
#######################################################
#                                                     #
#                        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 T0332TS168_3-D1
# Molecule2: number of CA atoms  153 ( 1194),  selected  153 , name T0332_D1.pdb
# PARAMETERS: T0332TS168_3-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          0.930
LGA    L       8      L       8          1.339
LGA    I       9      I       9          1.877
LGA    V      10      V      10          1.806
LGA    V      11      V      11          2.916
LGA    A      12      A      12          1.379
LGA    S      13      S      13          3.020
LGA    L      14      L      14          1.716
LGA    I      15      I      15          1.111
LGA    D      16      D      16          0.797
LGA    K      17      K      17          2.193
LGA    P      18      P      18          2.821
LGA    T      19      T      19          0.835
LGA    N      20      N      20          2.537
LGA    L      21      L      21          2.613
LGA    G      22      G      22          1.338
LGA    G      23      G      23          0.760
LGA    L      24      L      24          1.203
LGA    C      25      C      25          1.739
LGA    R      26      R      26          1.654
LGA    T      27      T      27          1.082
LGA    C      28      C      28          0.523
LGA    E      29      E      29          1.826
LGA    V      30      V      30          2.284
LGA    F      31      F      31          1.366
LGA    G      32      G      32          2.335
LGA    A      33      A      33          1.346
LGA    S      34      S      34          2.447
LGA    V      35      V      35          0.548
LGA    L      36      L      36          0.416
LGA    V      37      V      37          1.059
LGA    V      38      V      38          1.045
LGA    G      39      G      39          1.583
LGA    S      40      -       -           -
LGA    L      41      -       -           -
LGA    Q      42      S      40          4.469
LGA    C      43      L      41          5.348
LGA    I      44      Q      42          0.681
LGA    S      45      C      43           #
LGA    D      46      I      44           #
LGA    K      47      S      45          1.969
LGA    Q      48      D      46          2.624
LGA    -       -      K      47           -
LGA    F      49      Q      48           #
LGA    Q      50      F      49           #
LGA    H      51      Q      50          1.228
LGA    -       -      H      51           -
LGA    L      52      L      52          3.441
LGA    S      53      S      53          3.060
LGA    V      54      V      54          2.868
LGA    S      55      S      55          3.225
LGA    A      56      A      56          4.100
LGA    E      57      E      57          4.069
LGA    Q      58      Q      58          4.219
LGA    W      59      W      59          1.384
LGA    L      60      L      60          1.724
LGA    P      61      P      61          4.673
LGA    L      62      L      62          0.212
LGA    V      63      V      63          1.015
LGA    E      64      E      64          1.034
LGA    V      65      V      65          0.453
LGA    K      66      K      66          1.706
LGA    P      67      P      67           #
LGA    P      68      P      68          3.308
LGA    Q      69      Q      69          3.872
LGA    L      70      L      70          1.340
LGA    I      71      I      71          1.917
LGA    D      72      D      72          1.533
LGA    Y      73      Y      73          0.841
LGA    L      74      L      74          1.629
LGA    Q      75      Q      75          2.476
LGA    Q      76      Q      76          2.057
LGA    K      77      K      77          1.378
LGA    K      78      K      78          2.450
LGA    T      79      T      79          2.863
LGA    E      80      E      80          2.107
LGA    G      81      G      81          1.257
LGA    Y      82      Y      82          0.926
LGA    T      83      T      83           #
LGA    I      84      I      84           #
LGA    I      85      I      85           #
LGA    G      86      G      86          3.991
