    37      26.233  49.638  36.822  1.00 25.00           C
ATOM     38  CA  VAL    38      27.884  50.962  33.706  1.00 25.00           C
ATOM     39  CA  GLY    39      30.193  53.064  31.530  1.00 25.00           C
ATOM     40  CA  SER    40      31.463  56.640  31.258  1.00 25.00           C
ATOM     41  CA  LEU    41      31.660  56.173  27.536  1.00 25.00           C
ATOM     42  CA  GLN    42      29.011  57.785  25.261  1.00 25.00           C
ATOM     43  CA  CYS    43      27.149  58.085  28.594  1.00 25.00           C
ATOM     44  CA  ILE    44      23.815  59.682  29.660  1.00 25.00           C
ATOM     45  CA  SER    45      23.537  60.456  25.975  1.00 25.00           C
ATOM     46  CA  ASP    46      20.763  62.868  27.151  1.00 25.00           C
ATOM     47  CA  LYS    47      18.889  59.985  28.851  1.00 25.00           C
ATOM     48  CA  GLN    48      18.725  58.628  25.273  1.00 25.00           C
ATOM     49  CA  PHE    49      19.582  55.117  26.540  1.00 25.00           C
ATOM     50  CA  GLN    50      16.838  55.380  29.199  1.00 25.00           C
ATOM     51  CA  HIS    51      14.324  56.486  26.530  1.00 25.00           C
ATOM     52  CA  LEU    52      15.330  53.525  24.320  1.00 25.00           C
ATOM     53  CA  SER    53      14.884  51.134  27.277  1.00 25.00           C
ATOM     54  CA  VAL    54      11.527  52.199  28.555  1.00 25.00           C
ATOM     55  CA  SER    55      10.088  48.940  27.103  1.00 25.00           C
ATOM     56  CA  ALA    56      10.878  46.544  29.948  1.00 25.00           C
ATOM     57  CA  GLU    57      13.754  48.356  31.713  1.00 25.00           C
ATOM     58  CA  GLN    58      11.656  48.628  34.905  1.00 25.00           C
ATOM     59  CA  TRP    59      14.916  50.000  36.309  1.00 25.00           C
ATOM     60  CA  LEU    60      18.157  48.657  34.995  1.00 25.00           C
ATOM     61  CA  PRO    61      19.769  50.839  37.635  1.00 25.00           C
ATOM     62  CA  LEU    62      21.150  53.268  35.013  1.00 25.00           C
ATOM     63  CA  VAL    63      24.700  54.545  35.618  1.00 25.00           C
ATOM     64  CA  GLU    64      28.378  55.012  36.695  1.00 25.00           C
ATOM     65  CA  VAL    65      31.478  52.798  36.838  1.00 25.00           C
ATOM     66  CA  LYS    66      33.945  55.484  35.751  1.00 25.00           C
ATOM     67  CA  PRO    67      35.039  57.785  38.547  1.00 25.00           C
ATOM     68  CA  PRO    68      37.366  55.486  40.516  1.00 25.00           C
ATOM     69  CA  GLN    69      39.505  53.494  38.104  1.00 25.00           C
ATOM     70  CA  LEU    70      36.885  50.795  38.775  1.00 25.00           C
ATOM     71  CA  ILE    71      38.541  50.209  42.177  1.00 25.00           C
ATOM     72  CA  ASP    72      35.572  51.867  43.937  1.00 25.00           C
ATOM     73  CA  TYR    73      33.140  49.655  41.972  1.00 25.00           C
ATOM     74  CA  LEU    74      35.148  46.542  42.943  1.00 25.00           C
ATOM     75  CA  GLN    75      35.076  47.613  46.619  1.00 25.00           C
ATOM     76  CA  GLN    76      31.288  48.131  46.420  1.00 25.00           C
ATOM     77  CA  LYS    77      30.870  44.658  44.862  1.00 25.00           C
