
#######################################################
#                                                     #
#                        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  130 (  130),  selected  130 , name T0354TS599_3
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS599_3.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           #
LGA    E       2      E       2          3.463
LGA    I       3      I       3          3.329
LGA    Q       4      Q       4          1.667
LGA    E       5      E       5          1.423
LGA    I       6      I       6          1.605
LGA    S       7      S       7          1.581
LGA    K       8      K       8          0.991
LGA    L       9      L       9          1.532
LGA    A      10      A      10          1.895
LGA    I      11      I      11          1.643
LGA    E      12      E      12          2.223
LGA    A      13      A      13          2.932
LGA    L      14      L      14          2.456
LGA    E      15      E      15          2.989
LGA    D      16      D      16          4.445
LGA    I      17      I      17          3.387
LGA    K      18      K      18          2.015
LGA    G      19      G      19          1.694
LGA    K      20      K      20          1.675
LGA    D      21      D      21          2.732
LGA    I      22      I      22          1.676
LGA    I      23      I      23          2.561
LGA    E      24      E      24          1.889
LGA    L      25      L      25          1.167
LGA    D      26      D      26          1.878
LGA    T      27      T      27          2.450
LGA    S      28      S      28          3.947
LGA    K      29      -       -           -
LGA    L      30      K      29          0.831
LGA    T      31      L      30           #
LGA    -       -      T      31           -
LGA    S      32      S      32          2.461
LGA    L      33      L      33           #
LGA    F      34      -       -           -
LGA    Q      35      F      34          4.395
LGA    R      36      Q      35          2.763
LGA    M      37      R      36          1.489
LGA    I      38      M      37          1.177
LGA    V      39      I      38          1.276
LGA    A      40      V      39          1.370
LGA    T      41      A      40          2.085
LGA    G      42      T      41          1.961
LGA    D      43      G      42          1.524
LGA    S      44      D      43          2.470
LGA    -       -      S      44           -
LGA    N      45      N      45          2.836
LGA    R      46      R      46          2.258
LGA    Q      47      Q      47          2.308
LGA    V      48      V      48          3.051
LGA    K      49      K      49          2.404
LGA    A      50      A      50          2.145
LGA    L      51      L      51          2.919
LGA    A      52      A      52          2.747
LGA    N      53      N      53          2.125
LGA    S      54      S      54          2.492
LGA    V      55      V      55          2.400
LGA    Q      56      Q      56          1.813
LGA    V      57      V      57          2.347
LGA    K      58      K      58          2.668
LGA    L      59      L      59          1.978
LGA    K      60      K      60          1.837
LGA    E      61      E      61          2.597
LGA    A      62      A      62          2.895
LGA    G      63      G      63          2.293
LGA    V      64      V      64          1.963
LGA    D      65      D      65          1.979
LGA    I      66      I      66          2.383
LGA    V      67      V      67          4.807
LGA    G      68      G      68          0.675
LGA    S      69      S      69          1.332
LGA    E      70      E      70          2.210
LGA    G      71      G      71          3.519
LGA    H      72      H      72           -
LGA    E      73      E      73           -
LGA    S      74      S      74           -
LGA    -       -      G      75           -
LGA    G      75      E      76           #
LGA    E      76      W      77          3.792
LGA    W      77      V      78          3.386
LGA    V      78      L      79          2.323
LGA    L      79      V      80          2.035
LGA    V      80      D      81          1.180
LGA    D      81      A      82          1.855
LGA    A      82      G      83          3.477
LGA    G      83      -       -           -
LGA    D      84      D      84          1.232
LGA    V      85      V      85          1.952
LGA    V      86      V      86          1.534
LGA    V      87      V      87          1.857
LGA    H      88      H      88          2.050
