
#######################################################
#                                                     #
#                        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  147 (  147),  selected  147 , name T0373TS168_4
# Molecule2: number of CA atoms  140 ( 1047),  selected  140 , name T0373.pdb
# PARAMETERS: T0373TS168_4.T0373.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    P       2      -       -           -
LGA    T       3      -       -           -
LGA    N       4      -       -           -
LGA    Q       5      P       2           #
LGA    D       6      T       3           -
LGA    L       7      N       4           -
LGA    -       -      Q       5           -
LGA    -       -      D       6           -
LGA    Q       8      L       7           #
LGA    L       9      Q       8           -
LGA    A      10      L       9           -
LGA    A      11      -       -           -
LGA    H      12      A      10           #
LGA    L      13      A      11           -
LGA    R      14      H      12           -
LGA    S      15      L      13           -
LGA    Q      16      R      14          4.694
LGA    -       -      S      15           -
LGA    -       -      Q      16           -
LGA    -       -      V      17           -
LGA    V      17      T      18          5.088
LGA    T      18      -       -           -
LGA    T      19      T      19          5.609
LGA    L      20      L      20           #
LGA    -       -      T      21           -
LGA    T      21      R      22          5.244
LGA    R      22      -       -           -
LGA    R      23      -       -           -
LGA    L      24      R      23           #
LGA    R      25      L      24           -
LGA    R      26      R      25           -
LGA    E      27      R      26          5.089
LGA    A      28      E      27           -
LGA    Q      29      A      28           -
LGA    A      30      Q      29           -
LGA    D      31      -       -           -
LGA    P      32      A      30           #
LGA    V      33      D      31          3.396
LGA    -       -      P      32           -
LGA    -       -      V      33           -
LGA    Q      34      Q      34          1.681
LGA    F      35      F      35          3.470
LGA    S      36      S      36           #
LGA    Q      37      -       -           -
LGA    L      38      -       -           -
LGA    V      39      Q      37           #
LGA    V      40      L      38           -
LGA    L      41      V      39           -
LGA    G      42      V      40           #
LGA    A      43      L      41           -
LGA    I      44      G      42           -
LGA    D      45      -       -           -
LGA    R      46      A      43           #
LGA    L      47      I      44           -
LGA    G      48      D      45           -
LGA    G      49      R      46           -
LGA    D      50      -       -           -
LGA    V      51      L      47          2.196
LGA    T      52      G      48          2.267
LGA    P      53      G      49          1.608
LGA    S      54      D      50          3.172
LGA    E      55      V      51          0.710
LGA    L      56      T      52           #
LGA    A      57      P      53           #
LGA    A      58      S      54           #
LGA    A      59      E      55          3.187
LGA    E      60      L      56          3.488
LGA    -       -      A      57           -
LGA    -       -      A      58           -
LGA    -       -      A      59           -
LGA    -       -      E      60           -
LGA    -       -      R      61           -
LGA    -       -      M      62           -
LGA    -       -      R      63           -
LGA    -       -      S      64           -
LGA    -       -      S      65           -
LGA    -       -      N      66           -
LGA    R      61      L      67          2.244
LGA    M      62      A      68          1.817
LGA    -       -      A      69           -
LGA    -       -      L      70           -
LGA    R      63      L      71          3.205
LGA    S      64      R      72          3.677
LGA    S      65      E      73          4.247
LGA    N      66      -       -           -
LGA    L      67      -       -           -
