
#######################################################
#                                                     #
#                        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  133 (  133),  selected  133 , name T0307TS393_1
# Molecule2: number of CA atoms  132 ( 1005),  selected  132 , name T0307.pdb
# PARAMETERS: T0307TS393_1.T0307.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    G       2      G       2           -
LGA    L       3      L       3           -
LGA    G       4      G       4           -
LGA    R       5      R       5           -
LGA    Q       6      -       -           -
LGA    S       7      Q       6           #
LGA    -       -      S       7           -
LGA    L       8      L       8          1.730
LGA    N       9      N       9          4.098
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      F      13          4.745
LGA    L      18      S      14           #
LGA    T      19      G      15           #
LGA    A      20      Q      16           #
LGA    I      21      E      17          3.957
LGA    -       -      L      18           -
LGA    I      22      T      19           #
LGA    K      23      -       -           -
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      -       -           -
LGA    L      61      -       -           -
LGA    K      62      -       -           -
LGA    A      63      -       -           -
LGA    S      64      A      20          4.397
LGA    D      65      I      21          4.031
LGA    S      66      I      22          3.785
LGA    I      67      K      23          2.421
LGA    E      68      M      24          1.102
LGA    A      69      A      25          2.144
LGA    S      70      K      26          0.556
LGA    Q      71      S      27          1.850
LGA    A      72      M      28          3.200
LGA    V      73      V      29          3.226
LGA    A      74      M      30          3.593
LGA    L      75      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           -
LGA    -       -      L      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      S      64           -
LGA    -       -      D      65           -
LGA    -       -      S      66           -
LGA    -       -      I      67           -
LGA    -       -      E      68           -
LGA    -       -      A      69           -
LGA    -       -      S      70           -
LGA    -       -      Q      71           -
LGA    -       -      A      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      I      76           -
LGA    -       -      A      77           -
LGA    -       -      R      78           -
LGA    -       -      M      79           -
LGA    -       -      D      80           -
LGA    -       -      E      81           -
LGA    -       -      E      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    -       -      K      85           -
LGA    -       -      Y      86           -
LGA    -       -      V      87           -
LGA    -       -      A      88           -
LGA    -       -      S      89           -
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    -       -      G      92           -
LGA    -       -      V      93           -
LGA    I      76      I      94          4.897
LGA    A      77      M      95          5.382
LGA    R      78      A      96           -
LGA    M      79      -       -           -
LGA    D      80      S      97           #
LGA    E      81      D      98           -
LGA    -       -      G      99           -
LGA    -       -      D     100           -
LGA    E      82      I     101           #
LGA    R      83      D     102          5.196
LGA    K      84      -       -           -
LGA    K      85      -       -           -
LGA    Y      86      -       -           -
LGA    V      87      -       -           -
LGA    A      88      -       -           -
LGA    S      89      -       -           -
LGA    Y      90      -       -           -
LGA    L      91      -       -           -
LGA    G      92      -       -           -
LGA    V      93      -       -           -
LGA    I      94      -       -           -
LGA    M      95      -       -           -
LGA    A      96      -       -           -
LGA    S      97      -       -           -
LGA    D      98      -       -           -
