
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms  135 ( 1000),  selected  135 , name T0385_D1.pdb
# PARAMETERS: T0385TS393_5-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      L      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      A      29           -
LGA    -       -      L      30           -
LGA    -       -      A      31           -
LGA    -       -      V      32           -
LGA    -       -      E      33           -
LGA    -       -      H      34           -
LGA    -       -      A      35           -
LGA    -       -      T      36           -
LGA    -       -      I      37           -
LGA    -       -      Y      38           -
LGA    -       -      G      39           -
LGA    -       -      Y      40           -
LGA    -       -      G      41           -
LGA    C      27      I      42          3.654
LGA    D      28      V      43          4.633
LGA    -       -      S      44           -
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    A      29      S      47          1.526
LGA    L      30      P      48           #
LGA    A      31      P      49           -
LGA    -       -      G      50           -
LGA    -       -      V      51           -
LGA    V      32      N      52          3.220
LGA    E      33      F      53          4.907
LGA    H      34      L      54          5.338
LGA    A      35      V      55          4.873
LGA    T      36      A      56          3.741
LGA    I      37      D      57          1.926
LGA    Y      38      -       -           -
LGA    G      39      -       -           -
LGA    Y      40      -       -           -
LGA    G      41      -       -           -
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      -       -           -
LGA    N      52      -       -           -
LGA    F      53      -       -           -
LGA    L      54      -       -           -
LGA    V      55      -       -           -
LGA    A      56      -       -           -
LGA    D      57      -       -           -
LGA    A      58      -       -           -
LGA    L      59      -       -           -
LGA    K      60      -       -           -
LGA    Q      61      A      58          2.412
LGA    H      62      L      59          3.302
LGA    R      63      K      60          1.711
LGA    H      64      Q      61          4.600
LGA    R      65      H      62           #
LGA    R      66      -       -           -
LGA    D      67      R      63          4.768
LGA    D      68      H      64           -
LGA    V      69      R      65           -
LGA    I      70      R      66           -
LGA    -       -      D      67           -
LGA    -       -      D      68           -
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           -
LGA    -       -      P      81           -
LGA    -       -      I      82           -
LGA    V      71      A      83           #
LGA    M      72      A      84           -
LGA    L      73      -       -           -
LGA    S      74      A      85          3.682
LGA    A      75      G      86          1.928
LGA    R      76      -       -           -
LGA    G      77      -       -           -
LGA    V      78      Y      87          1.013
LGA    T      79      Q      88          2.839
LGA    A      80      -       -           -
LGA    P      81      -       -           -
LGA    I      82      L      89           #
LGA    A      83      P      90           #
LGA    A      84      M      91           -
LGA    A      85      Q      92           -
LGA    G      86      V      93           -
LGA    Y      87      S      94           -
LGA    Q      88      S      95           -
LGA    L      89      A      96           -
LGA    P      90      A      97           -
LGA    M      91      D      98           -
LGA    Q      92      -       -           -
LGA    V      93      -       -           -
LGA    S      94      -       -           -
LGA    S      95      A      99          4.444
LGA    A      96      A     100          2.121
LGA    A      97      R     101          2.221
LGA    D      98      L     102          2.744
LGA    A      99      A     103          1.882
LGA    A     100      V     104          0.604
LGA    R     101      R     105          1.490
LGA    L     102      M     106          1.197
LGA    A     103      E     107          0.543
LGA    V     104      N     108          0.682
LGA    R     105      D     109          0.727
LGA    M     106      G     110          0.543
LGA    E     107      A     111          1.314