LGA    A      68      L      74          4.932
LGA    A      69      E      75           -
LGA    L      70      R      76           -
LGA    -       -      G      77           -
LGA    -       -      G      78           -
LGA    L      71      L      79           #
LGA    R      72      -       -           -
LGA    E      73      -       -           -
LGA    L      74      -       -           -
LGA    E      75      -       -           -
LGA    R      76      -       -           -
LGA    G      77      -       -           -
LGA    G      78      -       -           -
LGA    L      79      -       -           -
LGA    I      80      -       -           -
LGA    V      81      -       -           -
LGA    R      82      -       -           -
LGA    H      83      -       -           -
LGA    A      84      -       -           -
LGA    D      85      -       -           -
LGA    P      86      -       -           -
LGA    Q      87      -       -           -
LGA    D      88      -       -           -
LGA    G      89      -       -           -
LGA    R      90      -       -           -
LGA    R      91      -       -           -
LGA    T      92      -       -           -
LGA    R      93      -       -           -
LGA    V      94      -       -           -
LGA    S      95      -       -           -
LGA    L      96      I      80          4.984
LGA    S      97      V      81           #
LGA    -       -      R      82           -
LGA    -       -      H      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      P      86           -
LGA    -       -      R      91           -
LGA    -       -      T      92           -
LGA    -       -      R      93           -
LGA    -       -      V      94           -
LGA    -       -      S      95           -
LGA    -       -      L      96           -
LGA    S      98      S      97          2.602
LGA    E      99      S      98          3.153
LGA    -       -      E      99           -
LGA    G     100      G     100          1.326
LGA    R     101      R     101          2.002
LGA    R     102      R     102          1.885
LGA    N     103      N     103          1.508
LGA    L     104      L     104          1.439
LGA    Y     105      Y     105          0.921
LGA    G     106      G     106          1.482
LGA    N     107      N     107          1.776
LGA    R     108      R     108          1.221
LGA    A     109      A     109          1.598
LGA    K     110      K     110          2.048
LGA    R     111      R     111          1.680
LGA    E     112      E     112          1.502
LGA    E     113      E     113          1.917
LGA    W     114      W     114          1.691
LGA    L     115      L     115          1.723
LGA    V     116      V     116          1.695
LGA    R     117      R     117          1.715
LGA    A     118      A     118          2.054
LGA    M     119      M     119          2.429
LGA    H     120      H     120          2.479
LGA    A     121      A     121          2.365
LGA    C     122      C     122          2.760
LGA    L     123      -       -           -
LGA    D     124      L     123          3.340
LGA    E     125      D     124           #
LGA    S     126      E     125           -
LGA    E     127      S     126           -
LGA    -       -      E     127           -
LGA    -       -      R     128           -
LGA    -       -      A     129           -
LGA    R     128      L     130           #
LGA    A     129      L     131          2.479
LGA    L     130      -       -           -
LGA    L     131      A     132           #
LGA    A     132      A     133          4.936
LGA    A     133      A     134          3.950
LGA    A     134      G     135          4.151
LGA    G     135      P     136          3.010
LGA    P     136      L     137          3.402
LGA    L     137      L     138          4.043
LGA    L     138      T     139          3.632
LGA    T     139      R     140           #
LGA    R     140      -       -           -
LGA    L     141      L     141           #
LGA    A     142      A     142           -
LGA    Q     143      Q     143           -
LGA    F     144      F     144           -
LGA    E     145      E     145           -