ATOM     78  CA  LYS    78      32.998  43.124  47.650  1.00 25.00           C
ATOM     79  CA  THR    79      30.871  44.907  50.289  1.00 25.00           C
ATOM     80  CA  GLU    80      27.602  43.038  49.476  1.00 25.00           C
ATOM     81  CA  GLY    81      29.033  39.636  48.421  1.00 25.00           C
ATOM     82  CA  TYR    82      28.869  39.463  44.615  1.00 25.00           C
ATOM     83  CA  THR    83      28.798  41.872  41.622  1.00 25.00           C
ATOM     84  CA  ILE    84      29.847  43.340  38.273  1.00 25.00           C
ATOM     85  CA  ILE    85      32.206  44.702  35.608  1.00 25.00           C
ATOM     86  CA  GLY    86      33.862  41.323  35.301  1.00 25.00           C
ATOM     87  CA  VAL    87      34.694  41.028  31.643  1.00 25.00           C
ATOM     88  CA  GLU    88      36.816  40.687  28.521  1.00 25.00           C
ATOM     89  CA  GLN    89      34.835  39.361  25.599  1.00 25.00           C
ATOM     90  CA  THR    90      33.283  37.373  22.698  1.00 25.00           C
ATOM     91  CA  ALA    91      32.621  34.294  20.504  1.00 25.00           C
ATOM     92  CA  LYS    92      33.746  30.688  20.945  1.00 25.00           C
ATOM     93  CA  SER    93      37.045  30.035  22.781  1.00 25.00           C
ATOM     94  CA  LEU    94      37.325  28.836  26.388  1.00 25.00           C
ATOM     95  CA  ASP    95      33.558  29.025  26.234  1.00 25.00           C
ATOM     96  CA  LEU    96      30.621  29.902  28.570  1.00 25.00           C
ATOM     97  CA  THR    97      30.393  26.090  28.871  1.00 25.00           C
ATOM     98  CA  GLN    98      32.926  26.141  31.743  1.00 25.00           C
ATOM     99  CA  TYR    99      32.186  29.189  33.884  1.00 25.00           C
ATOM    100  CA  CYS   100      29.820  28.630  36.814  1.00 25.00           C
ATOM    101  CA  PHE   101      26.772  30.971  36.505  1.00 25.00           C
ATOM    102  CA  PRO   102      24.676  30.709  39.675  1.00 25.00           C
ATOM    103  CA  GLU   103      28.018  31.135  41.404  1.00 25.00           C
ATOM    104  CA  LYS   104      26.650  34.582  42.186  1.00 25.00           C
ATOM    105  CA  SER   105      27.270  36.688  39.093  1.00 25.00           C
ATOM    106  CA  LEU   106      29.974  38.455  37.128  1.00 25.00           C
ATOM    107  CA  LEU   107      28.002  38.778  33.879  1.00 25.00           C
ATOM    108  CA  LEU   108      29.668  41.484  31.836  1.00 25.00           C
ATOM    109  CA  LEU   109      30.575  42.589  28.259  1.00 25.00           C
ATOM    110  CA  GLY   110      32.878  45.024  26.490  1.00 25.00           C
ATOM    111  CA  ASN   111      32.396  47.429  23.532  1.00 25.00           C
ATOM    112  CA  GLU   112      32.406  47.816  19.707  1.00 25.00           C
ATOM    113  CA  ARG   113      36.163  48.104  19.875  1.00 25.00           C
ATOM    114  CA  GLU   114      39.455  46.989  21.487  1.00 25.00           C
ATOM    115  CA  GLY   115      37.415  47.086  24.657  1.00 25.00           C
ATOM    116  CA  ILE   116      37.659  46.655  28.411  1.00 25.00           C
ATOM    117  CA  PRO   117      41.178  48.062  28.886  1.00 25.00           C
ATOM    118  CA  ALA   118      43.688  45.840  30.752  1.00 25.00           C