LGA    N     108      T     112          1.438
LGA    D     109      A     113          0.790
LGA    G     110      W     114          1.584
LGA    A     111      R     115          2.050
LGA    T     112      A     116          1.257
LGA    A     113      V     117          1.748
LGA    W     114      V     118          2.732
LGA    R     115      E     119          2.457
LGA    A     116      H     120          2.175
LGA    V     117      A     121          1.856
LGA    V     118      E     122          2.841
LGA    E     119      -       -           -
LGA    H     120      -       -           -
LGA    A     121      T     123          3.179
LGA    E     122      A     124          3.695
LGA    T     123      D     125          3.248
LGA    -       -      D     126           -
LGA    A     124      R     127          1.853
LGA    -       -      V     128           -
LGA    -       -      F     129           -
LGA    D     125      A     130          4.088
LGA    D     126      S     131          3.924
LGA    R     127      T     132          4.007
LGA    V     128      A     133          3.356
LGA    F     129      L     134          2.447
LGA    A     130      T     135          2.468
LGA    S     131      E     136          2.213
LGA    T     132      S     137          1.633
LGA    A     133      A     138          1.108
LGA    L     134      V     139          0.858
LGA    T     135      M     140          0.993
LGA    E     136      A     141          0.512
LGA    S     137      T     142          0.279
LGA    A     138      R     143          0.588
LGA    V     139      W     144          1.512
LGA    M     140      N     145          1.330
LGA    A     141      R     146          1.492
LGA    T     142      V     147          2.302
LGA    R     143      L     148          2.876
LGA    W     144      G     149          3.227
LGA    N     145      A     150          3.728
LGA    R     146      -       -           -
LGA    V     147      W     151          4.982
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    2.74     5.88     34.466     2.390

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.465117 * X  +   0.160706 * Y  +  -0.870540 * Z  +  26.940350
  Y_new =   0.478688 * X  +   0.781556 * Y  +   0.400036 * Z  +  15.686335
  Z_new =   0.744663 * X  +  -0.602781 * Y  +   0.286587 * Z  +  13.298059 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.126988    2.014605  [ DEG:   -64.5717    115.4283 ]
  Theta =  -0.840030   -2.301562  [ DEG:   -48.1302   -131.8698 ]
  Phi   =   0.799776   -2.341816  [ DEG:    45.8238   -134.1762 ]
 
# 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_5-D1                               
REMARK     2: T0385_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385TS393_5-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   2.74    5.88  34.466
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS393_5-D1
PFRMAT TS
TARGET T0385
MODEL 5
PARENT N/A
ATOM     17  CA  SER    17      14.570   1.856  -4.732  1.00 25.00           C
ATOM     18  CA  GLU    18      15.675  -0.366  -1.868  1.00 25.00           C
ATOM     19  CA  GLY    19      15.133  -0.315   1.914  1.00 25.00           C
ATOM     20  CA  SER    20      13.108   2.948   1.616  1.00 25.00           C
ATOM     21  CA  ALA    21      16.119   4.481   3.438  1.00 25.00           C
ATOM     22  CA  ASP    22      15.703   8.138   4.499  1.00 25.00           C
ATOM     23  CA  ASN    23      16.842   7.263   8.050  1.00 25.00           C
ATOM     24  CA  ALA    24      19.905   5.443   6.645  1.00 25.00           C
ATOM     25  CA  ALA    25      20.745   8.482   4.472  1.00 25.00           C
ATOM     26  CA  LEU    26      20.433  10.779   7.521  1.00 25.00           C
ATOM     27  CA  CYS    27      22.744   8.474   9.525  1.00 25.00           C
ATOM     28  CA  ASP    28      25.296   8.510   6.669  1.00 25.00           C
ATOM     29  CA  ALA    29      25.142  12.335   6.547  1.00 25.00           C
ATOM     30  CA  LEU    30      25.686  12.503  10.334  1.00 25.00           C
ATOM     31  CA  ALA    31      28.694  10.152  10.030  1.00 25.00           C
ATOM     32  CA  VAL    32      30.147  12.333   7.238  1.00 25.00           C
ATOM     33  CA  GLU    33      29.678  15.458   9.401  1.00 25.00           C
ATOM     34  CA  HIS    34      31.430  13.724  12.332  1.00 25.00           C
ATOM     35  CA  ALA    35      34.334  12.734  10.041  1.00 25.00           C
ATOM     36  CA  THR    36      34.616  16.344   8.795  1.00 25.00           C