LGA    E     146      -       -           -
LGA    P     147      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  147  140    5.0     56    3.06    53.57     27.079     1.774

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.218853 * X  +  -0.829946 * Y  +   0.513122 * Z  +  48.335258
  Y_new =  -0.509297 * X  +   0.545715 * Y  +   0.665442 * Z  +   1.444238
  Z_new =  -0.832298 * X  +  -0.115697 * Y  +  -0.542120 * Z  +  56.748363 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.931330    0.210262  [ DEG:  -167.9529     12.0471 ]
  Theta =   0.983241    2.158352  [ DEG:    56.3355    123.6645 ]
  Phi   =  -1.976655    1.164938  [ DEG:  -113.2540     66.7460 ]
 
# 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: T0373TS168_4                                  
REMARK     2: T0373.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0373TS168_4.T0373.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  147  140   5.0   56   3.06   53.57  27.079
REMARK  ---------------------------------------------------------- 
MOLECULE T0373TS168_4
PFRMAT TS
TARGET T0373
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      67.236 -18.599  62.811  1.00 25.00           C
ATOM      2  CA  PRO     2      65.950 -16.534  65.755  1.00 25.00           C
ATOM      3  CA  THR     3      68.915 -14.183  65.159  1.00 25.00           C
ATOM      4  CA  ASN     4      66.851 -11.278  66.454  1.00 25.00           C
ATOM      5  CA  GLN     5      67.284  -8.669  63.684  1.00 25.00           C
ATOM      6  CA  ASP     6      63.702  -9.308  62.489  1.00 25.00           C
ATOM      7  CA  LEU     7      62.408  -8.900  66.070  1.00 25.00           C
ATOM      8  CA  GLN     8      64.334  -5.608  66.419  1.00 25.00           C
ATOM      9  CA  LEU     9      62.854  -4.364  63.112  1.00 25.00           C
ATOM     10  CA  ALA    10      59.338  -5.294  64.309  1.00 25.00           C
ATOM     11  CA  ALA    11      59.934  -3.420  67.596  1.00 25.00           C
ATOM     12  CA  HIS    12      61.140  -0.347  65.654  1.00 25.00           C
ATOM     13  CA  LEU    13      58.019  -0.493  63.438  1.00 25.00           C
ATOM     14  CA  ARG    14      55.792  -0.721  66.546  1.00 25.00           C
ATOM     15  CA  SER    15      57.581   2.299  68.079  1.00 25.00           C
ATOM     16  CA  GLN    16      57.081   4.273  64.835  1.00 25.00           C
ATOM     17  CA  VAL    17      53.362   3.362  64.825  1.00 25.00           C
ATOM     18  CA  THR    18      53.049   4.499  68.469  1.00 25.00           C
ATOM     19  CA  THR    19      54.772   7.809  67.610  1.00 25.00           C
ATOM     20  CA  LEU    20      52.382   8.316  64.661  1.00 25.00           C
ATOM     21  CA  THR    21      49.383   7.625  66.941  1.00 25.00           C
ATOM     22  CA  ARG    22      50.711  10.152  69.494  1.00 25.00           C
ATOM     23  CA  ARG    23      51.144  12.761  66.724  1.00 25.00           C
ATOM     24  CA  LEU    24      47.561  12.122  65.529  1.00 25.00           C
ATOM     25  CA  ARG    25      46.268  12.529  69.110  1.00 25.00           C
ATOM     26  CA  ARG    26      48.195  15.822  69.458  1.00 25.00           C
ATOM     27  CA  GLU    27      46.714  17.065  66.152  1.00 25.00           C
ATOM     28  CA  ALA    28      44.258  19.308  67.978  1.00 25.00           C
ATOM     29  CA  GLN    29      41.630  18.015  70.351  1.00 25.00           C
ATOM     30  CA  ALA    30      37.998  17.788  69.285  1.00 25.00           C
ATOM     31  CA  ASP    31      36.929  14.235  70.339  1.00 25.00           C
ATOM     32  CA  PRO    32      37.892  11.538  67.791  1.00 25.00           C
ATOM     33  CA  VAL    33      39.340   9.710  64.831  1.00 25.00           C
ATOM     34  CA  GLN    34      39.999   6.103  65.878  1.00 25.00           C
ATOM     35  CA  PHE    35      42.788   3.843  67.118  1.00 25.00           C
ATOM     36  CA  SER    36      46.532   3.528  66.381  1.00 25.00           C
ATOM     37  CA  GLN    37      46.736   0.423  68.615  1.00 25.00           C
ATOM     38  CA  LEU    38      43.735  -1.111  66.798  1.00 25.00           C
ATOM     39  CA  VAL    39      45.387  -0.401  63.417  1.00 25.00           C
ATOM     40  CA  VAL    40      48.629  -2.041  64.630  1.00 25.00           C
