
#######################################################
#                                                     #
#                        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  135 (  135),  selected  135 , name T0385TS393_2-D1
# Molecule2: number of CA atoms  135 ( 1000),  selected  135 , name T0385_D1.pdb
# PARAMETERS: T0385TS393_2-D1.T0385_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      S      17           -
LGA    E      18      E      18           -
LGA    G      19      G      19           -
LGA    S      20      S      20           -
LGA    A      21      A      21           -
LGA    D      22      D      22           -
LGA    N      23      N      23           -
LGA    A      24      A      24           -
LGA    A      25      A      25           -
LGA    -       -      L      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      A      29           -
LGA    -       -      L      30           -
LGA    -       -      A      31           -
LGA    L      26      V      32           #
LGA    C      27      E      33           -
LGA    D      28      H      34           -
LGA    A      29      A      35           -
LGA    L      30      T      36          5.134
LGA    A      31      I      37           -
LGA    -       -      Y      38           -
LGA    V      32      G      39          4.691
LGA    E      33      Y      40          2.197
LGA    H      34      G      41          2.103
LGA    A      35      I      42          1.605
LGA    T      36      V      43          2.192
LGA    I      37      S      44          3.120
LGA    Y      38      A      45          3.143
LGA    G      39      L      46           -
LGA    Y      40      S      47           -
LGA    G      41      P      48           -
LGA    I      42      -       -           -
LGA    V      43      -       -           -
LGA    S      44      -       -           -
LGA    A      45      -       -           -
LGA    L      46      -       -           -
LGA    S      47      -       -           -
LGA    P      48      -       -           -
LGA    P      49      -       -           -
LGA    G      50      -       -           -
LGA    V      51      P      49           #
LGA    N      52      G      50          6.599
LGA    F      53      -       -           -
LGA    L      54      V      51           #
LGA    V      55      N      52          2.048
LGA    A      56      -       -           -
LGA    D      57      F      53          3.611
LGA    A      58      L      54          2.096
LGA    L      59      V      55          2.212
LGA    K      60      A      56          2.983
LGA    Q      61      D      57          3.796
LGA    H      62      A      58          4.293
LGA    R      63      L      59          4.738
LGA    -       -      K      60           -
LGA    H      64      Q      61           #
LGA    R      65      H      62          4.651
LGA    R      66      R      63           -
LGA    D      67      H      64           -
LGA    D      68      R      65           #
LGA    V      69      -       -           -
LGA    I      70      -       -           -
LGA    V      71      -       -           -
LGA    M      72      -       -           -
LGA    L      73      -       -           -
LGA    S      74      -       -           -
LGA    A      75      -       -           -
LGA    R      76      -       -           -
LGA    G      77      -       -           -
LGA    V      78      -       -           -
LGA    T      79      -       -           -
LGA    A      80      R      66          1.460
LGA    P      81      D      67          3.786
LGA    I      82      D      68           -
LGA    A      83      V      69           -
LGA    A      84      I      70           -
LGA    A      85      V      71           -
LGA    G      86      M      72           -
LGA    Y      87      L      73           -