LGA    G      99      -       -           -
LGA    D     100      -       -           -
LGA    I     101      -       -           -
LGA    D     102      D     103          3.782
LGA    D     103      N     104          2.058
LGA    N     104      E     105          2.700
LGA    E     105      L     106          2.261
LGA    L     106      A     107          1.264
LGA    A     107      L     108          1.587
LGA    L     108      W     109          1.685
LGA    W     109      T     110          0.914
LGA    T     110      L     111          0.776
LGA    L     111      I     112          1.549
LGA    I     112      S     113          0.473
LGA    S     113      T     114          1.784
LGA    T     114      L     115          2.632
LGA    L     115      C     116          1.464
LGA    C     116      G     117          4.312
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      L     118           #
LGA    A     126      P     119          3.506
LGA    I     127      -       -           -
LGA    N     128      -       -           -
LGA    N     129      T     120           #
LGA    M     130      M     121          4.058
LGA    -       -      T     122           -
LGA    -       -      V     123           -
LGA    -       -      M     124           -
LGA    -       -      E     125           -
LGA    K     131      A     126           #
LGA    N     132      I     127          3.983
LGA    L     133      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)  133  132    5.0     36    3.14    19.44     18.434     1.112

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.699612 * X  +   0.708753 * Y  +   0.090627 * Z  +  20.726439
  Y_new =   0.668857 * X  +  -0.604993 * Y  +  -0.431989 * Z  +   8.849177
  Z_new =  -0.251345 * X  +   0.362841 * Y  +  -0.897314 * Z  +  33.987385 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.757331   -0.384262  [ DEG:   157.9834    -22.0166 ]
  Theta =   0.254069    2.887523  [ DEG:    14.5571    165.4429 ]
  Phi   =   0.762928   -2.378665  [ DEG:    43.7126   -136.2874 ]
 
# 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_1                                  
REMARK     2: T0307.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307TS393_1.T0307.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  133  132   5.0   36   3.14   19.44  18.434
REMARK  ---------------------------------------------------------- 
MOLECULE T0307TS393_1
PFRMAT TS
TARGET T0307
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      12.455  16.036  62.057  1.00 25.00           C
ATOM      2  CA  GLY     2      11.955  19.766  61.911  1.00 25.00           C
ATOM      3  CA  LEU     3       9.163  20.619  59.462  1.00 25.00           C
ATOM      4  CA  GLY     4       7.526  21.453  56.104  1.00 25.00           C
ATOM      5  CA  ARG     5       4.440  20.729  54.010  1.00 25.00           C
ATOM      6  CA  GLN     6       2.113  19.903  51.068  1.00 25.00           C
ATOM      7  CA  SER     7      -0.114  18.854  48.149  1.00 25.00           C
ATOM      8  CA  LEU     8       0.256  17.510  44.613  1.00 25.00           C
ATOM      9  CA  ASN     9       0.585  17.248  40.880  1.00 25.00           C
ATOM     10  CA  ILE    10       1.783  16.474  37.394  1.00 25.00           C
ATOM     11  CA  MET    11       3.658  16.155  34.098  1.00 25.00           C
ATOM     12  CA  THR    12       6.555  18.279  32.841  1.00 25.00           C
ATOM     13  CA  PHE    13       9.887  18.760  31.176  1.00 25.00           C
ATOM     14  CA  SER    14      12.538  21.450  31.903  1.00 25.00           C
ATOM     15  CA  GLY    15      14.762  18.420  32.642  1.00 25.00           C
ATOM     16  CA  GLN    16      12.519  17.544  35.619  1.00 25.00           C
ATOM     17  CA  GLU    17      14.073  14.048  35.791  1.00 25.00           C
ATOM     18  CA  LEU    18      17.584  15.578  35.724  1.00 25.00           C
ATOM     19  CA  THR    19      16.616  17.981  38.545  1.00 25.00           C
ATOM     20  CA  ALA    20      15.249  15.055  40.603  1.00 25.00           C
ATOM     21  CA  ILE    21      18.497  13.106  40.036  1.00 25.00           C
ATOM     22  CA  ILE    22      20.544  16.148  41.145  1.00 25.00           C
ATOM     23  CA  LYS    23      18.391  16.479  44.295  1.00 25.00           C
ATOM     24  CA  MET    24      18.899  12.760  45.062  1.00 25.00           C
