
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  153 ( 1194),  selected  153 , name T0332_D1.pdb
# PARAMETERS: T0332TS168_4-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          0.975
LGA    L       8      L       8          2.053
LGA    I       9      I       9          3.668
LGA    V      10      V      10          2.591
LGA    V      11      V      11          2.771
LGA    A      12      A      12          2.288
LGA    S      13      S      13          3.998
LGA    L      14      L      14          1.231
LGA    I      15      I      15          2.344
LGA    D      16      D      16          2.358
LGA    K      17      K      17          2.155
LGA    P      18      P      18          1.980
LGA    T      19      T      19          1.422
LGA    N      20      N      20          0.886
LGA    L      21      L      21          1.295
LGA    G      22      G      22          1.252
LGA    G      23      G      23          1.053
LGA    L      24      L      24          0.950
LGA    C      25      C      25          0.886
LGA    R      26      R      26          0.864
LGA    T      27      T      27          0.485
LGA    C      28      C      28          0.420
LGA    E      29      E      29          0.907
LGA    V      30      V      30          1.222
LGA    F      31      F      31          2.123
LGA    G      32      G      32          2.363
LGA    A      33      A      33          1.273
LGA    S      34      S      34          1.890
LGA    V      35      V      35          2.002
LGA    L      36      L      36          0.475
LGA    V      37      V      37          2.353
LGA    V      38      V      38          2.740
LGA    G      39      -       -           -
LGA    S      40      G      39          0.956
LGA    L      41      -       -           -
LGA    Q      42      -       -           -
LGA    C      43      S      40          3.933
LGA    I      44      L      41          2.628
LGA    S      45      Q      42          2.816
LGA    D      46      C      43          4.621
LGA    K      47      I      44          3.320
LGA    Q      48      S      45          3.829
LGA    -       -      D      46           -
LGA    -       -      K      47           -
LGA    F      49      Q      48           #
LGA    Q      50      F      49           #
LGA    H      51      Q      50          2.652
LGA    -       -      H      51           -
LGA    L      52      L      52          3.720
LGA    S      53      S      53          2.564
LGA    V      54      V      54          3.421
LGA    S      55      S      55          4.461
LGA    A      56      A      56          4.217
LGA    E      57      E      57          4.367
LGA    Q      58      Q      58          3.978
LGA    W      59      W      59          2.373
LGA    L      60      L      60          1.863
LGA    P      61      P      61          2.115
LGA    L      62      L      62          1.716
LGA    V      63      V      63          1.321
LGA    E      64      E      64          0.310
LGA    V      65      V      65          0.573
LGA    K      66      K      66          2.178
LGA    P      67      P      67           #
LGA    P      68      P      68          4.806
LGA    Q      69      Q      69          3.590
LGA    L      70      L      70          1.979
LGA    I      71      I      71          1.944
LGA    D      72      D      72          1.350
LGA    Y      73      Y      73          0.984
LGA    L      74      L      74          1.201
LGA    Q      75      Q      75          2.448
LGA    Q      76      Q      76          2.649
LGA    K      77      K      77          2.300
LGA    K      78      K      78          2.916
LGA    T      79      T      79          3.866
LGA    E      80      E      80          1.672
LGA    G      81      G      81          0.706
LGA    Y      82      Y      82          0.520
LGA    T      83      T      83           #
LGA    I      84      I      84          5.166
LGA    I      85      -       -           -
LGA    G      86      I      85           #
LGA    V      87      G      86          4.040
LGA    E      88      V      87          2.476