LGA    V      89      V      89          2.952
LGA    M      90      M      90          2.895
LGA    L      91      L      91          3.233
LGA    P      92      P      92          2.994
LGA    A      93      A      93          2.392
LGA    V      94      V      94          3.024
LGA    R      95      R      95          2.017
LGA    D      96      D      96          2.534
LGA    Y      97      Y      97          3.811
LGA    -       -      Y      98           -
LGA    Y      98      D      99          2.974
LGA    D      99      I     100           #
LGA    I     100      -       -           -
LGA    E     101      E     101           #
LGA    A     102      A     102          3.851
LGA    L     103      L     103          5.043
LGA    W     104      W     104          5.067
LGA    G     105      G     105          2.867
LGA    G     106      G     106          4.585
LGA    Q     107      Q     107           -
LGA    K     108      K     108           -
LGA    P     109      P     109           -
LGA    S     110      S     110           -
LGA    F     111      F     111           -
LGA    A     112      A     112           -
LGA    V     113      V     113           -
LGA    G     114      G     114           -
LGA    A     115      A     115           -
LGA    A     116      A     116           -
LGA    K     117      K     117           -
LGA    P     118      P     118           -
LGA    W     119      W     119           -
LGA    S     120      S     120           -
LGA    A     121      A     121           -
LGA    V     122      V     122           -
LGA    L     123      -       -           -
LGA    E     124      -       -           -
LGA    H     125      -       -           -
LGA    H     126      -       -           -
LGA    H     127      -       -           -
LGA    H     128      -       -           -
LGA    H     129      -       -           -
LGA    H     130      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  130  122    5.0     93    2.61    79.57     49.317     3.429

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.086406 * X  +   0.990678 * Y  +   0.105316 * Z  +  40.151047
  Y_new =  -0.992078 * X  +   0.095237 * Y  +  -0.081916 * Z  +  24.682653
  Z_new =  -0.091182 * X  +  -0.097403 * Y  +   0.991059 * Z  +  20.051790 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.097967    3.043625  [ DEG:    -5.6131    174.3869 ]
  Theta =   0.091309    3.050284  [ DEG:     5.2316    174.7684 ]
  Phi   =  -1.483919    1.657673  [ DEG:   -85.0223     94.9777 ]
 
# 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: T0354TS599_3                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS599_3.T0354.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  130  122   5.0   93   2.61   79.57  49.317
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS599_3
PFRMAT TS                                                                       
TARGET T0354                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      51.786  21.354  15.539  1.00  0.00              
ATOM      2  CA  GLU     2      53.440  24.218  17.559  1.00  0.00              
ATOM      3  CA  ILE     3      49.549  23.800  17.856  1.00  0.00              
ATOM      4  CA  GLN     4      49.283  20.086  19.820  1.00  0.00              
ATOM      5  CA  GLU     5      51.820  21.646  22.088  1.00  0.00              
ATOM      6  CA  ILE     6      49.830  24.635  22.755  1.00  0.00              
ATOM      7  CA  SER     7      46.701  22.751  23.655  1.00  0.00              
ATOM      8  CA  LYS     8      48.552  20.536  26.032  1.00  0.00              
ATOM      9  CA  LEU     9      50.228  23.496  27.705  1.00  0.00              
ATOM     10  CA  ALA    10      46.918  25.341  28.152  1.00  0.00              
ATOM     11  CA  ILE    11      45.295  22.268  29.571  1.00  0.00              
ATOM     12  CA  GLU    12      48.094  21.707  32.031  1.00  0.00              
ATOM     13  CA  ALA    13      48.143  25.261  33.213  1.00  0.00              
ATOM     14  CA  LEU    14      44.403  25.250  33.764  1.00  0.00              
ATOM     15  CA  GLU    15      44.537  22.032  35.707  1.00  0.00              
ATOM     16  CA  ASP    16      47.320  23.277  37.941  1.00  0.00              
ATOM     17  CA  ILE    17      45.608  26.515  38.783  1.00  0.00              
ATOM     18  CA  LYS    18      42.340  24.885  39.691  1.00  0.00              
ATOM     19  CA  GLY    19      40.230  26.101  36.688  1.00  0.00              