ATOM     37  CA  ILE    37      34.656  17.613  12.409  1.00 25.00           C
ATOM     38  CA  TYR    38      37.403  15.094  13.289  1.00 25.00           C
ATOM     39  CA  GLY    39      39.390  16.629  16.160  1.00 25.00           C
ATOM     40  CA  TYR    40      38.403  16.924  19.862  1.00 25.00           C
ATOM     41  CA  GLY    41      37.533  17.817  23.456  1.00 25.00           C
ATOM     42  CA  ILE    42      34.574  15.413  23.466  1.00 25.00           C
ATOM     43  CA  VAL    43      31.944  18.026  24.182  1.00 25.00           C
ATOM     44  CA  SER    44      29.857  21.142  24.474  1.00 25.00           C
ATOM     45  CA  ALA    45      32.027  24.237  24.186  1.00 25.00           C
ATOM     46  CA  LEU    46      32.260  27.981  23.806  1.00 25.00           C
ATOM     47  CA  SER    47      29.351  30.410  23.158  1.00 25.00           C
ATOM     48  CA  PRO    48      31.622  31.525  20.271  1.00 25.00           C
ATOM     49  CA  PRO    49      34.524  33.838  21.108  1.00 25.00           C
ATOM     50  CA  GLY    50      35.786  34.283  17.518  1.00 25.00           C
ATOM     51  CA  VAL    51      36.588  32.241  14.379  1.00 25.00           C
ATOM     52  CA  ASN    52      39.009  30.058  16.388  1.00 25.00           C
ATOM     53  CA  PHE    53      36.327  29.503  19.065  1.00 25.00           C
ATOM     54  CA  LEU    54      33.797  28.523  16.361  1.00 25.00           C
ATOM     55  CA  VAL    55      36.319  26.062  14.860  1.00 25.00           C
ATOM     56  CA  ALA    56      36.932  24.541  18.320  1.00 25.00           C
ATOM     57  CA  ASP    57      33.159  24.174  18.856  1.00 25.00           C
ATOM     58  CA  ALA    58      32.815  22.468  15.445  1.00 25.00           C
ATOM     59  CA  LEU    59      35.669  20.071  16.329  1.00 25.00           C
ATOM     60  CA  LYS    60      33.982  19.254  19.669  1.00 25.00           C
ATOM     61  CA  GLN    61      30.674  18.578  17.860  1.00 25.00           C
ATOM     62  CA  HIS    62      32.470  16.274  15.384  1.00 25.00           C
ATOM     63  CA  ARG    63      34.115  14.395  18.288  1.00 25.00           C
ATOM     64  CA  HIS    64      30.707  13.996  19.991  1.00 25.00           C
ATOM     65  CA  ARG    65      29.208  12.658  16.732  1.00 25.00           C
ATOM     66  CA  ARG    66      32.095  10.166  16.396  1.00 25.00           C
ATOM     67  CA  ASP    67      31.553   9.014  20.008  1.00 25.00           C
ATOM     68  CA  ASP    68      27.814   8.551  19.324  1.00 25.00           C
ATOM     69  CA  VAL    69      28.615   6.508  16.186  1.00 25.00           C
ATOM     70  CA  ILE    70      31.037   4.325  18.195  1.00 25.00           C
ATOM     71  CA  VAL    71      28.355   3.770  20.871  1.00 25.00           C
ATOM     72  CA  MET    72      25.824   2.790  18.168  1.00 25.00           C
ATOM     73  CA  LEU    73      28.346   0.330  16.666  1.00 25.00           C
ATOM     74  CA  SER    74      28.960  -1.192  20.127  1.00 25.00           C
ATOM     75  CA  ALA    75      25.186  -1.559  20.662  1.00 25.00           C
ATOM     76  CA  ARG    76      23.249  -1.530  17.382  1.00 25.00           C
ATOM     77  CA  GLY    77      20.051  -0.757  19.233  1.00 25.00           C
ATOM     78  CA  VAL    78      21.674   2.175  21.136  1.00 25.00           C
ATOM     79  CA  THR    79      18.568   2.182  23.322  1.00 25.00           C
ATOM     80  CA  ALA    80      19.378   5.704  24.519  1.00 25.00           C
ATOM     81  CA  PRO    81      23.207   5.728  24.568  1.00 25.00           C
ATOM     82  CA  ILE    82      23.257   7.966  21.460  1.00 25.00           C
ATOM     83  CA  ALA    83      20.762  10.357  23.112  1.00 25.00           C
ATOM     84  CA  ALA    84      22.931  10.479  26.266  1.00 25.00           C
ATOM     85  CA  ALA    85      25.553  12.876  27.763  1.00 25.00           C
ATOM     86  CA  GLY    86      28.161  10.536  29.259  1.00 25.00           C
ATOM     87  CA  TYR    87      26.731   7.288  27.939  1.00 25.00           C
ATOM     88  CA  GLN    88      29.442   4.892  29.070  1.00 25.00           C
ATOM     89  CA  LEU    89      31.567   6.898  26.652  1.00 25.00           C
ATOM     90  CA  PRO    90      30.667  10.136  24.919  1.00 25.00           C
ATOM     91  CA  MET    91      27.612  11.680  23.237  1.00 25.00           C
ATOM     92  CA  GLN    92      24.724  12.856  21.107  1.00 25.00           C
ATOM     93  CA  VAL    93      24.508  13.967  17.424  1.00 25.00           C
ATOM     94  CA  SER    94      24.951  15.466  13.970  1.00 25.00           C