ATOM     25  CA  ALA    25      22.682  13.160  44.616  1.00 25.00           C
ATOM     26  CA  LYS    26      22.666  16.178  46.974  1.00 25.00           C
ATOM     27  CA  SER    27      20.696  14.169  49.571  1.00 25.00           C
ATOM     28  CA  MET    28      23.202  11.288  49.281  1.00 25.00           C
ATOM     29  CA  VAL    29      26.108  13.736  49.753  1.00 25.00           C
ATOM     30  CA  MET    30      24.399  15.206  52.849  1.00 25.00           C
ATOM     31  CA  ALA    31      25.884  18.060  54.959  1.00 25.00           C
ATOM     32  CA  ASP    32      28.004  19.423  57.770  1.00 25.00           C
ATOM     33  CA  GLY    33      30.169  20.810  60.649  1.00 25.00           C
ATOM     34  CA  LYS    34      32.305  21.938  63.628  1.00 25.00           C
ATOM     35  CA  ILE    35      34.769  22.509  66.394  1.00 25.00           C
ATOM     36  CA  LYS    36      37.216  22.795  69.347  1.00 25.00           C
ATOM     37  CA  PRO    37      39.199  20.962  72.025  1.00 25.00           C
ATOM     38  CA  ALA    38      41.492  18.453  70.259  1.00 25.00           C
ATOM     39  CA  GLU    39      38.647  15.892  70.149  1.00 25.00           C
ATOM     40  CA  ILE    40      36.295  18.533  68.677  1.00 25.00           C
ATOM     41  CA  ALA    41      38.910  19.419  66.024  1.00 25.00           C
ATOM     42  CA  VAL    42      39.307  15.713  65.141  1.00 25.00           C
ATOM     43  CA  MET    43      35.507  15.357  64.826  1.00 25.00           C
ATOM     44  CA  THR    44      35.383  18.429  62.543  1.00 25.00           C
ATOM     45  CA  ARG    45      38.180  16.961  60.375  1.00 25.00           C
ATOM     46  CA  GLU    46      36.285  13.641  60.136  1.00 25.00           C
ATOM     47  CA  PHE    47      33.100  15.505  59.111  1.00 25.00           C
ATOM     48  CA  MET    48      35.053  17.420  56.431  1.00 25.00           C
ATOM     49  CA  ARG    49      36.513  14.135  55.112  1.00 25.00           C
ATOM     50  CA  PHE    50      33.005  12.603  54.975  1.00 25.00           C
ATOM     51  CA  GLY    51      31.717  15.663  53.066  1.00 25.00           C
ATOM     52  CA  ILE    52      34.626  15.374  50.591  1.00 25.00           C
ATOM     53  CA  LEU    53      33.857  11.658  50.084  1.00 25.00           C
ATOM     54  CA  GLN    54      30.169  12.479  49.460  1.00 25.00           C
ATOM     55  CA  ASP    55      31.172  15.154  46.908  1.00 25.00           C
ATOM     56  CA  GLN    56      33.464  12.646  45.143  1.00 25.00           C
ATOM     57  CA  VAL    57      30.619  10.085  45.032  1.00 25.00           C
ATOM     58  CA  ASP    58      28.267  12.725  43.560  1.00 25.00           C
ATOM     59  CA  LEU    59      30.882  13.611  40.907  1.00 25.00           C
ATOM     60  CA  LEU    60      31.279   9.906  40.025  1.00 25.00           C
ATOM     61  CA  LEU    61      27.479   9.549  39.710  1.00 25.00           C
ATOM     62  CA  LYS    62      27.355  12.621  37.427  1.00 25.00           C
ATOM     63  CA  ALA    63      30.152  11.153  35.260  1.00 25.00           C
ATOM     64  CA  SER    64      28.258   7.834  35.021  1.00 25.00           C
ATOM     65  CA  ASP    65      25.072   9.697  33.995  1.00 25.00           C
ATOM     66  CA  SER    66      27.026  11.613  31.315  1.00 25.00           C
ATOM     67  CA  ILE    67      28.485   8.326  29.995  1.00 25.00           C
ATOM     68  CA  GLU    68      24.978   6.795  29.858  1.00 25.00           C
ATOM     69  CA  ALA    69      23.689   9.855  27.950  1.00 25.00           C
ATOM     70  CA  SER    70      26.598   9.566  25.475  1.00 25.00           C
ATOM     71  CA  GLN    71      25.829   5.849  24.968  1.00 25.00           C
ATOM     72  CA  ALA    72      22.141   6.672  24.344  1.00 25.00           C
ATOM     73  CA  VAL    73      23.143   9.346  21.793  1.00 25.00           C
ATOM     74  CA  ALA    74      25.436   6.837  20.027  1.00 25.00           C
ATOM     75  CA  LEU    75      22.591   4.277  19.917  1.00 25.00           C
ATOM     76  CA  ILE    76      20.240   6.918  18.445  1.00 25.00           C
ATOM     77  CA  ALA    77      22.855   7.803  15.792  1.00 25.00           C
ATOM     78  CA  ARG    78      23.251   4.097  14.909  1.00 25.00           C