ATOM     20  CA  LYS    20      37.307  23.768  37.002  1.00  0.00              
ATOM     21  CA  ASP    21      35.907  23.241  33.586  1.00  0.00              
ATOM     22  CA  ILE    22      38.186  22.619  30.665  1.00  0.00              
ATOM     23  CA  ILE    23      36.969  20.836  27.510  1.00  0.00              
ATOM     24  CA  GLU    24      39.484  20.054  24.875  1.00  0.00              
ATOM     25  CA  LEU    25      38.624  19.111  21.343  1.00  0.00              
ATOM     26  CA  ASP    26      41.475  17.813  19.085  1.00  0.00              
ATOM     27  CA  THR    27      40.922  17.801  15.538  1.00  0.00              
ATOM     28  CA  SER    28      43.583  15.338  14.340  1.00  0.00              
ATOM     29  CA  LYS    29      41.374  13.074  12.200  1.00  0.00              
ATOM     30  CA  LEU    30      39.689  15.991  10.437  1.00  0.00              
ATOM     31  CA  THR    31      42.736  17.502   8.690  1.00  0.00              
ATOM     32  CA  SER    32      41.467  21.080   8.831  1.00  0.00              
ATOM     33  CA  LEU    33      40.666  20.607  12.520  1.00  0.00              
ATOM     34  CA  PHE    34      44.161  19.278  13.200  1.00  0.00              
ATOM     35  CA  GLN    35      45.628  22.508  11.905  1.00  0.00              
ATOM     36  CA  ARG    36      43.171  24.084  14.309  1.00  0.00              
ATOM     37  CA  MET    37      42.732  22.944  17.954  1.00  0.00              
ATOM     38  CA  ILE    38      39.575  24.010  19.903  1.00  0.00              
ATOM     39  CA  VAL    39      39.719  24.492  23.542  1.00  0.00              
ATOM     40  CA  ALA    40      36.560  25.036  25.462  1.00  0.00              
ATOM     41  CA  THR    41      36.865  26.583  28.722  1.00  0.00              
ATOM     42  CA  GLY    42      34.067  26.978  31.138  1.00  0.00              
ATOM     43  CA  ASP    43      35.518  28.198  34.381  1.00  0.00              
ATOM     44  CA  SER    44      34.880  31.422  35.981  1.00  0.00              
ATOM     45  CA  ASN    45      35.791  34.391  33.870  1.00  0.00              
ATOM     46  CA  ARG    46      38.597  35.519  36.186  1.00  0.00              
ATOM     47  CA  GLN    47      40.280  32.097  36.386  1.00  0.00              
ATOM     48  CA  VAL    48      40.166  31.854  32.618  1.00  0.00              
ATOM     49  CA  LYS    49      41.650  35.252  32.055  1.00  0.00              
ATOM     50  CA  ALA    50      44.569  34.440  34.292  1.00  0.00              
ATOM     51  CA  LEU    51      45.178  31.137  32.438  1.00  0.00              
ATOM     52  CA  ALA    52      44.971  32.852  29.059  1.00  0.00              
ATOM     53  CA  ASN    53      47.417  35.524  30.137  1.00  0.00              
ATOM     54  CA  SER    54      49.821  32.687  31.102  1.00  0.00              
ATOM     55  CA  VAL    55      49.271  31.045  27.719  1.00  0.00              
ATOM     56  CA  GLN    56      49.835  34.240  25.770  1.00  0.00              
ATOM     57  CA  VAL    57      53.143  34.652  27.540  1.00  0.00              
ATOM     58  CA  LYS    58      54.139  31.013  26.767  1.00  0.00              
ATOM     59  CA  LEU    59      53.234  31.412  23.132  1.00  0.00              
ATOM     60  CA  LYS    60      55.227  34.679  22.861  1.00  0.00              
ATOM     61  CA  GLU    61      58.273  33.069  24.421  1.00  0.00              
ATOM     62  CA  ALA    62      58.067  30.362  21.741  1.00  0.00              
ATOM     63  CA  GLY    63      57.796  32.849  18.958  1.00  0.00              
ATOM     64  CA  VAL    64      54.116  32.470  17.995  1.00  0.00              
ATOM     65  CA  ASP    65      52.693  35.820  16.874  1.00  0.00              
ATOM     66  CA  ILE    66      49.331  36.699  17.925  1.00  0.00              
ATOM     67  CA  VAL    67      46.820  36.757  20.486  1.00  0.00              
ATOM     68  CA  GLY    68      43.621  37.859  18.941  1.00  0.00              
ATOM     69  CA  SER    69      40.569  38.604  21.011  1.00  0.00              
ATOM     70  CA  GLU    70      37.213  38.626  19.347  1.00  0.00              
ATOM     71  CA  GLY    71      34.255  39.844  21.274  1.00  0.00              
ATOM     72  CA  HIS    72      31.276  37.741  20.059  1.00  0.00              
ATOM     73  CA  GLU    73      28.514  39.509  21.884  1.00  0.00              
ATOM     74  CA  SER    74      26.147  36.675  22.579  1.00  0.00              
ATOM     75  CA  GLY    75      27.611  35.247  25.744  1.00  0.00              