LGA    Q      89      E      88          4.252
LGA    T      90      Q      89           #
LGA    A      91      T      90           -
LGA    K      92      A      91           -
LGA    -       -      K      92           -
LGA    S      93      S      93          4.305
LGA    L      94      L      94          1.887
LGA    D      95      D      95          1.586
LGA    L      96      L      96          1.095
LGA    T      97      T      97          2.560
LGA    Q      98      Q      98          2.914
LGA    Y      99      Y      99          2.819
LGA    C     100      C     100          1.713
LGA    F     101      F     101          2.048
LGA    P     102      P     102          4.031
LGA    E     103      E     103          1.551
LGA    K     104      K     104          1.628
LGA    S     105      S     105          1.863
LGA    L     106      L     106          3.553
LGA    L     107      L     107          4.193
LGA    L     108      L     108          0.729
LGA    L     109      L     109          0.595
LGA    G     110      G     110          1.683
LGA    N     111      N     111          1.766
LGA    E     112      E     112          0.704
LGA    R     113      R     113          0.399
LGA    E     114      E     114          2.160
LGA    G     115      G     115          1.391
LGA    I     116      I     116          1.472
LGA    P     117      P     117          2.386
LGA    A     118      A     118          1.891
LGA    N     119      N     119          1.959
LGA    L     120      L     120          1.925
LGA    I     121      I     121          1.771
LGA    Q     122      Q     122          1.903
LGA    Q     123      Q     123          1.398
LGA    L     124      L     124          1.926
LGA    D     125      D     125          1.651
LGA    V     126      V     126          1.364
LGA    C     127      C     127          1.515
LGA    V     128      V     128          2.792
LGA    E     129      E     129          4.986
LGA    I     130      I     130           #
LGA    P     131      P     131          5.203
LGA    Q     132      Q     132          2.548
LGA    Q     133      Q     133          3.691
LGA    G     134      G     134          3.085
LGA    I     135      I     135          3.572
LGA    I     136      I     136          4.419
LGA    R     137      R     137          3.550
LGA    S     138      S     138          1.132
LGA    L     139      L     139          2.124
LGA    N     140      N     140          2.007
LGA    V     141      V     141          0.649
LGA    H     142      H     142          0.164
LGA    V     143      V     143          0.649
LGA    S     144      S     144          0.601
LGA    G     145      G     145          0.289
LGA    A     146      A     146          0.310
LGA    L     147      L     147          0.535
LGA    L     148      L     148          0.377
LGA    I     149      I     149          0.638
LGA    W     150      W     150          1.037
LGA    E     151      E     151          0.819
LGA    Y     152      Y     152          0.237
LGA    T     153      T     153          1.239
LGA    R     154      R     154          1.693
LGA    Q     155      Q     155          1.073
LGA    Q     156      Q     156          0.707
LGA    L     157      L     157          1.489
LGA    L     158      L     158          1.636
LGA    S     159      S     159          4.286

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  153  153    5.0    140    2.44    92.14     57.758     5.508

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.389957 * X  +   0.161828 * Y  +   0.906502 * Z  +  27.245771
  Y_new =  -0.472360 * X  +   0.809892 * Y  +  -0.347780 * Z  +  42.808212
  Z_new =  -0.790449 * X  +  -0.563814 * Y  +  -0.239382 * Z  +  31.105717 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.972307    1.169285  [ DEG:  -113.0049     66.9951 ]
  Theta =   0.911542    2.230051  [ DEG:    52.2275    127.7725 ]
  Phi   =  -2.260923    0.880669  [ DEG:  -129.5414     50.4586 ]
 
# 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_4-D1                               
REMARK     2: T0332_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0332TS168_4-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  140   2.44   92.14  57.758
