
#######################################################
#                                                     #
#                        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 T0319TS393_4
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319TS393_4.T0319.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          4.097
LGA    K       2      K       2           #
LGA    F       3      F       3          4.278
LGA    L       4      L       4          5.080
LGA    T       5      T       5          3.874
LGA    T       6      T       6           #
LGA    N       7      N       7          3.788
LGA    F       8      F       8          4.364
LGA    L       9      -       -           -
LGA    K      10      -       -           -
LGA    C      11      -       -           -
LGA    S      12      -       -           -
LGA    V      13      -       -           -
LGA    K      14      -       -           -
LGA    A      15      -       -           -
LGA    C      16      -       -           -
LGA    D      17      -       -           -
LGA    T      18      L       9           #
LGA    S      19      K      10          1.871
LGA    -       -      C      11           -
LGA    -       -      S      12           -
LGA    -       -      V      13           -
LGA    -       -      K      14           -
LGA    -       -      A      15           -
LGA    -       -      C      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      N      20           -
LGA    -       -      D      21           -
LGA    N      20      N      22           #
LGA    D      21      F      23          3.355
LGA    N      22      P      24          4.241
LGA    F      23      L      25           #
LGA    P      24      Q      26           -
LGA    L      25      Y      27           -
LGA    Q      26      D      28           -
LGA    Y      27      G      29           -
LGA    D      28      S      30           -
LGA    G      29      K      31           -
LGA    -       -      C      32           -
LGA    -       -      Q      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      D      37           -
LGA    -       -      E      38           -
LGA    -       -      S      39           -
LGA    -       -      I      40           -
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      P      44           -
LGA    S      30      E      45          3.820
LGA    K      31      F      46          2.859
LGA    C      32      L      47          3.167
LGA    Q      33      L      48           #
LGA    -       -      N      49           -
LGA    -       -      I      50           -
LGA    -       -      V      51           -
LGA    -       -      D      52           -
LGA    -       -      R      53           -
LGA    -       -      V      54           -
LGA    L      34      D      55           #
LGA    -       -      W      56           -
LGA    -       -      P      57           -
LGA    V      35      A      58           #
LGA    Q      36      V      59          2.302
LGA    -       -      L      60           -
LGA    -       -      T      61           -
LGA    D      37      V      62          1.156
LGA    -       -      A      63           -
LGA    -       -      A      64           -
LGA    E      38      E      65          3.020
LGA    S      39      L      66           #
LGA    I      40      -       -           -
LGA    E      41      -       -           -
LGA    F      42      -       -           -
LGA    N      43      G      67          2.812
LGA    P      44      N      68          3.014
LGA    E      45      -       -           -
LGA    F      46      -       -           -
LGA    L      47      -       -           -
LGA    L      48      N      69          2.450
LGA    N      49      A      70          2.804
LGA    I      50      L      71          3.963
LGA    V      51      -       -           -
LGA    D      52      P      72          2.640
LGA    R      53      P      73          3.230
LGA    V      54      T      74          2.800
LGA    D      55      K      75          2.217
LGA    W      56      -       -           -