ATOM     79  CA  MET    79      19.452   3.741  14.594  1.00 25.00           C
ATOM     80  CA  ASP    80      19.328   6.813  12.310  1.00 25.00           C
ATOM     81  CA  GLU    81      22.124   5.345  10.143  1.00 25.00           C
ATOM     82  CA  GLU    82      20.229   2.026   9.904  1.00 25.00           C
ATOM     83  CA  ARG    83      17.044   3.889   8.879  1.00 25.00           C
ATOM     84  CA  LYS    84      18.998   5.805   6.198  1.00 25.00           C
ATOM     85  CA  LYS    85      20.458   2.519   4.880  1.00 25.00           C
ATOM     86  CA  TYR    86      16.950   0.987   4.743  1.00 25.00           C
ATOM     87  CA  VAL    87      15.662   4.047   2.834  1.00 25.00           C
ATOM     88  CA  ALA    88      18.570   3.758   0.359  1.00 25.00           C
ATOM     89  CA  SER    89      17.801   0.041  -0.148  1.00 25.00           C
ATOM     90  CA  TYR    90      14.114   0.864  -0.773  1.00 25.00           C
ATOM     91  CA  LEU    91      15.116   3.537  -3.324  1.00 25.00           C
ATOM     92  CA  GLY    92      17.409   1.029  -5.089  1.00 25.00           C
ATOM     93  CA  VAL    93      14.563  -1.532  -5.200  1.00 25.00           C
ATOM     94  CA  ILE    94      12.211   1.109  -6.672  1.00 25.00           C
ATOM     95  CA  MET    95      14.827   1.995  -9.325  1.00 25.00           C
ATOM     96  CA  ALA    96      15.223  -1.711 -10.207  1.00 25.00           C
ATOM     97  CA  SER    97      17.502  -3.555  -7.782  1.00 25.00           C
ATOM     98  CA  ASP    98      18.029  -4.228  -4.134  1.00 25.00           C
ATOM     99  CA  GLY    99      18.262  -4.448  -0.362  1.00 25.00           C
ATOM    100  CA  ASP   100      18.339  -4.315   3.466  1.00 25.00           C
ATOM    101  CA  ILE   101      18.433  -4.084   7.279  1.00 25.00           C
ATOM    102  CA  ASP   102      18.530  -3.468  11.090  1.00 25.00           C
ATOM    103  CA  ASP   103      18.650  -2.891  14.855  1.00 25.00           C
ATOM    104  CA  ASN   104      16.989   0.066  16.635  1.00 25.00           C
ATOM    105  CA  GLU   105      15.098  -2.346  18.932  1.00 25.00           C
ATOM    106  CA  LEU   106      18.362  -4.182  19.734  1.00 25.00           C
ATOM    107  CA  ALA   107      20.067  -0.849  20.538  1.00 25.00           C
ATOM    108  CA  LEU   108      17.159   0.114  22.836  1.00 25.00           C
ATOM    109  CA  TRP   109      17.410  -3.270  24.613  1.00 25.00           C
ATOM    110  CA  THR   110      21.179  -2.773  25.077  1.00 25.00           C
ATOM    111  CA  LEU   111      20.566   0.722  26.519  1.00 25.00           C
ATOM    112  CA  ILE   112      17.957  -0.705  28.932  1.00 25.00           C
ATOM    113  CA  SER   113      20.424  -3.420  30.032  1.00 25.00           C
ATOM    114  CA  THR   114      23.122  -0.767  30.615  1.00 25.00           C
ATOM    115  CA  LEU   115      20.666   1.311  32.692  1.00 25.00           C
ATOM    116  CA  CYS   116      20.785   0.011  36.268  1.00 25.00           C
ATOM    117  CA  GLY   117      22.557  -2.228  38.749  1.00 25.00           C
ATOM    118  CA  LEU   118      21.147   0.116  41.413  1.00 25.00           C
ATOM    119  CA  PRO   119      19.023  -2.813  42.538  1.00 25.00           C
ATOM    120  CA  THR   120      15.605  -2.065  41.003  1.00 25.00           C
ATOM    121  CA  MET   121      13.826  -0.958  37.772  1.00 25.00           C
ATOM    122  CA  THR   122      10.834  -0.134  40.031  1.00 25.00           C
ATOM    123  CA  VAL   123       7.440   0.084  38.270  1.00 25.00           C
ATOM    124  CA  MET   124       7.780   3.892  38.035  1.00 25.00           C
ATOM    125  CA  GLU   125      11.295   3.513  36.563  1.00 25.00           C
ATOM    126  CA  ALA   126       9.973   0.999  33.994  1.00 25.00           C
ATOM    127  CA  ILE   127       7.156   3.413  33.043  1.00 25.00           C
ATOM    128  CA  ASN   128       9.694   6.250  32.628  1.00 25.00           C
ATOM    129  CA  ASN   129      11.869   4.012  30.406  1.00 25.00           C
ATOM    130  CA  MET   130       8.814   3.113  28.279  1.00 25.00           C
ATOM    131  CA  LYS   131       5.696   5.177  27.525  1.00 25.00           C
ATOM    132  CA  ASN   132       7.957   7.101  25.084  1.00 25.00           C
ATOM    133  CA  LEU   133      11.261   7.720  26.776  1.00 25.00           C
TER
END