LGA    Q      88      S      74           -
LGA    L      89      A      75           -
LGA    P      90      R      76           -
LGA    M      91      G      77           -
LGA    Q      92      V      78           -
LGA    V      93      T      79           -
LGA    S      94      A      80           -
LGA    -       -      P      81           -
LGA    -       -      I      82           -
LGA    -       -      A      83           -
LGA    -       -      A      84           -
LGA    -       -      A      85           -
LGA    -       -      G      86           -
LGA    -       -      Y      87           -
LGA    -       -      Q      88           -
LGA    -       -      L      89           -
LGA    -       -      P      90           -
LGA    -       -      M      91           -
LGA    -       -      Q      92           -
LGA    -       -      V      93           -
LGA    -       -      S      94           -
LGA    -       -      S      95           -
LGA    -       -      A      96           -
LGA    -       -      A      97           -
LGA    -       -      D      98           -
LGA    S      95      A      99          5.601
LGA    A      96      A     100          0.433
LGA    A      97      R     101          0.599
LGA    D      98      L     102          1.345
LGA    A      99      A     103          1.165
LGA    A     100      V     104          0.332
LGA    R     101      R     105          1.497
LGA    L     102      M     106          2.073
LGA    A     103      E     107          1.155
LGA    V     104      N     108          0.966
LGA    R     105      D     109          2.373
LGA    M     106      G     110          2.300
LGA    E     107      A     111          0.999
LGA    N     108      T     112          1.840
LGA    D     109      A     113          2.780
LGA    G     110      W     114          1.997
LGA    A     111      R     115          0.999
LGA    T     112      A     116          2.122
LGA    A     113      V     117          2.076
LGA    W     114      V     118          0.812
LGA    R     115      E     119          1.614
LGA    A     116      H     120          2.595
LGA    V     117      A     121          1.849
LGA    V     118      -       -           -
LGA    E     119      E     122          3.941
LGA    H     120      T     123          4.844
LGA    A     121      A     124           #
LGA    E     122      D     125           #
LGA    -       -      D     126           -
LGA    T     123      R     127          3.298
LGA    A     124      V     128          2.356
LGA    -       -      F     129           -
LGA    -       -      A     130           -
LGA    D     125      S     131          1.324
LGA    D     126      T     132          2.069
LGA    R     127      A     133          1.932
LGA    V     128      L     134          1.028
LGA    F     129      T     135          1.331
LGA    A     130      E     136          1.528
LGA    S     131      S     137          1.049
LGA    T     132      A     138          0.953
LGA    A     133      V     139          1.291
LGA    L     134      M     140          1.164
LGA    T     135      A     141          0.935
LGA    E     136      T     142          1.550
LGA    S     137      R     143          1.726
LGA    A     138      W     144          1.437
LGA    V     139      N     145          1.570
LGA    M     140      R     146          2.057
LGA    A     141      V     147          1.640
LGA    T     142      L     148          1.249
LGA    R     143      G     149          1.697
LGA    W     144      A     150          1.583
LGA    N     145      W     151          1.282
LGA    R     146      -       -           -
LGA    V     147      -       -           -
LGA    L     148      -       -           -
LGA    G     149      -       -           -
LGA    A     150      -       -           -