ATOM     41  CA  LEU    41      46.665  -5.109  65.811  1.00 25.00           C
ATOM     42  CA  GLY    42      44.919  -5.332  62.409  1.00 25.00           C
ATOM     43  CA  ALA    43      48.305  -5.115  60.631  1.00 25.00           C
ATOM     44  CA  ILE    44      49.688  -7.895  62.872  1.00 25.00           C
ATOM     45  CA  ASP    45      46.637 -10.074  62.094  1.00 25.00           C
ATOM     46  CA  ARG    46      47.127  -9.464  58.344  1.00 25.00           C
ATOM     47  CA  LEU    47      45.613 -12.954  57.933  1.00 25.00           C
ATOM     48  CA  GLY    48      45.837 -16.594  58.768  1.00 25.00           C
ATOM     49  CA  GLY    49      43.380 -17.339  56.031  1.00 25.00           C
ATOM     50  CA  ASP    50      41.978 -14.856  53.540  1.00 25.00           C
ATOM     51  CA  VAL    51      41.905 -11.055  53.543  1.00 25.00           C
ATOM     52  CA  THR    52      39.390  -8.513  52.211  1.00 25.00           C
ATOM     53  CA  PRO    53      36.050  -6.992  53.141  1.00 25.00           C
ATOM     54  CA  SER    54      33.516  -8.858  55.323  1.00 25.00           C
ATOM     55  CA  GLU    55      36.050 -11.670  55.904  1.00 25.00           C
ATOM     56  CA  LEU    56      38.714  -9.098  56.883  1.00 25.00           C
ATOM     57  CA  ALA    57      36.265  -7.452  59.323  1.00 25.00           C
ATOM     58  CA  ALA    58      35.462 -10.866  60.860  1.00 25.00           C
ATOM     59  CA  ALA    59      39.201 -11.598  61.247  1.00 25.00           C
ATOM     60  CA  GLU    60      39.716  -8.201  62.938  1.00 25.00           C
ATOM     61  CA  ARG    61      37.573  -8.655  66.047  1.00 25.00           C
ATOM     62  CA  MET    62      33.899  -7.960  66.514  1.00 25.00           C
ATOM     63  CA  ARG    63      32.884  -6.885  63.028  1.00 25.00           C
ATOM     64  CA  SER    64      32.694  -3.442  64.565  1.00 25.00           C
ATOM     65  CA  SER    65      34.997  -1.296  66.746  1.00 25.00           C
ATOM     66  CA  ASN    66      38.064  -3.084  65.309  1.00 25.00           C
ATOM     67  CA  LEU    67      36.780  -2.478  61.752  1.00 25.00           C
ATOM     68  CA  ALA    68      36.243   1.229  62.549  1.00 25.00           C
ATOM     69  CA  ALA    69      39.799   1.466  63.955  1.00 25.00           C
ATOM     70  CA  LEU    70      41.185  -0.193  60.794  1.00 25.00           C
ATOM     71  CA  LEU    71      39.233   2.275  58.613  1.00 25.00           C
ATOM     72  CA  ARG    72      40.609   5.207  60.656  1.00 25.00           C
ATOM     73  CA  GLU    73      44.167   3.851  60.254  1.00 25.00           C
ATOM     74  CA  LEU    74      43.640   3.520  56.475  1.00 25.00           C
ATOM     75  CA  GLU    75      42.349   7.123  56.315  1.00 25.00           C
ATOM     76  CA  ARG    76      45.409   8.331  58.275  1.00 25.00           C
ATOM     77  CA  GLY    77      48.452   6.287  57.135  1.00 25.00           C
ATOM     78  CA  GLY    78      48.513   2.831  55.417  1.00 25.00           C
ATOM     79  CA  LEU    79      48.733   0.952  58.762  1.00 25.00           C
ATOM     80  CA  ILE    80      46.996  -2.004  57.051  1.00 25.00           C
ATOM     81  CA  VAL    81      47.890  -4.267  54.153  1.00 25.00           C
ATOM     82  CA  ARG    82      45.400  -6.295  52.105  1.00 25.00           C
ATOM     83  CA  HIS    83      43.635  -5.379  48.833  1.00 25.00           C
ATOM     84  CA  ALA    84      43.327  -5.139  45.054  1.00 25.00           C
ATOM     85  CA  ASP    85      42.299  -6.938  41.821  1.00 25.00           C
ATOM     86  CA  PRO    86      42.386  -7.513  38.048  1.00 25.00           C
ATOM     87  CA  GLN    87      43.381  -4.884  35.489  1.00 25.00           C
ATOM     88  CA  ASP    88      44.275  -1.709  37.287  1.00 25.00           C
ATOM     89  CA  GLY    89      44.660  -1.321  41.014  1.00 25.00           C
ATOM     90  CA  ARG    90      46.009  -0.786  44.532  1.00 25.00           C
ATOM     91  CA  ARG    91      48.452  -1.230  47.416  1.00 25.00           C
ATOM     92  CA  THR    92      46.196  -1.188  50.417  1.00 25.00           C
ATOM     93  CA  ARG    93      43.690  -1.598  53.307  1.00 25.00           C