REMARK  ---------------------------------------------------------- 
MOLECULE T0332TS168_4-D1
PFRMAT TS
TARGET T0332
MODEL 4
PARENT N/A
ATOM      7  CA  ARG     7      22.048  37.921  40.073  1.00 25.00           C
ATOM      8  CA  LEU     8      24.740  39.632  37.947  1.00 25.00           C
ATOM      9  CA  ILE     9      23.493  39.805  34.395  1.00 25.00           C
ATOM     10  CA  VAL    10      23.845  42.608  31.833  1.00 25.00           C
ATOM     11  CA  VAL    11      27.058  44.592  31.434  1.00 25.00           C
ATOM     12  CA  ALA    12      27.592  46.993  28.502  1.00 25.00           C
ATOM     13  CA  SER    13      30.861  48.794  28.750  1.00 25.00           C
ATOM     14  CA  LEU    14      32.636  52.075  28.336  1.00 25.00           C
ATOM     15  CA  ILE    15      30.571  53.066  25.319  1.00 25.00           C
ATOM     16  CA  ASP    16      30.198  54.472  21.807  1.00 25.00           C
ATOM     17  CA  LYS    17      26.855  55.649  20.396  1.00 25.00           C
ATOM     18  CA  PRO    18      25.022  54.372  23.453  1.00 25.00           C
ATOM     19  CA  THR    19      23.097  52.209  20.946  1.00 25.00           C
ATOM     20  CA  ASN    20      24.979  49.097  22.146  1.00 25.00           C
ATOM     21  CA  LEU    21      24.154  49.971  25.783  1.00 25.00           C
ATOM     22  CA  GLY    22      20.461  50.410  24.864  1.00 25.00           C
ATOM     23  CA  GLY    23      20.473  47.016  23.093  1.00 25.00           C
ATOM     24  CA  LEU    24      22.065  45.386  26.172  1.00 25.00           C
ATOM     25  CA  CYS    25      19.404  46.979  28.420  1.00 25.00           C
ATOM     26  CA  ARG    26      16.640  45.686  26.106  1.00 25.00           C
ATOM     27  CA  THR    27      18.163  42.174  26.208  1.00 25.00           C
ATOM     28  CA  CYS    28      18.302  42.317  30.033  1.00 25.00           C
ATOM     29  CA  GLU    29      14.634  43.411  30.148  1.00 25.00           C
ATOM     30  CA  VAL    30      13.673  40.518  27.830  1.00 25.00           C
ATOM     31  CA  PHE    31      16.216  37.838  28.731  1.00 25.00           C
ATOM     32  CA  GLY    32      15.699  37.971  32.461  1.00 25.00           C
ATOM     33  CA  ALA    33      18.047  40.050  34.583  1.00 25.00           C
ATOM     34  CA  SER    34      17.513  42.344  37.534  1.00 25.00           C
ATOM     35  CA  VAL    35      20.903  43.784  36.451  1.00 25.00           C
ATOM     36  CA  LEU    36      22.011  46.824  34.346  1.00 25.00           C
ATOM     37  CA  VAL    37      25.595  47.223  35.676  1.00 25.00           C
ATOM     38  CA  VAL    38      25.810  49.573  32.654  1.00 25.00           C
ATOM     39  CA  GLY    39      28.971  51.625  32.346  1.00 25.00           C
ATOM     40  CA  SER    40      29.343  55.408  32.081  1.00 25.00           C
ATOM     41  CA  LEU    41      31.843  56.880  29.584  1.00 25.00           C
ATOM     42  CA  GLN    42      28.686  57.997  27.793  1.00 25.00           C
ATOM     43  CA  CYS    43      24.909  57.936  28.493  1.00 25.00           C
ATOM     44  CA  ILE    44      23.259  59.812  31.380  1.00 25.00           C
ATOM     45  CA  SER    45      23.498  62.854  29.113  1.00 25.00           C
ATOM     46  CA  ASP    46      20.164  61.674  27.847  1.00 25.00           C
ATOM     47  CA  LYS    47      16.933  59.741  27.753  1.00 25.00           C
ATOM     48  CA  GLN    48      17.163  58.105  24.297  1.00 25.00           C
ATOM     49  CA  PHE    49      19.005  55.108  25.812  1.00 25.00           C
ATOM     50  CA  GLN    50      16.307  54.783  28.511  1.00 25.00           C
ATOM     51  CA  HIS    51      13.575  54.893  25.829  1.00 25.00           C
ATOM     52  CA  LEU    52      15.395  52.178  23.831  1.00 25.00           C
ATOM     53  CA  SER    53      15.667  50.011  26.978  1.00 25.00           C
ATOM     54  CA  VAL    54      12.121  48.630  26.951  1.00 25.00           C
ATOM     55  CA  SER    55      11.693  48.411  30.725  1.00 25.00           C