LGA    V      87      V      87          2.300
LGA    E      88      E      88          3.107
LGA    Q      89      Q      89           #
LGA    T      90      T      90           #
LGA    A      91      -       -           -
LGA    K      92      A      91           #
LGA    -       -      K      92           -
LGA    S      93      S      93          2.253
LGA    L      94      L      94          2.039
LGA    D      95      D      95          1.781
LGA    L      96      L      96          2.978
LGA    T      97      T      97          3.910
LGA    Q      98      Q      98          2.794
LGA    Y      99      Y      99          2.852
LGA    C     100      C     100          2.727
LGA    F     101      F     101          1.668
LGA    P     102      P     102          3.602
LGA    E     103      E     103          2.614
LGA    K     104      K     104          4.050
LGA    S     105      S     105          5.139
LGA    L     106      L     106          4.626
LGA    L     107      L     107          4.498
LGA    L     108      L     108          0.978
LGA    L     109      L     109          2.273
LGA    G     110      G     110          2.867
LGA    N     111      N     111          1.744
LGA    E     112      E     112          1.411
LGA    R     113      R     113          1.003
LGA    E     114      E     114          2.593
LGA    G     115      G     115          0.775
LGA    I     116      I     116          0.343
LGA    P     117      P     117          0.802
LGA    A     118      A     118          0.964
LGA    N     119      N     119          1.708
LGA    L     120      L     120          1.620
LGA    I     121      I     121          1.706
LGA    Q     122      Q     122          1.880
LGA    Q     123      Q     123          1.295
LGA    L     124      L     124          1.539
LGA    D     125      D     125          0.641
LGA    V     126      V     126          0.845
LGA    C     127      C     127          1.825
LGA    V     128      V     128          1.864
LGA    E     129      E     129          4.200
LGA    I     130      I     130          5.836
LGA    P     131      P     131          4.852
LGA    Q     132      Q     132          0.695
LGA    Q     133      Q     133          2.145
LGA    G     134      G     134          1.397
LGA    I     135      I     135          2.078
LGA    I     136      I     136          2.877
LGA    R     137      R     137          3.542
LGA    S     138      S     138          1.317
LGA    L     139      L     139          1.658
LGA    N     140      N     140          1.692
LGA    V     141      V     141          1.012
LGA    H     142      H     142          1.364
LGA    V     143      V     143          1.163
LGA    S     144      S     144          1.031
LGA    G     145      G     145          1.498
LGA    A     146      A     146          1.635
LGA    L     147      L     147          1.340
LGA    L     148      L     148          1.351
LGA    I     149      I     149          2.098
LGA    W     150      W     150          2.120
LGA    E     151      E     151          1.352
LGA    Y     152      Y     152          1.812
LGA    T     153      T     153          2.635
LGA    R     154      R     154          2.258
LGA    Q     155      Q     155          1.253
LGA    Q     156      Q     156          2.370
LGA    L     157      L     157          3.676
LGA    L     158      L     158          2.786
LGA    S     159      S     159          3.698

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  153  153    5.0    139    2.40    95.68     59.351     5.552

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.527412 * X  +   0.797720 * Y  +   0.292368 * Z  +  27.211201
  Y_new =  -0.258416 * X  +   0.478436 * Y  +  -0.839238 * Z  +  42.848164
  Z_new =  -0.809356 * X  +   0.367072 * Y  +   0.458476 * Z  +  30.980045 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.675127   -2.466465  [ DEG:    38.6819   -141.3181 ]
  Theta =   0.943055    2.198537  [ DEG:    54.0331    125.9669 ]
  Phi   =  -0.455591    2.686001  [ DEG:   -26.1035    153.8965 ]
 
