
#######################################################
#                                                     #
#                        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  123 (  123),  selected  123 , name T0307TS393_3-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307TS393_3-D1.T0307_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I      10      I      10           -
LGA    M      11      M      11           -
LGA    T      12      T      12           -
LGA    -       -      F      13           -
LGA    -       -      S      14           -
LGA    -       -      G      15           -
LGA    -       -      Q      16           -
LGA    -       -      E      17           -
LGA    -       -      L      18           -
LGA    -       -      T      19           -
LGA    -       -      A      20           -
LGA    -       -      I      21           -
LGA    -       -      I      22           -
LGA    F      13      K      23           #
LGA    S      14      M      24           -
LGA    -       -      A      25           -
LGA    G      15      K      26          4.489
LGA    Q      16      S      27          4.807
LGA    E      17      M      28          3.409
LGA    L      18      V      29          2.570
LGA    T      19      M      30          2.545
LGA    A      20      A      31          3.806
LGA    -       -      D      32           -
LGA    I      21      G      33           #
LGA    I      22      K      34          3.051
LGA    K      23      I      35          4.472
LGA    M      24      -       -           -
LGA    A      25      -       -           -
LGA    K      26      -       -           -
LGA    S      27      -       -           -
LGA    M      28      -       -           -
LGA    V      29      -       -           -
LGA    M      30      -       -           -
LGA    A      31      -       -           -
LGA    D      32      -       -           -
LGA    G      33      -       -           -
LGA    K      34      -       -           -
LGA    I      35      -       -           -
LGA    K      36      -       -           -
LGA    P      37      -       -           -
LGA    A      38      -       -           -
LGA    E      39      -       -           -
LGA    I      40      -       -           -
LGA    A      41      -       -           -
LGA    V      42      -       -           -
LGA    M      43      -       -           -
LGA    T      44      -       -           -
LGA    R      45      -       -           -
LGA    E      46      -       -           -
LGA    F      47      -       -           -
LGA    M      48      -       -           -
LGA    R      49      -       -           -
LGA    F      50      -       -           -
LGA    G      51      -       -           -
LGA    I      52      -       -           -
LGA    L      53      -       -           -
LGA    Q      54      -       -           -
LGA    D      55      -       -           -
LGA    Q      56      -       -           -
LGA    V      57      -       -           -
LGA    D      58      -       -           -
LGA    L      59      -       -           -
LGA    L      60      K      36          4.030
LGA    L      61      P      37          3.845
LGA    K      62      A      38          3.523
LGA    A      63      E      39          2.883
LGA    S      64      I      40          2.427
LGA    D      65      A      41          2.283
LGA    S      66      V      42          1.403
LGA    I      67      M      43          0.839
LGA    E      68      T      44          1.109
LGA    A      69      R      45          1.348
LGA    S      70      E      46          1.330
LGA    Q      71      F      47          0.883
LGA    A      72      M      48          0.593
LGA    V      73      R      49          0.590
LGA    A      74      F      50          2.097
LGA    L      75      G      51          2.528
LGA    I      76      -       -           -
LGA    A      77      -       -           -
LGA    R      78      -       -           -
LGA    M      79      I      52           #
LGA    D      80      L      53           -
LGA    E      81      Q      54           -
LGA    E      82      D      55           -
LGA    R      83      Q      56           -
LGA    K      84      V      57           -
LGA    K      85      D      58           -
LGA    Y      86      L      59           -
LGA    V      87      L      60           -
LGA    A      88      L      61           -
LGA    S      89      K      62           -
LGA    Y      90      A      63           -
LGA    L      91      S      64           -