LGA    W     151      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  135  135    5.0     68    2.58     7.35     39.821     2.537

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.505838 * X  +   0.860592 * Y  +  -0.059237 * Z  +  21.365238
  Y_new =  -0.462945 * X  +   0.328770 * Y  +   0.823160 * Z  +  14.799891
  Z_new =   0.727880 * X  +  -0.388962 * Y  +   0.564711 * Z  +  15.898532 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.603156    2.538436  [ DEG:   -34.5583    145.4417 ]
  Theta =  -0.815225   -2.326367  [ DEG:   -46.7090   -133.2910 ]
  Phi   =  -0.741152    2.400441  [ DEG:   -42.4649    137.5351 ]
 
# 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: T0385TS393_2-D1                               
REMARK     2: T0385_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385TS393_2-D1.T0385_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  135  135   5.0   68   2.58    7.35  39.821
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS393_2-D1
PFRMAT TS
TARGET T0385
MODEL 2
PARENT N/A
ATOM     17  CA  SER    17       0.916   8.785  18.879  1.00 25.00           C
ATOM     18  CA  GLU    18       0.376   5.608  20.829  1.00 25.00           C
ATOM     19  CA  GLY    19       3.673   6.377  22.566  1.00 25.00           C
ATOM     20  CA  SER    20       5.926   5.903  25.596  1.00 25.00           C
ATOM     21  CA  ALA    21       9.127   7.446  24.381  1.00 25.00           C
ATOM     22  CA  ASP    22      12.116   9.606  25.414  1.00 25.00           C
ATOM     23  CA  ASN    23      14.347   6.496  25.552  1.00 25.00           C
ATOM     24  CA  ALA    24      13.154   5.454  22.066  1.00 25.00           C
ATOM     25  CA  ALA    25      13.908   8.964  20.732  1.00 25.00           C
ATOM     26  CA  LEU    26      17.410   8.825  22.277  1.00 25.00           C
ATOM     27  CA  CYS    27      18.010   5.401  20.669  1.00 25.00           C
ATOM     28  CA  ASP    28      16.870   6.768  17.277  1.00 25.00           C
ATOM     29  CA  ALA    29      19.238   9.754  17.658  1.00 25.00           C
ATOM     30  CA  LEU    30      22.125   7.389  18.511  1.00 25.00           C
ATOM     31  CA  ALA    31      21.327   5.261  15.428  1.00 25.00           C
ATOM     32  CA  VAL    32      21.287   8.404  13.240  1.00 25.00           C
ATOM     33  CA  GLU    33      24.671   9.477  14.677  1.00 25.00           C
ATOM     34  CA  HIS    34      26.106   5.999  13.961  1.00 25.00           C
ATOM     35  CA  ALA    35      24.794   6.172  10.367  1.00 25.00           C
ATOM     36  CA  THR    36      26.385   9.628   9.925  1.00 25.00           C
ATOM     37  CA  ILE    37      29.715   8.293  11.267  1.00 25.00           C
ATOM     38  CA  TYR    38      29.538   5.339   8.837  1.00 25.00           C
ATOM     39  CA  GLY    39      33.125   6.707   8.605  1.00 25.00           C
ATOM     40  CA  TYR    40      34.657   7.417  12.043  1.00 25.00           C
ATOM     41  CA  GLY    41      33.415   7.804  15.665  1.00 25.00           C
ATOM     42  CA  ILE    42      35.859  10.549  16.527  1.00 25.00           C
ATOM     43  CA  VAL    43      35.664  14.068  18.102  1.00 25.00           C
ATOM     44  CA  SER    44      35.899  17.688  16.856  1.00 25.00           C
ATOM     45  CA  ALA    45      33.459  20.379  15.939  1.00 25.00           C
ATOM     46  CA  LEU    46      36.042  22.606  14.161  1.00 25.00           C
ATOM     47  CA  SER    47      36.788  22.454  10.436  1.00 25.00           C
ATOM     48  CA  PRO    48      39.628  21.954   7.953  1.00 25.00           C
ATOM     49  CA  PRO    49      40.038  21.382   4.274  1.00 25.00           C
ATOM     50  CA  GLY    50      39.492  19.344   1.130  1.00 25.00           C
ATOM     51  CA  VAL    51      35.672  19.599   1.028  1.00 25.00           C
ATOM     52  CA  ASN    52      35.386  15.790   1.300  1.00 25.00           C
ATOM     53  CA  PHE    53      37.773  15.800   4.296  1.00 25.00           C