# 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: T0332TS168_3-D1                               
REMARK     2: T0332_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0332TS168_3-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  139   2.40   95.68  59.351
REMARK  ---------------------------------------------------------- 
MOLECULE T0332TS168_3-D1
PFRMAT TS
TARGET T0332
MODEL 3
PARENT N/A
ATOM      7  CA  ARG     7      21.947  37.813  40.081  1.00 25.00           C
ATOM      8  CA  LEU     8      23.376  37.702  36.543  1.00 25.00           C
ATOM      9  CA  ILE     9      22.927  41.467  36.806  1.00 25.00           C
ATOM     10  CA  VAL    10      24.258  42.180  33.366  1.00 25.00           C
ATOM     11  CA  VAL    11      26.504  44.615  31.572  1.00 25.00           C
ATOM     12  CA  ALA    12      28.849  47.429  30.544  1.00 25.00           C
ATOM     13  CA  SER    13      31.954  49.623  30.365  1.00 25.00           C
ATOM     14  CA  LEU    14      33.240  52.338  28.112  1.00 25.00           C
ATOM     15  CA  ILE    15      29.812  51.888  26.430  1.00 25.00           C
ATOM     16  CA  ASP    16      29.252  54.159  23.397  1.00 25.00           C
ATOM     17  CA  LYS    17      26.772  55.926  21.047  1.00 25.00           C
ATOM     18  CA  PRO    18      24.880  52.659  21.072  1.00 25.00           C
ATOM     19  CA  THR    19      21.588  51.209  19.754  1.00 25.00           C
ATOM     20  CA  ASN    20      22.944  47.657  20.206  1.00 25.00           C
ATOM     21  CA  LEU    21      24.003  48.490  23.790  1.00 25.00           C
ATOM     22  CA  GLY    22      20.519  49.905  24.517  1.00 25.00           C
ATOM     23  CA  GLY    23      18.909  46.730  23.104  1.00 25.00           C
ATOM     24  CA  LEU    24      21.191  44.569  25.292  1.00 25.00           C
ATOM     25  CA  CYS    25      20.247  46.644  28.368  1.00 25.00           C
ATOM     26  CA  ARG    26      16.531  46.235  27.535  1.00 25.00           C
ATOM     27  CA  THR    27      17.005  42.451  27.171  1.00 25.00           C
ATOM     28  CA  CYS    28      18.794  42.325  30.555  1.00 25.00           C
ATOM     29  CA  GLU    29      15.938  44.302  32.167  1.00 25.00           C
ATOM     30  CA  VAL    30      13.379  41.892  30.647  1.00 25.00           C
ATOM     31  CA  PHE    31      15.256  38.591  29.958  1.00 25.00           C
ATOM     32  CA  GLY    32      15.906  37.302  33.511  1.00 25.00           C
ATOM     33  CA  ALA    33      17.915  39.963  35.221  1.00 25.00           C
ATOM     34  CA  SER    34      17.786  43.472  36.793  1.00 25.00           C
ATOM     35  CA  VAL    35      20.529  46.099  36.976  1.00 25.00           C
ATOM     36  CA  LEU    36      22.594  47.101  33.942  1.00 25.00           C
ATOM     37  CA  VAL    37      25.877  48.782  34.599  1.00 25.00           C
ATOM     38  CA  VAL    38      26.532  51.654  32.223  1.00 25.00           C
ATOM     39  CA  GLY    39      29.629  53.895  31.962  1.00 25.00           C
ATOM     40  CA  SER    40      31.681  57.043  31.262  1.00 25.00           C
ATOM     41  CA  LEU    41      29.947  56.779  27.821  1.00 25.00           C
ATOM     42  CA  GLN    42      28.137  59.928  28.978  1.00 25.00           C
ATOM     43  CA  CYS    43      24.730  58.493  28.071  1.00 25.00           C
ATOM     44  CA  ILE    44      22.582  60.305  30.604  1.00 25.00           C
ATOM     45  CA  SER    45      20.672  63.030  28.731  1.00 25.00           C
ATOM     46  CA  ASP    46      21.508  61.818  25.239  1.00 25.00           C
ATOM     47  CA  LYS    47      18.249  59.855  25.596  1.00 25.00           C
ATOM     48  CA  GLN    48      18.695  57.148  22.923  1.00 25.00           C
ATOM     49  CA  PHE    49      19.496  54.566  25.636  1.00 25.00           C
ATOM     50  CA  GLN    50      16.368  55.606  27.584  1.00 25.00           C
ATOM     51  CA  HIS    51      14.249  55.264  24.412  1.00 25.00           C
ATOM     52  CA  LEU    52      15.709  51.780  23.782  1.00 25.00           C
ATOM     53  CA  SER    53      14.916  50.769  27.390  1.00 25.00           C
ATOM     54  CA  VAL    54      12.210  48.338  26.125  1.00 25.00           C