ATOM     95  CA  SER    95      22.132  15.885  11.394  1.00 25.00           C
ATOM     96  CA  ALA    96      18.422  15.940  10.390  1.00 25.00           C
ATOM     97  CA  ALA    97      15.597  16.930  12.779  1.00 25.00           C
ATOM     98  CA  ASP    98      16.274  13.819  14.908  1.00 25.00           C
ATOM     99  CA  ALA    99      20.004  14.678  15.021  1.00 25.00           C
ATOM    100  CA  ALA   100      19.172  18.259  16.094  1.00 25.00           C
ATOM    101  CA  ARG   101      16.872  16.925  18.850  1.00 25.00           C
ATOM    102  CA  LEU   102      19.643  14.577  20.061  1.00 25.00           C
ATOM    103  CA  ALA   103      22.122  17.495  20.126  1.00 25.00           C
ATOM    104  CA  VAL   104      19.630  19.599  22.133  1.00 25.00           C
ATOM    105  CA  ARG   105      19.157  16.718  24.612  1.00 25.00           C
ATOM    106  CA  MET   106      22.954  16.383  24.984  1.00 25.00           C
ATOM    107  CA  GLU   107      23.248  20.149  25.617  1.00 25.00           C
ATOM    108  CA  ASN   108      20.491  19.946  28.266  1.00 25.00           C
ATOM    109  CA  ASP   109      22.295  17.019  29.955  1.00 25.00           C
ATOM    110  CA  GLY   110      25.567  19.008  29.960  1.00 25.00           C
ATOM    111  CA  ALA   111      23.767  22.013  31.511  1.00 25.00           C
ATOM    112  CA  THR   112      22.260  19.749  34.208  1.00 25.00           C
ATOM    113  CA  ALA   113      25.724  18.300  34.962  1.00 25.00           C
ATOM    114  CA  TRP   114      27.168  21.836  35.244  1.00 25.00           C
ATOM    115  CA  ARG   115      24.344  22.825  37.633  1.00 25.00           C
ATOM    116  CA  ALA   116      25.020  19.715  39.762  1.00 25.00           C
ATOM    117  CA  VAL   117      28.752  20.574  39.875  1.00 25.00           C
ATOM    118  CA  VAL   118      27.919  24.155  40.948  1.00 25.00           C
ATOM    119  CA  GLU   119      25.618  22.821  43.703  1.00 25.00           C
ATOM    120  CA  HIS   120      28.390  20.472  44.915  1.00 25.00           C
ATOM    121  CA  ALA   121      30.869  23.391  44.979  1.00 25.00           C
ATOM    122  CA  GLU   122      32.611  23.618  41.642  1.00 25.00           C
ATOM    123  CA  THR   123      31.742  24.903  38.138  1.00 25.00           C
ATOM    124  CA  ALA   124      30.016  25.997  34.970  1.00 25.00           C
ATOM    125  CA  ASP   125      26.934  25.448  32.839  1.00 25.00           C
ATOM    126  CA  ASP   126      25.530  28.410  30.857  1.00 25.00           C
ATOM    127  CA  ARG   127      28.563  28.315  28.521  1.00 25.00           C
ATOM    128  CA  VAL   128      28.074  24.554  27.997  1.00 25.00           C
ATOM    129  CA  PHE   129      24.371  25.121  27.200  1.00 25.00           C
ATOM    130  CA  ALA   130      25.307  27.852  24.683  1.00 25.00           C
ATOM    131  CA  SER   131      27.845  25.503  23.039  1.00 25.00           C
ATOM    132  CA  THR   132      25.189  22.754  22.809  1.00 25.00           C
ATOM    133  CA  ALA   133      22.733  25.225  21.217  1.00 25.00           C
ATOM    134  CA  LEU   134      25.402  26.282  18.683  1.00 25.00           C
ATOM    135  CA  THR   135      26.091  22.611  17.839  1.00 25.00           C
ATOM    136  CA  GLU   136      22.343  21.995  17.350  1.00 25.00           C
ATOM    137  CA  SER   137      22.117  25.047  15.048  1.00 25.00           C
ATOM    138  CA  ALA   138      25.103  23.770  13.020  1.00 25.00           C
ATOM    139  CA  VAL   139      23.453  20.327  12.710  1.00 25.00           C
ATOM    140  CA  MET   140      20.199  21.967  11.530  1.00 25.00           C
ATOM    141  CA  ALA   141      22.140  24.006   8.933  1.00 25.00           C
ATOM    142  CA  THR   142      23.881  20.825   7.700  1.00 25.00           C
ATOM    143  CA  ARG   143      20.495  19.057   7.408  1.00 25.00           C
ATOM    144  CA  TRP   144      19.092  22.019   5.426  1.00 25.00           C
ATOM    145  CA  ASN   145      22.125  21.925   3.090  1.00 25.00           C
ATOM    146  CA  ARG   146      21.072  25.171   1.372  1.00 25.00           C
ATOM    147  CA  VAL   147      19.202  24.176  -1.826  1.00 25.00           C
ATOM    148  CA  LEU   148      22.472  22.373  -2.674  1.00 25.00           C
ATOM    149  CA  GLY   149      21.536  21.655  -6.294  1.00 25.00           C
ATOM    150  CA  ALA   150      18.322  20.757  -8.153  1.00 25.00           C
ATOM    151  CA  TRP   151      18.322  17.313  -9.897  1.00 25.00           C
TER
END