ATOM     54  CA  LEU    54      35.696  18.548   5.971  1.00 25.00           C
ATOM     55  CA  VAL    55      32.499  16.525   5.381  1.00 25.00           C
ATOM     56  CA  ALA    56      34.152  13.421   6.898  1.00 25.00           C
ATOM     57  CA  ASP    57      35.243  15.464   9.949  1.00 25.00           C
ATOM     58  CA  ALA    58      31.677  16.800  10.360  1.00 25.00           C
ATOM     59  CA  LEU    59      30.292  13.235  10.154  1.00 25.00           C
ATOM     60  CA  LYS    60      32.805  12.080  12.803  1.00 25.00           C
ATOM     61  CA  GLN    61      31.785  14.987  15.077  1.00 25.00           C
ATOM     62  CA  HIS    62      28.093  14.074  14.626  1.00 25.00           C
ATOM     63  CA  ARG    63      28.862  10.425  15.497  1.00 25.00           C
ATOM     64  CA  HIS    64      30.754  11.547  18.632  1.00 25.00           C
ATOM     65  CA  ARG    65      27.794  13.748  19.660  1.00 25.00           C
ATOM     66  CA  ARG    66      25.398  10.805  19.156  1.00 25.00           C
ATOM     67  CA  ASP    67      27.657   8.567  21.291  1.00 25.00           C
ATOM     68  CA  ASP    68      27.737  11.230  24.042  1.00 25.00           C
ATOM     69  CA  VAL    69      23.916  11.485  23.940  1.00 25.00           C
ATOM     70  CA  ILE    70      23.631   7.675  24.212  1.00 25.00           C
ATOM     71  CA  VAL    71      26.016   7.686  27.208  1.00 25.00           C
ATOM     72  CA  MET    72      23.940  10.433  28.883  1.00 25.00           C
ATOM     73  CA  LEU    73      20.742   8.410  28.294  1.00 25.00           C
ATOM     74  CA  SER    74      22.396   5.307  29.811  1.00 25.00           C
ATOM     75  CA  ALA    75      23.487   7.350  32.861  1.00 25.00           C
ATOM     76  CA  ARG    76      26.564   5.072  32.716  1.00 25.00           C
ATOM     77  CA  GLY    77      29.666   4.399  30.588  1.00 25.00           C
ATOM     78  CA  VAL    78      31.905   7.443  29.803  1.00 25.00           C
ATOM     79  CA  THR    79      34.340  10.336  30.295  1.00 25.00           C
ATOM     80  CA  ALA    80      32.985  13.138  28.107  1.00 25.00           C
ATOM     81  CA  PRO    81      35.658  13.715  25.425  1.00 25.00           C
ATOM     82  CA  ILE    82      32.934  14.377  22.816  1.00 25.00           C
ATOM     83  CA  ALA    83      31.242  16.871  25.180  1.00 25.00           C
ATOM     84  CA  ALA    84      34.589  18.644  25.744  1.00 25.00           C
ATOM     85  CA  ALA    85      36.154  19.079  22.328  1.00 25.00           C
ATOM     86  CA  GLY    86      38.497  21.409  20.413  1.00 25.00           C
ATOM     87  CA  TYR    87      35.398  23.521  19.869  1.00 25.00           C
ATOM     88  CA  GLN    88      36.060  27.224  19.197  1.00 25.00           C
ATOM     89  CA  LEU    89      33.474  28.918  16.899  1.00 25.00           C
ATOM     90  CA  PRO    90      31.527  25.720  16.047  1.00 25.00           C
ATOM     91  CA  MET    91      28.226  25.948  14.152  1.00 25.00           C
ATOM     92  CA  GLN    92      28.714  22.593  12.344  1.00 25.00           C
ATOM     93  CA  VAL    93      28.490  19.580  14.655  1.00 25.00           C
ATOM     94  CA  SER    94      25.984  18.409  12.032  1.00 25.00           C
ATOM     95  CA  SER    95      24.051  16.687   9.285  1.00 25.00           C
ATOM     96  CA  ALA    96      20.342  16.346   9.824  1.00 25.00           C
ATOM     97  CA  ALA    97      17.618  15.279  12.296  1.00 25.00           C
ATOM     98  CA  ASP    98      20.078  12.902  14.018  1.00 25.00           C
ATOM     99  CA  ALA    99      22.662  15.717  14.270  1.00 25.00           C
ATOM    100  CA  ALA   100      20.019  18.040  15.783  1.00 25.00           C
ATOM    101  CA  ARG   101      19.068  15.341  18.328  1.00 25.00           C
ATOM    102  CA  LEU   102      22.756  14.879  19.253  1.00 25.00           C