LGA    P      57      P      76          3.024
LGA    A      58      -       -           -
LGA    V      59      -       -           -
LGA    L      60      -       -           -
LGA    T      61      S      77          2.027
LGA    V      62      F      78          4.308
LGA    A      63      -       -           -
LGA    A      64      -       -           -
LGA    E      65      P      79          2.651
LGA    L      66      S      80          4.442
LGA    G      67      S      81           -
LGA    N      68      I      82           -
LGA    N      69      -       -           -
LGA    A      70      -       -           -
LGA    L      71      -       -           -
LGA    P      72      -       -           -
LGA    P      73      -       -           -
LGA    T      74      -       -           -
LGA    K      75      -       -           -
LGA    P      76      -       -           -
LGA    S      77      -       -           -
LGA    F      78      -       -           -
LGA    P      79      -       -           -
LGA    S      80      -       -           -
LGA    S      81      -       -           -
LGA    I      82      Q      83           #
LGA    Q      83      E      84           -
LGA    E      84      -       -           -
LGA    L      85      L      85          5.019
LGA    T      86      T      86          0.921
LGA    D      87      D      87          1.448
LGA    D      88      D      88          1.131
LGA    D      89      D      89          0.548
LGA    M      90      M      90          0.720
LGA    A      91      A      91          0.796
LGA    I      92      I      92          1.130
LGA    L      93      L      93          1.002
LGA    N      94      N      94          0.694
LGA    D      95      D      95          1.288
LGA    L      96      L      96          1.590
LGA    H      97      H      97          1.208
LGA    T      98      T      98          1.125
LGA    L      99      L      99          1.764
LGA    L     100      L     100          2.465
LGA    L     101      L     101          1.930
LGA    -       -      Q     102           -
LGA    Q     102      T     103          1.434
LGA    T     103      S     104           #
LGA    S     104      I     105           #
LGA    I     105      A     106           -
LGA    -       -      E     107           -
LGA    -       -      G     108           -
LGA    -       -      E     109           -
LGA    -       -      M     110           -
LGA    -       -      K     111           -
LGA    -       -      C     112           -
LGA    -       -      R     113           -
LGA    -       -      N     114           -
LGA    -       -      C     115           -
LGA    -       -      G     116           -
LGA    -       -      H     117           -
LGA    -       -      I     118           -
LGA    -       -      Y     119           -
LGA    -       -      Y     120           -
LGA    -       -      I     121           -
LGA    -       -      K     122           -
LGA    -       -      N     123           -
LGA    -       -      G     124           -
LGA    -       -      I     125           -
LGA    -       -      P     126           -
LGA    -       -      N     127           -
LGA    -       -      L     128           -
LGA    -       -      L     129           -
LGA    A     106      L     130          5.296
LGA    E     107      P     131           -
LGA    G     108      P     132           #
LGA    -       -      H     133           -
LGA    E     109      L     134          5.566
LGA    M     110      V     135           -
LGA    K     111      -       -           -
LGA    C     112      -       -           -
LGA    R     113      -       -           -
LGA    N     114      -       -           -
LGA    C     115      -       -           -
LGA    G     116      -       -           -
LGA    H     117      -       -           -
LGA    I     118      -       -           -
LGA    Y     119      -       -           -
LGA    Y     120      -       -           -
LGA    I     121      -       -           -
LGA    K     122      -       -           -