ATOM     56  CA  ALA    56      13.194  51.704  31.730  1.00 25.00           C
ATOM     57  CA  GLU    57      14.419  53.793  34.696  1.00 25.00           C
ATOM     58  CA  GLN    58      11.616  52.377  36.885  1.00 25.00           C
ATOM     59  CA  TRP    59      12.825  48.850  35.945  1.00 25.00           C
ATOM     60  CA  LEU    60      16.378  48.379  34.593  1.00 25.00           C
ATOM     61  CA  PRO    61      17.756  50.865  37.187  1.00 25.00           C
ATOM     62  CA  LEU    62      20.060  51.273  34.223  1.00 25.00           C
ATOM     63  CA  VAL    63      22.926  51.946  36.718  1.00 25.00           C
ATOM     64  CA  GLU    64      25.203  55.006  37.125  1.00 25.00           C
ATOM     65  CA  VAL    65      28.856  54.189  36.956  1.00 25.00           C
ATOM     66  CA  LYS    66      32.573  55.168  36.814  1.00 25.00           C
ATOM     67  CA  PRO    67      31.943  57.229  39.947  1.00 25.00           C
ATOM     68  CA  PRO    68      35.397  56.452  41.338  1.00 25.00           C
ATOM     69  CA  GLN    69      38.139  54.872  39.331  1.00 25.00           C
ATOM     70  CA  LEU    70      36.091  51.702  39.035  1.00 25.00           C
ATOM     71  CA  ILE    71      37.786  49.784  41.884  1.00 25.00           C
ATOM     72  CA  ASP    72      35.372  51.352  44.409  1.00 25.00           C
ATOM     73  CA  TYR    73      32.394  50.367  42.212  1.00 25.00           C
ATOM     74  CA  LEU    74      33.722  46.782  41.977  1.00 25.00           C
ATOM     75  CA  GLN    75      34.118  46.654  45.784  1.00 25.00           C
ATOM     76  CA  GLN    76      30.532  47.924  46.224  1.00 25.00           C
ATOM     77  CA  LYS    77      29.260  45.253  43.792  1.00 25.00           C
ATOM     78  CA  LYS    78      31.167  42.551  45.724  1.00 25.00           C
ATOM     79  CA  THR    79      29.655  43.802  49.013  1.00 25.00           C
ATOM     80  CA  GLU    80      28.065  40.317  49.010  1.00 25.00           C
ATOM     81  CA  GLY    81      29.862  37.509  47.142  1.00 25.00           C
ATOM     82  CA  TYR    82      30.338  38.130  43.361  1.00 25.00           C
ATOM     83  CA  THR    83      28.651  40.743  41.156  1.00 25.00           C
ATOM     84  CA  ILE    84      29.886  42.870  38.252  1.00 25.00           C
ATOM     85  CA  ILE    85      28.556  41.456  35.004  1.00 25.00           C
ATOM     86  CA  GLY    86      29.334  39.798  31.654  1.00 25.00           C
ATOM     87  CA  VAL    87      32.242  38.305  29.735  1.00 25.00           C
ATOM     88  CA  GLU    88      33.052  38.994  26.066  1.00 25.00           C
ATOM     89  CA  GLN    89      34.367  38.567  22.471  1.00 25.00           C
ATOM     90  CA  THR    90      33.944  34.806  23.115  1.00 25.00           C
ATOM     91  CA  ALA    91      33.354  31.665  21.034  1.00 25.00           C
ATOM     92  CA  LYS    92      36.736  30.056  21.898  1.00 25.00           C
ATOM     93  CA  SER    93      38.895  31.530  24.662  1.00 25.00           C
ATOM     94  CA  LEU    94      38.895  29.562  27.927  1.00 25.00           C
ATOM     95  CA  ASP    95      35.319  28.391  27.624  1.00 25.00           C
ATOM     96  CA  LEU    96      32.136  30.383  27.870  1.00 25.00           C
ATOM     97  CA  THR    97      30.306  27.036  28.205  1.00 25.00           C
ATOM     98  CA  GLN    98      32.260  26.260  31.406  1.00 25.00           C
ATOM     99  CA  TYR    99      32.111  29.055  33.961  1.00 25.00           C
ATOM    100  CA  CYS   100      28.949  27.842  35.619  1.00 25.00           C
ATOM    101  CA  PHE   101      26.550  30.840  35.808  1.00 25.00           C
ATOM    102  CA  PRO   102      24.945  29.254  38.914  1.00 25.00           C
ATOM    103  CA  GLU   103      26.547  31.939  41.081  1.00 25.00           C
ATOM    104  CA  LYS   104      27.390  35.569  40.183  1.00 25.00           C
ATOM    105  CA  SER   105      28.068  35.845  36.444  1.00 25.00           C
ATOM    106  CA  LEU   106      31.313  37.746  36.107  1.00 25.00           C
ATOM    107  CA  LEU   107      33.572  40.377  34.425  1.00 25.00           C