ATOM     76  CA  GLU    76      30.334  33.285  24.044  1.00  0.00              
ATOM     77  CA  TRP    77      33.858  34.803  23.873  1.00  0.00              
ATOM     78  CA  VAL    78      36.300  33.637  21.236  1.00  0.00              
ATOM     79  CA  LEU    79      40.040  33.810  21.844  1.00  0.00              
ATOM     80  CA  VAL    80      42.299  33.310  18.891  1.00  0.00              
ATOM     81  CA  ASP    81      45.845  32.272  19.453  1.00  0.00              
ATOM     82  CA  ALA    82      48.121  32.399  16.636  1.00  0.00              
ATOM     83  CA  GLY    83      49.470  28.898  15.790  1.00  0.00              
ATOM     84  CA  ASP    84      46.176  27.063  15.163  1.00  0.00              
ATOM     85  CA  VAL    85      44.710  27.436  18.661  1.00  0.00              
ATOM     86  CA  VAL    86      41.126  28.540  19.067  1.00  0.00              
ATOM     87  CA  VAL    87      39.977  29.200  22.637  1.00  0.00              
ATOM     88  CA  HIS    88      36.310  29.380  23.151  1.00  0.00              
ATOM     89  CA  VAL    89      35.165  30.861  26.308  1.00  0.00              
ATOM     90  CA  MET    90      31.624  30.049  27.246  1.00  0.00              
ATOM     91  CA  LEU    91      29.522  31.749  29.933  1.00  0.00              
ATOM     92  CA  PRO    92      27.628  29.645  32.512  1.00  0.00              
ATOM     93  CA  ALA    93      24.278  29.307  30.808  1.00  0.00              
ATOM     94  CA  VAL    94      25.876  28.184  27.491  1.00  0.00              
ATOM     95  CA  ARG    95      28.048  25.584  29.120  1.00  0.00              
ATOM     96  CA  ASP    96      25.255  23.938  31.046  1.00  0.00              
ATOM     97  CA  TYR    97      22.998  23.707  27.932  1.00  0.00              
ATOM     98  CA  TYR    98      25.604  22.165  25.656  1.00  0.00              
ATOM     99  CA  ASP    99      27.312  19.590  27.889  1.00  0.00              
ATOM    100  CA  ILE   100      31.017  20.435  27.511  1.00  0.00              
ATOM    101  CA  GLU   101      32.449  17.133  26.505  1.00  0.00              
ATOM    102  CA  ALA   102      29.761  16.737  23.803  1.00  0.00              
ATOM    103  CA  LEU   103      30.378  20.229  22.395  1.00  0.00              
ATOM    104  CA  TRP   104      34.175  19.697  22.241  1.00  0.00              
ATOM    105  CA  GLY   105      33.794  16.403  20.453  1.00  0.00              
ATOM    106  CA  GLY   106      31.582  18.090  17.918  1.00  0.00              
ATOM    107  CA  GLN   107      33.731  21.126  16.989  1.00  0.00              
ATOM    108  CA  LYS   108      32.921  21.307  13.338  1.00  0.00              
ATOM    109  CA  PRO   109      32.764  17.712  12.215  1.00  0.00              
ATOM    110  CA  SER   110      34.000  17.965   8.599  1.00  0.00              
ATOM    111  CA  PHE   111      32.303  15.465   6.338  1.00  0.00              
ATOM    112  CA  ALA   112      34.886  13.623   4.367  1.00  0.00              
ATOM    113  CA  VAL   113      33.932  13.311   0.659  1.00  0.00              
ATOM    114  CA  GLY   114      35.587  10.079  -0.302  1.00  0.00              
ATOM    115  CA  ALA   115      33.136   8.555  -2.821  1.00  0.00              
ATOM    116  CA  ALA   116      35.166   7.697  -5.936  1.00  0.00              
ATOM    117  CA  LYS   117      34.744   3.977  -6.224  1.00  0.00              
ATOM    118  CA  PRO   118      38.077   2.270  -5.956  1.00  0.00              
ATOM    119  CA  TRP   119      39.852   1.214  -9.082  1.00  0.00              
ATOM    120  CA  SER   120      41.607   4.478 -10.009  1.00  0.00              
ATOM    121  CA  ALA   121      41.753   6.114  -6.554  1.00  0.00              
ATOM    122  CA  VAL   122      39.688   9.245  -6.302  1.00  0.00              
ATOM    123  CA  LEU   123      40.711  11.007  -3.099  1.00  0.00              
ATOM    124  CA  GLU   124      40.979  14.579  -4.443  1.00  0.00              
ATOM    125  CA  HIS   125      38.399  16.264  -2.197  1.00  0.00              
ATOM    126  CA  HIS   126      35.997  18.068  -4.563  1.00  0.00              
ATOM    127  CA  HIS   127      34.911  20.133  -1.530  1.00  0.00              
ATOM    128  CA  HIS   128      35.433  18.356   2.267  1.00  0.00              
ATOM    129  CA  HIS   129      36.131  22.244   3.701  1.00  0.00              
ATOM    130  CA  HIS   130      36.955  21.967   7.219  1.00  0.00              
TER                                                                             
END