ATOM     55  CA  SER    55      10.864  48.889  29.678  1.00 25.00           C
ATOM     56  CA  ALA    56      12.589  51.588  31.748  1.00 25.00           C
ATOM     57  CA  GLU    57      14.358  52.691  34.961  1.00 25.00           C
ATOM     58  CA  GLN    58      11.834  50.714  37.058  1.00 25.00           C
ATOM     59  CA  TRP    59      12.354  47.532  34.967  1.00 25.00           C
ATOM     60  CA  LEU    60      16.068  48.022  35.628  1.00 25.00           C
ATOM     61  CA  PRO    61      18.070  49.799  32.916  1.00 25.00           C
ATOM     62  CA  LEU    62      19.901  51.054  35.969  1.00 25.00           C
ATOM     63  CA  VAL    63      23.231  52.399  37.093  1.00 25.00           C
ATOM     64  CA  GLU    64      25.790  54.944  35.938  1.00 25.00           C
ATOM     65  CA  VAL    65      29.246  54.124  37.203  1.00 25.00           C
ATOM     66  CA  LYS    66      32.555  55.957  36.524  1.00 25.00           C
ATOM     67  CA  PRO    67      32.477  56.780  40.272  1.00 25.00           C
ATOM     68  CA  PRO    68      36.230  56.226  39.987  1.00 25.00           C
ATOM     69  CA  GLN    69      37.857  53.386  37.994  1.00 25.00           C
ATOM     70  CA  LEU    70      35.085  51.053  39.174  1.00 25.00           C
ATOM     71  CA  ILE    71      37.350  49.564  41.879  1.00 25.00           C
ATOM     72  CA  ASP    72      35.078  51.000  44.606  1.00 25.00           C
ATOM     73  CA  TYR    73      32.008  49.504  42.871  1.00 25.00           C
ATOM     74  CA  LEU    74      33.755  46.101  42.664  1.00 25.00           C
ATOM     75  CA  GLN    75      34.625  46.293  46.388  1.00 25.00           C
ATOM     76  CA  GLN    76      30.984  47.142  47.220  1.00 25.00           C
ATOM     77  CA  LYS    77      29.785  44.169  45.124  1.00 25.00           C
ATOM     78  CA  LYS    78      32.249  41.866  46.938  1.00 25.00           C
ATOM     79  CA  THR    79      30.999  43.152  50.322  1.00 25.00           C
ATOM     80  CA  GLU    80      28.586  40.269  49.971  1.00 25.00           C
ATOM     81  CA  GLY    81      29.346  37.526  47.375  1.00 25.00           C
ATOM     82  CA  TYR    82      29.830  38.570  43.757  1.00 25.00           C
ATOM     83  CA  THR    83      27.535  40.978  41.903  1.00 25.00           C
ATOM     84  CA  ILE    84      27.791  41.672  38.120  1.00 25.00           C
ATOM     85  CA  ILE    85      28.721  39.879  34.889  1.00 25.00           C
ATOM     86  CA  GLY    86      32.331  38.968  34.196  1.00 25.00           C
ATOM     87  CA  VAL    87      32.414  39.141  30.412  1.00 25.00           C
ATOM     88  CA  GLU    88      33.657  40.229  26.998  1.00 25.00           C
ATOM     89  CA  GLN    89      32.935  38.180  23.903  1.00 25.00           C
ATOM     90  CA  THR    90      33.367  34.437  24.494  1.00 25.00           C
ATOM     91  CA  ALA    91      34.844  31.740  22.301  1.00 25.00           C
ATOM     92  CA  LYS    92      38.357  30.601  23.399  1.00 25.00           C
ATOM     93  CA  SER    93      39.201  32.122  26.767  1.00 25.00           C
ATOM     94  CA  LEU    94      38.220  28.737  28.300  1.00 25.00           C
ATOM     95  CA  ASP    95      34.483  29.368  27.654  1.00 25.00           C
ATOM     96  CA  LEU    96      31.815  31.210  29.579  1.00 25.00           C
ATOM     97  CA  THR    97      29.945  27.883  29.270  1.00 25.00           C
ATOM     98  CA  GLN    98      32.608  26.158  31.415  1.00 25.00           C
ATOM     99  CA  TYR    99      32.078  28.850  34.090  1.00 25.00           C
ATOM    100  CA  CYS   100      29.758  28.131  36.976  1.00 25.00           C
ATOM    101  CA  PHE   101      27.065  30.731  36.415  1.00 25.00           C
ATOM    102  CA  PRO   102      24.865  30.885  39.535  1.00 25.00           C
ATOM    103  CA  GLU   103      27.298  33.707  40.444  1.00 25.00           C
ATOM    104  CA  LYS   104      29.751  36.375  39.207  1.00 25.00           C
ATOM    105  CA  SER   105      32.195  39.293  39.308  1.00 25.00           C
ATOM    106  CA  LEU   106      32.703  42.686  37.629  1.00 25.00           C
ATOM    107  CA  LEU   107      30.551  44.605  35.060  1.00 25.00           C