LGA    G      92      D      65           -
LGA    V      93      S      66           -
LGA    I      94      I      67           -
LGA    M      95      E      68           -
LGA    A      96      A      69           -
LGA    S      97      S      70           -
LGA    D      98      Q      71           -
LGA    G      99      A      72           -
LGA    D     100      V      73           -
LGA    I     101      A      74           -
LGA    D     102      L      75           -
LGA    D     103      I      76           -
LGA    -       -      A      77           -
LGA    -       -      R      78           -
LGA    -       -      M      79           -
LGA    -       -      D      80           -
LGA    -       -      E      81           -
LGA    N     104      E      82          4.085
LGA    E     105      R      83          1.192
LGA    L     106      K      84          3.322
LGA    A     107      K      85          3.174
LGA    L     108      Y      86          1.309
LGA    W     109      V      87          3.981
LGA    T     110      A      88          4.620
LGA    L     111      S      89          1.371
LGA    I     112      Y      90          4.179
LGA    S     113      L      91           #
LGA    T     114      G      92          4.806
LGA    L     115      V      93          3.194
LGA    C     116      I      94           -
LGA    -       -      M      95           -
LGA    -       -      A      96           -
LGA    G     117      S      97           #
LGA    -       -      D      98           -
LGA    -       -      G      99           -
LGA    -       -      D     100           -
LGA    -       -      I     101           -
LGA    L     118      D     102          2.071
LGA    P     119      D     103          4.075
LGA    T     120      N     104          5.330
LGA    M     121      E     105           #
LGA    T     122      L     106          4.589
LGA    V     123      A     107          4.166
LGA    M     124      L     108          3.699
LGA    E     125      W     109          2.522
LGA    A     126      T     110          1.237
LGA    I     127      L     111          2.069
LGA    N     128      I     112          0.575
LGA    N     129      S     113          1.527
LGA    M     130      T     114          2.778
LGA    K     131      L     115          2.858
LGA    N     132      C     116          3.211
LGA    -       -      G     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      T     120           -
LGA    -       -      M     121           -
LGA    -       -      T     122           -
LGA    -       -      V     123           -
LGA    -       -      M     124           -
LGA    -       -      E     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      N     128           -
LGA    -       -      N     129           -
LGA    -       -      M     130           -
LGA    -       -      K     131           -
LGA    -       -      N     132           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  123  123    5.0     49    3.09     2.04     24.236     1.537

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.833856 * X  +   0.426542 * Y  +  -0.350352 * Z  +  21.519232
  Y_new =  -0.456163 * X  +  -0.889893 * Y  +   0.002276 * Z  +  10.193643
  Z_new =  -0.310805 * X  +   0.161716 * Y  +   0.936615 * Z  +  21.200775 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.170974   -2.970619  [ DEG:     9.7961   -170.2039 ]
  Theta =   0.316040    2.825553  [ DEG:    18.1078    161.8922 ]
  Phi   =  -2.641015    0.500578  [ DEG:  -151.3190     28.6810 ]
 
# 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: T0307TS393_3-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307TS393_3-D1.T0307_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  123  123   5.0   49   3.09    2.04  24.236
REMARK  ---------------------------------------------------------- 
MOLECULE T0307TS393_3-D1
PFRMAT TS
TARGET T0307
MODEL 3
PARENT N/A
ATOM     10  CA  ILE    10      35.562  -4.416  25.508  1.00 25.00           C
ATOM     11  CA  MET    11      33.768  -1.899  27.676  1.00 25.00           C
ATOM     12  CA  THR    12      34.299   1.733  28.801  1.00 25.00           C
ATOM     13  CA  PHE    13      31.405   4.249  28.369  1.00 25.00           C
ATOM     14  CA  SER    14      33.786   6.849  26.841  1.00 25.00           C
ATOM     15  CA  GLY    15      30.664   7.726  24.798  1.00 25.00           C
ATOM     16  CA  GLN    16      31.298   4.642  22.618  1.00 25.00           C
ATOM     17  CA  GLU    17      27.576   4.473  21.731  1.00 25.00           C