ATOM     94  CA  VAL    94      42.215  -3.589  56.228  1.00 25.00           C
ATOM     95  CA  SER    95      38.587  -2.361  55.865  1.00 25.00           C
ATOM     96  CA  LEU    96      35.446  -1.793  57.880  1.00 25.00           C
ATOM     97  CA  SER    97      33.423  -1.473  54.607  1.00 25.00           C
ATOM     98  CA  SER    98      31.763  -0.042  51.460  1.00 25.00           C
ATOM     99  CA  GLU    99      31.061   3.482  52.784  1.00 25.00           C
ATOM    100  CA  GLY   100      33.981   3.166  55.243  1.00 25.00           C
ATOM    101  CA  ARG   101      36.279   2.019  52.403  1.00 25.00           C
ATOM    102  CA  ARG   102      35.173   5.000  50.269  1.00 25.00           C
ATOM    103  CA  ASN   103      35.869   7.380  53.189  1.00 25.00           C
ATOM    104  CA  LEU   104      39.346   5.839  53.647  1.00 25.00           C
ATOM    105  CA  TYR   105      40.053   6.263  49.906  1.00 25.00           C
ATOM    106  CA  GLY   106      38.942   9.923  50.086  1.00 25.00           C
ATOM    107  CA  ASN   107      41.232  10.496  53.102  1.00 25.00           C
ATOM    108  CA  ARG   108      44.159   8.903  51.213  1.00 25.00           C
ATOM    109  CA  ALA   109      43.464  11.151  48.192  1.00 25.00           C
ATOM    110  CA  LYS   110      43.389  14.230  50.469  1.00 25.00           C
ATOM    111  CA  ARG   111      46.721  13.180  52.038  1.00 25.00           C
ATOM    112  CA  GLU   112      48.249  12.733  48.555  1.00 25.00           C
ATOM    113  CA  GLU   113      46.999  16.206  47.533  1.00 25.00           C
ATOM    114  CA  TRP   114      48.515  17.715  50.710  1.00 25.00           C
ATOM    115  CA  LEU   115      51.851  15.986  49.967  1.00 25.00           C
ATOM    116  CA  VAL   116      51.786  17.345  46.387  1.00 25.00           C
ATOM    117  CA  ARG   117      51.085  20.869  47.712  1.00 25.00           C
ATOM    118  CA  ALA   118      54.004  20.553  50.170  1.00 25.00           C
ATOM    119  CA  MET   119      56.304  19.406  47.330  1.00 25.00           C
ATOM    120  CA  HIS   120      55.197  22.388  45.197  1.00 25.00           C
ATOM    121  CA  ALA   121      55.893  24.766  48.117  1.00 25.00           C
ATOM    122  CA  CYS   122      58.775  23.625  50.224  1.00 25.00           C
ATOM    123  CA  LEU   123      59.545  20.061  51.449  1.00 25.00           C
ATOM    124  CA  ASP   124      63.279  19.351  51.577  1.00 25.00           C
ATOM    125  CA  GLU   125      62.203  15.782  50.814  1.00 25.00           C
ATOM    126  CA  SER   126      61.838  13.681  53.995  1.00 25.00           C
ATOM    127  CA  GLU   127      58.234  12.810  53.036  1.00 25.00           C
ATOM    128  CA  ARG   128      59.389  11.785  49.532  1.00 25.00           C
ATOM    129  CA  ALA   129      62.131   9.584  51.051  1.00 25.00           C
ATOM    130  CA  LEU   130      59.563   7.945  53.372  1.00 25.00           C
ATOM    131  CA  LEU   131      57.251   7.286  50.391  1.00 25.00           C
ATOM    132  CA  ALA   132      60.161   5.725  48.449  1.00 25.00           C
ATOM    133  CA  ALA   133      61.000   3.498  51.449  1.00 25.00           C
ATOM    134  CA  ALA   134      57.338   2.404  51.692  1.00 25.00           C
ATOM    135  CA  GLY   135      57.310   1.583  47.952  1.00 25.00           C
ATOM    136  CA  PRO   136      60.520  -0.466  48.352  1.00 25.00           C
ATOM    137  CA  LEU   137      58.973  -2.362  51.297  1.00 25.00           C
ATOM    138  CA  LEU   138      55.838  -3.082  49.218  1.00 25.00           C
ATOM    139  CA  THR   139      58.013  -4.365  46.338  1.00 25.00           C
ATOM    140  CA  ARG   140      59.931  -6.627  48.761  1.00 25.00           C
ATOM    141  CA  LEU   141      56.629  -7.988  50.143  1.00 25.00           C
ATOM    142  CA  ALA   142      55.396  -8.681  46.583  1.00 25.00           C
ATOM    143  CA  GLN   143      58.665 -10.508  45.782  1.00 25.00           C
ATOM    144  CA  PHE   144      60.519 -13.759  45.604  1.00 25.00           C
ATOM    145  CA  GLU   145      63.962 -13.728  44.030  1.00 25.00           C
ATOM    146  CA  GLU   146      67.321 -12.135  44.959  1.00 25.00           C
ATOM    147  CA  PRO   147      66.733  -8.969  42.952  1.00 25.00           C
TER
END