ATOM    108  CA  LEU   108      32.407  44.048  31.768  1.00 25.00           C
ATOM    109  CA  LEU   109      33.341  45.549  28.379  1.00 25.00           C
ATOM    110  CA  GLY   110      31.882  46.337  24.956  1.00 25.00           C
ATOM    111  CA  ASN   111      33.073  49.574  23.355  1.00 25.00           C
ATOM    112  CA  GLU   112      33.214  47.975  19.940  1.00 25.00           C
ATOM    113  CA  ARG   113      36.758  49.232  19.992  1.00 25.00           C
ATOM    114  CA  GLU   114      39.414  47.199  21.901  1.00 25.00           C
ATOM    115  CA  GLY   115      37.092  46.865  24.841  1.00 25.00           C
ATOM    116  CA  ILE   116      38.336  45.800  28.269  1.00 25.00           C
ATOM    117  CA  PRO   117      40.543  48.605  29.629  1.00 25.00           C
ATOM    118  CA  ALA   118      43.394  46.580  30.945  1.00 25.00           C
ATOM    119  CA  ASN   119      42.401  47.350  34.563  1.00 25.00           C
ATOM    120  CA  LEU   120      38.843  46.113  33.875  1.00 25.00           C
ATOM    121  CA  ILE   121      40.233  42.892  32.338  1.00 25.00           C
ATOM    122  CA  GLN   122      42.470  42.366  35.402  1.00 25.00           C
ATOM    123  CA  GLN   123      39.463  42.888  37.717  1.00 25.00           C
ATOM    124  CA  LEU   124      37.382  40.016  36.417  1.00 25.00           C
ATOM    125  CA  ASP   125      38.485  36.705  37.874  1.00 25.00           C
ATOM    126  CA  VAL   126      38.414  35.522  34.226  1.00 25.00           C
ATOM    127  CA  CYS   127      37.473  38.055  31.565  1.00 25.00           C
ATOM    128  CA  VAL   128      36.066  36.054  28.653  1.00 25.00           C
ATOM    129  CA  GLU   129      38.100  37.363  25.788  1.00 25.00           C
ATOM    130  CA  ILE   130      37.386  36.559  22.190  1.00 25.00           C
ATOM    131  CA  PRO   131      36.424  35.026  18.846  1.00 25.00           C
ATOM    132  CA  GLN   132      34.567  32.658  16.524  1.00 25.00           C
ATOM    133  CA  GLN   133      36.482  31.000  13.673  1.00 25.00           C
ATOM    134  CA  GLY   134      35.140  31.649  10.235  1.00 25.00           C
ATOM    135  CA  ILE   135      34.741  35.382   9.685  1.00 25.00           C
ATOM    136  CA  ILE   136      36.886  36.761  12.558  1.00 25.00           C
ATOM    137  CA  ARG   137      34.211  39.524  12.476  1.00 25.00           C
ATOM    138  CA  SER   138      33.386  39.924  16.166  1.00 25.00           C
ATOM    139  CA  LEU   139      30.095  41.504  17.223  1.00 25.00           C
ATOM    140  CA  ASN   140      27.836  44.474  17.788  1.00 25.00           C
ATOM    141  CA  VAL   141      28.230  43.973  21.530  1.00 25.00           C
ATOM    142  CA  HIS   142      24.424  43.590  21.720  1.00 25.00           C
ATOM    143  CA  VAL   143      24.639  40.262  19.838  1.00 25.00           C
ATOM    144  CA  SER   144      27.357  39.047  22.247  1.00 25.00           C
ATOM    145  CA  GLY   145      25.184  40.044  25.240  1.00 25.00           C
ATOM    146  CA  ALA   146      22.207  38.159  23.737  1.00 25.00           C
ATOM    147  CA  LEU   147      24.401  35.064  23.214  1.00 25.00           C
ATOM    148  CA  LEU   148      25.601  35.270  26.845  1.00 25.00           C
ATOM    149  CA  ILE   149      21.978  35.541  28.053  1.00 25.00           C
ATOM    150  CA  TRP   150      21.021  32.487  25.949  1.00 25.00           C
ATOM    151  CA  GLU   151      23.963  30.524  27.418  1.00 25.00           C
ATOM    152  CA  TYR   152      22.884  31.507  30.958  1.00 25.00           C
ATOM    153  CA  THR   153      19.303  30.375  30.207  1.00 25.00           C
ATOM    154  CA  ARG   154      20.613  27.032  28.873  1.00 25.00           C
ATOM    155  CA  GLN   155      22.724  26.571  32.034  1.00 25.00           C
ATOM    156  CA  GLN   156      19.668  27.321  34.216  1.00 25.00           C
ATOM    157  CA  LEU   157      18.191  24.350  32.356  1.00 25.00           C
ATOM    158  CA  LEU   158      20.324  21.427  33.486  1.00 25.00           C
ATOM    159  CA  SER   159      22.444  21.814  36.586  1.00 25.00           C
TER
END