LGA    N     123      -       -           -
LGA    G     124      -       -           -
LGA    I     125      -       -           -
LGA    P     126      -       -           -
LGA    N     127      -       -           -
LGA    L     128      -       -           -
LGA    L     129      -       -           -
LGA    L     130      -       -           -
LGA    P     131      -       -           -
LGA    P     132      -       -           -
LGA    H     133      -       -           -
LGA    L     134      -       -           -
LGA    V     135      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  135  135    5.0     49    3.00    51.02     22.851     1.582

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.148367 * X  +  -0.145398 * Y  +   0.978186 * Z  +  26.301575
  Y_new =  -0.961865 * X  +   0.251051 * Y  +  -0.108575 * Z  +  -5.291182
  Z_new =  -0.229788 * X  +  -0.956992 * Y  +  -0.177100 * Z  +  13.381041 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.753786    1.387807  [ DEG:  -100.4845     79.5155 ]
  Theta =   0.231860    2.909733  [ DEG:    13.2846    166.7154 ]
  Phi   =  -1.723839    1.417754  [ DEG:   -98.7687     81.2313 ]
 
# 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: T0319TS393_4                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319TS393_4.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  135  135   5.0   49   3.00   51.02  22.851
REMARK  ---------------------------------------------------------- 
MOLECULE T0319TS393_4
PFRMAT TS
TARGET T0319
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      16.270   8.605  15.742  1.00 25.00           C
ATOM      2  CA  LYS     2      17.863   6.720  12.874  1.00 25.00           C
ATOM      3  CA  PHE     3      19.830   4.966  10.130  1.00 25.00           C
ATOM      4  CA  LEU     4      18.179   1.856  11.411  1.00 25.00           C
ATOM      5  CA  THR     5      19.332  -1.078  13.506  1.00 25.00           C
ATOM      6  CA  THR     6      20.045  -4.759  14.296  1.00 25.00           C
ATOM      7  CA  ASN     7      16.373  -5.776  14.590  1.00 25.00           C
ATOM      8  CA  PHE     8      15.906  -4.960  18.335  1.00 25.00           C
ATOM      9  CA  LEU     9      18.666  -7.566  18.697  1.00 25.00           C
ATOM     10  CA  LYS    10      17.347 -10.485  20.753  1.00 25.00           C
ATOM     11  CA  CYS    11      15.838 -11.746  17.522  1.00 25.00           C
ATOM     12  CA  SER    12      12.817 -13.346  19.225  1.00 25.00           C
ATOM     13  CA  VAL    13       9.423 -12.629  17.700  1.00 25.00           C
ATOM     14  CA  LYS    14       8.417 -12.333  14.025  1.00 25.00           C
ATOM     15  CA  ALA    15      10.331  -9.150  13.008  1.00 25.00           C
ATOM     16  CA  CYS    16      11.455  -7.097  16.051  1.00 25.00           C
ATOM     17  CA  ASP    17       8.710  -7.090  18.700  1.00 25.00           C
ATOM     18  CA  THR    18       7.770  -3.529  17.602  1.00 25.00           C
ATOM     19  CA  SER    19       7.889  -2.075  14.090  1.00 25.00           C
ATOM     20  CA  ASN    20       6.388  -5.403  12.998  1.00 25.00           C
ATOM     21  CA  ASP    21       7.843  -5.489   9.515  1.00 25.00           C
ATOM     22  CA  ASN    22      11.591  -5.152   9.494  1.00 25.00           C
ATOM     23  CA  PHE    23      14.083  -2.551  10.673  1.00 25.00           C
ATOM     24  CA  PRO    24      16.653  -4.943   9.299  1.00 25.00           C
ATOM     25  CA  LEU    25      15.575  -8.331  10.760  1.00 25.00           C
ATOM     26  CA  GLN    26      17.331 -11.218  12.581  1.00 25.00           C
ATOM     27  CA  TYR    27      20.511  -9.854  14.161  1.00 25.00           C
ATOM     28  CA  ASP    28      22.213 -11.138  17.345  1.00 25.00           C
ATOM     29  CA  GLY    29      23.917 -12.689  20.380  1.00 25.00           C
ATOM     30  CA  SER    30      27.512 -11.568  20.104  1.00 25.00           C
ATOM     31  CA  LYS    31      28.173  -7.864  19.272  1.00 25.00           C
ATOM     32  CA  CYS    32      26.873  -8.292  15.731  1.00 25.00           C