ATOM    108  CA  LEU   108      32.514  43.558  32.641  1.00 25.00           C
ATOM    109  CA  LEU   109      31.958  43.955  28.895  1.00 25.00           C
ATOM    110  CA  GLY   110      33.470  44.987  25.502  1.00 25.00           C
ATOM    111  CA  ASN   111      32.790  48.427  24.011  1.00 25.00           C
ATOM    112  CA  GLU   112      33.082  49.113  20.299  1.00 25.00           C
ATOM    113  CA  ARG   113      36.616  50.178  19.439  1.00 25.00           C
ATOM    114  CA  GLU   114      38.703  47.830  21.562  1.00 25.00           C
ATOM    115  CA  GLY   115      38.268  47.316  25.283  1.00 25.00           C
ATOM    116  CA  ILE   116      37.066  46.480  28.803  1.00 25.00           C
ATOM    117  CA  PRO   117      39.208  49.234  30.246  1.00 25.00           C
ATOM    118  CA  ALA   118      42.409  47.219  30.972  1.00 25.00           C
ATOM    119  CA  ASN   119      42.020  47.439  34.776  1.00 25.00           C
ATOM    120  CA  LEU   120      38.602  45.725  34.550  1.00 25.00           C
ATOM    121  CA  ILE   121      40.112  42.946  32.389  1.00 25.00           C
ATOM    122  CA  GLN   122      42.938  42.472  34.931  1.00 25.00           C
ATOM    123  CA  GLN   123      40.380  42.262  37.773  1.00 25.00           C
ATOM    124  CA  LEU   124      37.533  39.762  37.897  1.00 25.00           C
ATOM    125  CA  ASP   125      39.990  36.842  38.341  1.00 25.00           C
ATOM    126  CA  VAL   126      39.429  35.277  34.875  1.00 25.00           C
ATOM    127  CA  CYS   127      38.273  37.462  32.028  1.00 25.00           C
ATOM    128  CA  VAL   128      37.252  36.266  28.534  1.00 25.00           C
ATOM    129  CA  GLU   129      38.591  38.015  25.472  1.00 25.00           C
ATOM    130  CA  ILE   130      38.868  36.106  22.213  1.00 25.00           C
ATOM    131  CA  PRO   131      37.303  34.945  18.927  1.00 25.00           C
ATOM    132  CA  GLN   132      36.704  31.686  16.995  1.00 25.00           C
ATOM    133  CA  GLN   133      38.041  29.471  14.170  1.00 25.00           C
ATOM    134  CA  GLY   134      35.001  30.145  11.979  1.00 25.00           C
ATOM    135  CA  ILE   135      34.121  33.607  10.625  1.00 25.00           C
ATOM    136  CA  ILE   136      31.457  36.381  10.969  1.00 25.00           C
ATOM    137  CA  ARG   137      34.241  38.118  12.923  1.00 25.00           C
ATOM    138  CA  SER   138      33.858  40.361  15.995  1.00 25.00           C
ATOM    139  CA  LEU   139      31.048  42.135  17.848  1.00 25.00           C
ATOM    140  CA  ASN   140      28.911  45.080  18.952  1.00 25.00           C
ATOM    141  CA  VAL   141      29.303  44.145  22.587  1.00 25.00           C
ATOM    142  CA  HIS   142      25.492  43.788  22.703  1.00 25.00           C
ATOM    143  CA  VAL   143      25.732  40.396  20.940  1.00 25.00           C
ATOM    144  CA  SER   144      28.387  39.251  23.451  1.00 25.00           C
ATOM    145  CA  GLY   145      26.151  40.360  26.357  1.00 25.00           C
ATOM    146  CA  ALA   146      23.200  38.439  24.852  1.00 25.00           C
ATOM    147  CA  LEU   147      25.386  35.317  24.483  1.00 25.00           C
ATOM    148  CA  LEU   148      26.506  35.641  28.132  1.00 25.00           C
ATOM    149  CA  ILE   149      22.857  35.970  29.248  1.00 25.00           C
ATOM    150  CA  TRP   150      21.933  32.851  27.227  1.00 25.00           C
ATOM    151  CA  GLU   151      24.830  30.925  28.828  1.00 25.00           C
ATOM    152  CA  TYR   152      23.675  32.032  32.307  1.00 25.00           C
ATOM    153  CA  THR   153      20.106  30.893  31.513  1.00 25.00           C
ATOM    154  CA  ARG   154      21.427  27.501  30.324  1.00 25.00           C
ATOM    155  CA  GLN   155      23.464  27.137  33.546  1.00 25.00           C
ATOM    156  CA  GLN   156      20.362  27.976  35.631  1.00 25.00           C
ATOM    157  CA  LEU   157      17.727  25.745  34.144  1.00 25.00           C
ATOM    158  CA  LEU   158      20.091  22.719  33.834  1.00 25.00           C
ATOM    159  CA  SER   159      22.355  20.900  36.343  1.00 25.00           C
TER
END