ATOM     18  CA  LEU    18      27.605   8.189  20.801  1.00 25.00           C
ATOM     19  CA  THR    19      30.688   7.639  18.596  1.00 25.00           C
ATOM     20  CA  ALA    20      28.959   4.687  16.874  1.00 25.00           C
ATOM     21  CA  ILE    21      25.848   6.834  16.261  1.00 25.00           C
ATOM     22  CA  ILE    22      28.028   9.612  14.778  1.00 25.00           C
ATOM     23  CA  LYS    23      29.753   7.072  12.489  1.00 25.00           C
ATOM     24  CA  MET    24      26.344   5.748  11.350  1.00 25.00           C
ATOM     25  CA  ALA    25      25.174   9.320  10.618  1.00 25.00           C
ATOM     26  CA  LYS    26      28.360   9.976   8.595  1.00 25.00           C
ATOM     27  CA  SER    27      27.794   6.748   6.614  1.00 25.00           C
ATOM     28  CA  MET    28      24.176   7.786   5.908  1.00 25.00           C
ATOM     29  CA  VAL    29      25.369  11.226   4.718  1.00 25.00           C
ATOM     30  CA  MET    30      27.944   9.565   2.420  1.00 25.00           C
ATOM     31  CA  ALA    31      27.688  10.252  -1.291  1.00 25.00           C
ATOM     32  CA  ASP    32      29.233  11.238  -4.631  1.00 25.00           C
ATOM     33  CA  GLY    33      30.815  12.484  -7.887  1.00 25.00           C
ATOM     34  CA  LYS    34      32.567  13.709 -11.027  1.00 25.00           C
ATOM     35  CA  ILE    35      34.452  14.653 -14.238  1.00 25.00           C
ATOM     36  CA  LYS    36      37.294  16.112 -16.328  1.00 25.00           C
ATOM     37  CA  PRO    37      40.793  17.360 -17.131  1.00 25.00           C
ATOM     38  CA  ALA    38      41.975  14.714 -14.626  1.00 25.00           C
ATOM     39  CA  GLU    39      43.115  17.466 -12.219  1.00 25.00           C
ATOM     40  CA  ILE    40      39.714  19.196 -12.547  1.00 25.00           C
ATOM     41  CA  ALA    41      37.932  15.884 -11.828  1.00 25.00           C
ATOM     42  CA  VAL    42      40.128  15.345  -8.738  1.00 25.00           C
ATOM     43  CA  MET    43      39.324  18.885  -7.518  1.00 25.00           C
ATOM     44  CA  THR    44      35.583  18.234  -8.021  1.00 25.00           C
ATOM     45  CA  ARG    45      35.863  14.960  -6.054  1.00 25.00           C
ATOM     46  CA  GLU    46      37.684  16.788  -3.223  1.00 25.00           C
ATOM     47  CA  PHE    47      34.948  19.468  -3.162  1.00 25.00           C
ATOM     48  CA  MET    48      32.255  16.750  -3.002  1.00 25.00           C
ATOM     49  CA  ARG    49      34.102  15.054  -0.107  1.00 25.00           C
ATOM     50  CA  PHE    50      34.330  18.402   1.740  1.00 25.00           C
ATOM     51  CA  GLY    51      30.580  18.974   1.215  1.00 25.00           C
ATOM     52  CA  ILE    52      29.831  15.469   2.562  1.00 25.00           C
ATOM     53  CA  LEU    53      32.017  16.153   5.630  1.00 25.00           C
ATOM     54  CA  GLN    54      30.184  19.462   6.229  1.00 25.00           C
ATOM     55  CA  ASP    55      26.810  17.668   5.965  1.00 25.00           C
ATOM     56  CA  GLN    56      27.993  15.023   8.470  1.00 25.00           C
ATOM     57  CA  VAL    57      29.133  17.775  10.876  1.00 25.00           C
ATOM     58  CA  ASP    58      25.730  19.505  10.548  1.00 25.00           C
ATOM     59  CA  LEU    59      23.949  16.192  11.267  1.00 25.00           C
ATOM     60  CA  LEU    60      26.145  15.653  14.357  1.00 25.00           C
ATOM     61  CA  LEU    61      25.341  19.193  15.577  1.00 25.00           C
ATOM     62  CA  LYS    62      21.600  18.543  15.074  1.00 25.00           C
ATOM     63  CA  ALA    63      21.881  15.269  17.041  1.00 25.00           C
ATOM     64  CA  SER    64      23.700  17.097  19.872  1.00 25.00           C
ATOM     65  CA  ASP    65      20.965  19.776  19.933  1.00 25.00           C
ATOM     66  CA  SER    66      18.272  17.058  20.093  1.00 25.00           C
ATOM     67  CA  ILE    67      20.119  15.363  22.988  1.00 25.00           C
ATOM     68  CA  GLU    68      20.347  18.710  24.835  1.00 25.00           C
ATOM     69  CA  ALA    69      16.598  19.284  24.310  1.00 25.00           C
ATOM     70  CA  SER    70      15.848  15.777  25.657  1.00 25.00           C
ATOM     71  CA  GLN    71      18.035  16.463  28.726  1.00 25.00           C
ATOM     72  CA  ALA    72      16.201  19.770  29.325  1.00 25.00           C
ATOM     73  CA  VAL    73      12.828  17.977  29.060  1.00 25.00           C
ATOM     74  CA  ALA    74      14.009  15.332  31.565  1.00 25.00           C