ATOM     33  CA  GLN    33      24.297  -6.538  13.542  1.00 25.00           C
ATOM     34  CA  LEU    34      24.008  -3.517  11.166  1.00 25.00           C
ATOM     35  CA  VAL    35      22.257  -0.680   9.320  1.00 25.00           C
ATOM     36  CA  GLN    36      19.671  -1.272   6.618  1.00 25.00           C
ATOM     37  CA  ASP    37      18.301   1.676   4.671  1.00 25.00           C
ATOM     38  CA  GLU    38      16.662   3.064   1.546  1.00 25.00           C
ATOM     39  CA  SER    39      17.933   6.235  -0.076  1.00 25.00           C
ATOM     40  CA  ILE    40      20.143   5.476  -3.090  1.00 25.00           C
ATOM     41  CA  GLU    41      20.852   1.812  -2.511  1.00 25.00           C
ATOM     42  CA  PHE    42      24.538   2.723  -3.161  1.00 25.00           C
ATOM     43  CA  ASN    43      24.594   5.541  -0.627  1.00 25.00           C
ATOM     44  CA  PRO    44      25.552   6.230   3.030  1.00 25.00           C
ATOM     45  CA  GLU    45      28.989   4.940   1.939  1.00 25.00           C
ATOM     46  CA  PHE    46      29.561   3.448   5.420  1.00 25.00           C
ATOM     47  CA  LEU    47      26.135   1.742   5.278  1.00 25.00           C
ATOM     48  CA  LEU    48      26.962   0.311   1.823  1.00 25.00           C
ATOM     49  CA  ASN    49      30.312  -0.999   3.141  1.00 25.00           C
ATOM     50  CA  ILE    50      28.530  -2.629   6.115  1.00 25.00           C
ATOM     51  CA  VAL    51      26.011  -4.267   3.741  1.00 25.00           C
ATOM     52  CA  ASP    52      28.877  -5.583   1.568  1.00 25.00           C
ATOM     53  CA  ARG    53      26.894  -8.340  -0.234  1.00 25.00           C
ATOM     54  CA  VAL    54      24.420  -9.055   2.521  1.00 25.00           C
ATOM     55  CA  ASP    55      22.649 -10.354   5.660  1.00 25.00           C
ATOM     56  CA  TRP    56      23.926  -7.785   8.109  1.00 25.00           C
ATOM     57  CA  PRO    57      27.334  -9.297   7.231  1.00 25.00           C
ATOM     58  CA  ALA    58      28.255  -9.440  10.946  1.00 25.00           C
ATOM     59  CA  VAL    59      24.926 -11.167  11.729  1.00 25.00           C
ATOM     60  CA  LEU    60      25.562 -13.711   8.938  1.00 25.00           C
ATOM     61  CA  THR    61      29.069 -14.388  10.320  1.00 25.00           C
ATOM     62  CA  VAL    62      27.615 -14.896  13.827  1.00 25.00           C
ATOM     63  CA  ALA    63      25.013 -17.330  12.423  1.00 25.00           C
ATOM     64  CA  ALA    64      27.770 -19.264  10.600  1.00 25.00           C
ATOM     65  CA  GLU    65      29.814 -19.446  13.833  1.00 25.00           C
ATOM     66  CA  LEU    66      26.747 -20.736  15.729  1.00 25.00           C
ATOM     67  CA  GLY    67      27.448 -24.336  14.788  1.00 25.00           C
ATOM     68  CA  ASN    68      25.407 -27.503  14.159  1.00 25.00           C
ATOM     69  CA  ASN    69      26.404 -28.520  10.598  1.00 25.00           C
ATOM     70  CA  ALA    70      29.076 -29.448   8.016  1.00 25.00           C
ATOM     71  CA  LEU    71      31.705 -29.526  10.770  1.00 25.00           C
ATOM     72  CA  PRO    72      31.714 -32.548  13.108  1.00 25.00           C
ATOM     73  CA  PRO    73      35.119 -34.292  13.628  1.00 25.00           C
ATOM     74  CA  THR    74      38.008 -32.474  15.342  1.00 25.00           C
ATOM     75  CA  LYS    75      39.327 -31.859  11.807  1.00 25.00           C
ATOM     76  CA  PRO    76      42.733 -32.898  13.146  1.00 25.00           C
ATOM     77  CA  SER    77      44.825 -31.010  10.592  1.00 25.00           C
ATOM     78  CA  PHE    78      45.390 -27.823  12.531  1.00 25.00           C
ATOM     79  CA  PRO    79      48.607 -28.503  14.356  1.00 25.00           C
ATOM     80  CA  SER    80      48.012 -25.586  16.801  1.00 25.00           C
ATOM     81  CA  SER    81      47.472 -23.037  14.088  1.00 25.00           C
ATOM     82  CA  ILE    82      47.419 -19.395  15.171  1.00 25.00           C
ATOM     83  CA  GLN    83      47.810 -17.231  12.049  1.00 25.00           C