ATOM    119  CA  ASN   119      42.267  47.012  34.110  1.00 25.00           C
ATOM    120  CA  LEU   120      38.898  45.392  33.277  1.00 25.00           C
ATOM    121  CA  ILE   121      40.668  42.122  32.362  1.00 25.00           C
ATOM    122  CA  GLN   122      42.602  42.215  35.667  1.00 25.00           C
ATOM    123  CA  GLN   123      39.340  42.792  37.587  1.00 25.00           C
ATOM    124  CA  LEU   124      38.273  39.206  36.770  1.00 25.00           C
ATOM    125  CA  ASP   125      38.501  35.811  38.480  1.00 25.00           C
ATOM    126  CA  VAL   126      38.153  34.407  34.944  1.00 25.00           C
ATOM    127  CA  CYS   127      36.859  36.341  31.863  1.00 25.00           C
ATOM    128  CA  VAL   128      34.414  35.360  29.097  1.00 25.00           C
ATOM    129  CA  GLU   129      35.942  34.167  25.803  1.00 25.00           C
ATOM    130  CA  ILE   130      37.738  35.102  22.582  1.00 25.00           C
ATOM    131  CA  PRO   131      37.709  33.703  19.046  1.00 25.00           C
ATOM    132  CA  GLN   132      35.731  34.033  15.849  1.00 25.00           C
ATOM    133  CA  GLN   133      35.274  31.509  13.100  1.00 25.00           C
ATOM    134  CA  GLY   134      36.223  33.003   9.679  1.00 25.00           C
ATOM    135  CA  ILE   135      37.990  36.207  10.552  1.00 25.00           C
ATOM    136  CA  ILE   136      34.749  37.976  11.453  1.00 25.00           C
ATOM    137  CA  ARG   137      37.001  39.773  13.959  1.00 25.00           C
ATOM    138  CA  SER   138      33.802  40.604  15.700  1.00 25.00           C
ATOM    139  CA  LEU   139      30.536  40.000  17.504  1.00 25.00           C
ATOM    140  CA  ASN   140      28.359  43.009  16.796  1.00 25.00           C
ATOM    141  CA  VAL   141      28.070  43.626  20.569  1.00 25.00           C
ATOM    142  CA  HIS   142      24.869  44.033  22.633  1.00 25.00           C
ATOM    143  CA  VAL   143      23.189  41.239  20.625  1.00 25.00           C
ATOM    144  CA  SER   144      26.217  38.967  21.206  1.00 25.00           C
ATOM    145  CA  GLY   145      26.090  39.717  24.960  1.00 25.00           C
ATOM    146  CA  ALA   146      22.349  38.894  25.023  1.00 25.00           C
ATOM    147  CA  LEU   147      23.020  35.596  23.195  1.00 25.00           C
ATOM    148  CA  LEU   148      25.771  34.730  25.715  1.00 25.00           C
ATOM    149  CA  ILE   149      23.389  35.496  28.615  1.00 25.00           C
ATOM    150  CA  TRP   150      20.709  33.261  27.036  1.00 25.00           C
ATOM    151  CA  GLU   151      23.265  30.439  26.632  1.00 25.00           C
ATOM    152  CA  TYR   152      24.301  30.818  30.299  1.00 25.00           C
ATOM    153  CA  THR   153      20.630  30.675  31.376  1.00 25.00           C
ATOM    154  CA  ARG   154      20.112  27.510  29.282  1.00 25.00           C
ATOM    155  CA  GLN   155      23.208  25.918  30.879  1.00 25.00           C
ATOM    156  CA  GLN   156      21.893  26.802  34.366  1.00 25.00           C
ATOM    157  CA  LEU   157      20.041  23.517  34.766  1.00 25.00           C
ATOM    158  CA  LEU   158      22.528  20.908  35.981  1.00 25.00           C
ATOM    159  CA  SER   159      22.511  22.535  39.350  1.00 25.00           C
TER
END