ATOM     75  CA  LEU    75      15.149  18.085  33.971  1.00 25.00           C
ATOM     76  CA  ILE    76      11.748  19.814  33.642  1.00 25.00           C
ATOM     77  CA  ALA    77       9.966  16.501  34.362  1.00 25.00           C
ATOM     78  CA  ARG    78      12.163  15.962  37.453  1.00 25.00           C
ATOM     79  CA  MET    79      11.359  19.503  38.671  1.00 25.00           C
ATOM     80  CA  ASP    80       7.618  18.853  38.169  1.00 25.00           C
ATOM     81  CA  GLU    81       7.898  15.578  40.136  1.00 25.00           C
ATOM     82  CA  GLU    82       9.717  17.406  42.967  1.00 25.00           C
ATOM     83  CA  ARG    83       6.982  20.085  43.029  1.00 25.00           C
ATOM     84  CA  LYS    84       4.289  17.367  43.188  1.00 25.00           C
ATOM     85  CA  LYS    85       6.137  15.672  46.083  1.00 25.00           C
ATOM     86  CA  TYR    86       6.365  19.020  47.929  1.00 25.00           C
ATOM     87  CA  VAL    87       2.614  19.592  47.405  1.00 25.00           C
ATOM     88  CA  ALA    88       1.866  16.086  48.752  1.00 25.00           C
ATOM     89  CA  SER    89       4.052  16.771  51.821  1.00 25.00           C
ATOM     90  CA  TYR    90       2.218  20.080  52.420  1.00 25.00           C
ATOM     91  CA  LEU    91      -1.155  18.286  52.155  1.00 25.00           C
ATOM     92  CA  GLY    92       0.027  15.641  54.659  1.00 25.00           C
ATOM     93  CA  VAL    93       1.166  18.393  57.067  1.00 25.00           C
ATOM     94  CA  ILE    94      -2.235  20.123  56.737  1.00 25.00           C
ATOM     95  CA  MET    95      -4.017  16.809  57.457  1.00 25.00           C
ATOM     96  CA  ALA    96      -1.820  16.272  60.548  1.00 25.00           C
ATOM     97  CA  SER    97      -0.522  13.498  58.371  1.00 25.00           C
ATOM     98  CA  ASP    98       0.796  11.653  55.362  1.00 25.00           C
ATOM     99  CA  GLY    99       2.211  10.625  51.983  1.00 25.00           C
ATOM    100  CA  ASP   100       3.796   9.631  48.670  1.00 25.00           C
ATOM    101  CA  ILE   101       5.007   8.629  45.258  1.00 25.00           C
ATOM    102  CA  ASP   102       6.528   8.147  41.758  1.00 25.00           C
ATOM    103  CA  ASP   103       7.871   7.744  38.195  1.00 25.00           C
ATOM    104  CA  ASN   104       9.963  10.297  36.254  1.00 25.00           C
ATOM    105  CA  GLU   105      12.729   7.694  35.760  1.00 25.00           C
ATOM    106  CA  LEU   106      10.150   5.159  34.498  1.00 25.00           C
ATOM    107  CA  ALA   107       8.755   7.758  32.055  1.00 25.00           C
ATOM    108  CA  LEU   108      12.292   8.505  30.791  1.00 25.00           C
ATOM    109  CA  TRP   109      12.933   4.761  30.298  1.00 25.00           C
ATOM    110  CA  THR   110       9.648   4.430  28.358  1.00 25.00           C
ATOM    111  CA  LEU   111      10.621   7.403  26.151  1.00 25.00           C
ATOM    112  CA  ILE   112      14.043   5.817  25.482  1.00 25.00           C
ATOM    113  CA  SER   113      12.354   2.509  24.547  1.00 25.00           C
ATOM    114  CA  THR   114       9.993   4.359  22.166  1.00 25.00           C
ATOM    115  CA  LEU   115      12.976   6.139  20.553  1.00 25.00           C
ATOM    116  CA  CYS   116      13.291   4.619  17.032  1.00 25.00           C
ATOM    117  CA  GLY   117      11.277   3.209  14.167  1.00 25.00           C
ATOM    118  CA  LEU   118      14.174   0.665  14.020  1.00 25.00           C
ATOM    119  CA  PRO   119      12.692  -2.820  14.627  1.00 25.00           C
ATOM    120  CA  THR   120      15.851  -4.635  15.506  1.00 25.00           C
ATOM    121  CA  MET   121      15.808  -2.817  18.895  1.00 25.00           C
ATOM    122  CA  THR   122      19.305  -4.258  19.290  1.00 25.00           C
ATOM    123  CA  VAL   123      20.675  -6.195  22.297  1.00 25.00           C
ATOM    124  CA  MET   124      23.029  -3.290  23.126  1.00 25.00           C
ATOM    125  CA  GLU   125      20.104  -0.827  22.913  1.00 25.00           C
ATOM    126  CA  ALA   126      18.030  -3.051  25.239  1.00 25.00           C
ATOM    127  CA  ILE   127      20.939  -3.205  27.726  1.00 25.00           C
ATOM    128  CA  ASN   128      21.266   0.609  27.617  1.00 25.00           C
ATOM    129  CA  ASN   129      17.507   0.974  28.250  1.00 25.00           C
ATOM    130  CA  MET   130      17.749  -1.430  31.220  1.00 25.00           C
ATOM    131  CA  LYS   131      21.051  -0.100  32.563  1.00 25.00           C
ATOM    132  CA  ASN   132      21.570   3.167  34.322  1.00 25.00           C
TER
END