ATOM    103  CA  ALA   103      23.141  18.662  19.708  1.00 25.00           C
ATOM    104  CA  VAL   104      20.034  18.733  21.947  1.00 25.00           C
ATOM    105  CA  ARG   105      21.443  15.848  24.035  1.00 25.00           C
ATOM    106  CA  MET   106      24.774  17.702  24.393  1.00 25.00           C
ATOM    107  CA  GLU   107      22.923  20.867  25.502  1.00 25.00           C
ATOM    108  CA  ASN   108      20.949  18.836  28.081  1.00 25.00           C
ATOM    109  CA  ASP   109      24.200  17.300  29.399  1.00 25.00           C
ATOM    110  CA  GLY   110      25.759  20.787  29.684  1.00 25.00           C
ATOM    111  CA  ALA   111      22.681  22.035  31.589  1.00 25.00           C
ATOM    112  CA  THR   112      22.905  19.038  33.964  1.00 25.00           C
ATOM    113  CA  ALA   113      26.621  19.754  34.556  1.00 25.00           C
ATOM    114  CA  TRP   114      25.821  23.425  35.298  1.00 25.00           C
ATOM    115  CA  ARG   115      23.098  22.358  37.770  1.00 25.00           C
ATOM    116  CA  ALA   116      25.558  19.981  39.491  1.00 25.00           C
ATOM    117  CA  VAL   117      28.141  22.797  39.743  1.00 25.00           C
ATOM    118  CA  VAL   118      25.498  25.119  41.256  1.00 25.00           C
ATOM    119  CA  GLU   119      24.547  22.420  43.800  1.00 25.00           C
ATOM    120  CA  HIS   120      28.235  21.958  44.725  1.00 25.00           C
ATOM    121  CA  ALA   121      28.619  25.741  45.181  1.00 25.00           C
ATOM    122  CA  GLU   122      29.744  27.097  41.825  1.00 25.00           C
ATOM    123  CA  THR   123      29.520  27.340  38.069  1.00 25.00           C
ATOM    124  CA  ALA   124      29.698  26.830  34.263  1.00 25.00           C
ATOM    125  CA  ASP   125      28.137  26.773  30.757  1.00 25.00           C
ATOM    126  CA  ASP   126      30.517  27.131  27.779  1.00 25.00           C
ATOM    127  CA  ARG   127      29.884  23.481  26.804  1.00 25.00           C
ATOM    128  CA  VAL   128      26.104  24.056  27.013  1.00 25.00           C
ATOM    129  CA  PHE   129      26.430  27.169  24.807  1.00 25.00           C
ATOM    130  CA  ALA   130      28.477  25.179  22.256  1.00 25.00           C
ATOM    131  CA  SER   131      25.821  22.420  22.240  1.00 25.00           C
ATOM    132  CA  THR   132      23.075  25.033  21.689  1.00 25.00           C
ATOM    133  CA  ALA   133      25.066  26.548  18.789  1.00 25.00           C
ATOM    134  CA  LEU   134      25.499  23.073  17.239  1.00 25.00           C
ATOM    135  CA  THR   135      21.738  22.429  17.569  1.00 25.00           C
ATOM    136  CA  GLU   136      20.991  25.792  15.896  1.00 25.00           C
ATOM    137  CA  SER   137      23.391  24.932  13.039  1.00 25.00           C
ATOM    138  CA  ALA   138      21.685  21.531  12.596  1.00 25.00           C
ATOM    139  CA  VAL   139      18.257  23.236  12.499  1.00 25.00           C
ATOM    140  CA  MET   140      19.534  25.708   9.868  1.00 25.00           C
ATOM    141  CA  ALA   141      20.899  22.809   7.770  1.00 25.00           C
ATOM    142  CA  THR   142      17.528  21.008   8.023  1.00 25.00           C
ATOM    143  CA  ARG   143      15.714  24.197   6.924  1.00 25.00           C
ATOM    144  CA  TRP   144      18.094  24.554   3.945  1.00 25.00           C
ATOM    145  CA  ASN   145      17.461  20.905   2.971  1.00 25.00           C
ATOM    146  CA  ARG   146      13.746  21.657   2.647  1.00 25.00           C
ATOM    147  CA  VAL   147      10.044  21.784   3.622  1.00 25.00           C
ATOM    148  CA  LEU   148       8.654  20.229   6.811  1.00 25.00           C
ATOM    149  CA  GLY   149       5.152  20.089   5.404  1.00 25.00           C
ATOM    150  CA  ALA   150       5.537  16.366   4.492  1.00 25.00           C
ATOM    151  CA  TRP   151       3.684  13.678   2.550  1.00 25.00           C
TER
END