ATOM     84  CA  GLU    84      46.283 -13.974  13.058  1.00 25.00           C
ATOM     85  CA  LEU    85      42.605 -14.733  13.481  1.00 25.00           C
ATOM     86  CA  THR    86      40.503 -14.905  10.341  1.00 25.00           C
ATOM     87  CA  ASP    87      41.446 -11.372   9.203  1.00 25.00           C
ATOM     88  CA  ASP    88      38.250 -11.170   7.102  1.00 25.00           C
ATOM     89  CA  ASP    89      36.171 -12.313  10.108  1.00 25.00           C
ATOM     90  CA  MET    90      37.843  -9.658  12.305  1.00 25.00           C
ATOM     91  CA  ALA    91      37.095  -6.976   9.674  1.00 25.00           C
ATOM     92  CA  ILE    92      33.437  -8.102   9.531  1.00 25.00           C
ATOM     93  CA  LEU    93      33.209  -7.932  13.350  1.00 25.00           C
ATOM     94  CA  ASN    94      34.700  -4.404  13.305  1.00 25.00           C
ATOM     95  CA  ASP    95      32.163  -3.340  10.641  1.00 25.00           C
ATOM     96  CA  LEU    96      29.307  -4.777  12.750  1.00 25.00           C
ATOM     97  CA  HIS    97      30.590  -2.881  15.821  1.00 25.00           C
ATOM     98  CA  THR    98      30.754   0.358  13.785  1.00 25.00           C
ATOM     99  CA  LEU    99      27.169  -0.201  12.560  1.00 25.00           C
ATOM    100  CA  LEU   100      26.004  -0.786  16.161  1.00 25.00           C
ATOM    101  CA  LEU   101      27.747   2.437  17.275  1.00 25.00           C
ATOM    102  CA  GLN   102      26.060   4.363  14.426  1.00 25.00           C
ATOM    103  CA  THR   103      22.938   2.487  13.225  1.00 25.00           C
ATOM    104  CA  SER   104      21.301   2.659  16.642  1.00 25.00           C
ATOM    105  CA  ILE   105      17.904   1.374  17.775  1.00 25.00           C
ATOM    106  CA  ALA   106      16.578   2.422  21.121  1.00 25.00           C
ATOM    107  CA  GLU   107      16.780   3.230  24.784  1.00 25.00           C
ATOM    108  CA  GLY   108      18.626  -0.066  25.199  1.00 25.00           C
ATOM    109  CA  GLU   109      19.413  -2.317  22.238  1.00 25.00           C
ATOM    110  CA  MET   110      20.740  -2.758  18.690  1.00 25.00           C
ATOM    111  CA  LYS   111      23.611  -5.157  18.458  1.00 25.00           C
ATOM    112  CA  CYS   112      22.870  -6.093  22.060  1.00 25.00           C
ATOM    113  CA  ARG   113      25.011  -7.567  24.888  1.00 25.00           C
ATOM    114  CA  ASN   114      27.910  -6.145  26.982  1.00 25.00           C
ATOM    115  CA  CYS   115      30.599  -6.810  24.378  1.00 25.00           C
ATOM    116  CA  GLY   116      32.561  -3.568  24.093  1.00 25.00           C
ATOM    117  CA  HIS   117      30.474  -2.518  21.130  1.00 25.00           C
ATOM    118  CA  ILE   118      27.134  -3.514  22.632  1.00 25.00           C
ATOM    119  CA  TYR   119      24.950  -0.618  21.488  1.00 25.00           C
ATOM    120  CA  TYR   120      22.230   1.963  22.040  1.00 25.00           C
ATOM    121  CA  ILE   121      24.210   4.719  20.345  1.00 25.00           C
ATOM    122  CA  LYS   122      26.399   7.513  21.832  1.00 25.00           C
ATOM    123  CA  ASN   123      26.391   9.942  24.758  1.00 25.00           C
ATOM    124  CA  GLY   124      27.607  13.046  26.611  1.00 25.00           C
ATOM    125  CA  ILE   125      28.805  16.026  24.607  1.00 25.00           C
ATOM    126  CA  PRO   126      27.473  19.369  25.920  1.00 25.00           C
ATOM    127  CA  ASN   127      26.581  20.826  22.521  1.00 25.00           C
ATOM    128  CA  LEU   128      29.181  21.409  19.820  1.00 25.00           C
ATOM    129  CA  LEU   129      31.890  19.957  17.688  1.00 25.00           C
ATOM    130  CA  LEU   130      35.134  21.816  18.308  1.00 25.00           C
ATOM    131  CA  PRO   131      37.720  20.971  15.703  1.00 25.00           C
ATOM    132  CA  PRO   132      36.638  21.545  12.035  1.00 25.00           C
ATOM    133  CA  HIS   133      33.655  23.530  10.857  1.00 25.00           C
ATOM    134  CA  LEU   134      32.107  26.190   8.718  1.00 25.00           C
ATOM    135  CA  VAL   135      29.905  28.237   6.339  1.00 25.00           C
TER
END
