
#######################################################
#                                                     #
#                        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  112 (  112),  selected  112 , name T0283TS393_2
# Molecule2: number of CA atoms  112 (  888),  selected  112 , name T0283
# PARAMETERS: T0283TS393_2.T0283  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          5.686
LGA    S       2      S       2          5.203
LGA    F       3      F       3          3.149
LGA    I       4      I       4          2.037
LGA    E       5      E       5          2.839
LGA    K       6      K       6          3.015
LGA    M       7      M       7          1.819
LGA    I       8      I       8          1.328
LGA    G       9      G       9          2.053
LGA    S      10      S      10          1.885
LGA    L      11      L      11          0.801
LGA    N      12      N      12          0.670
LGA    D      13      D      13          1.107
LGA    K      14      K      14          1.092
LGA    R      15      R      15          0.707
LGA    E      16      E      16          0.260
LGA    W      17      W      17          1.069
LGA    K      18      K      18          1.525
LGA    A      19      A      19          1.055
LGA    M      20      M      20          0.673
LGA    E      21      E      21          1.568
LGA    A      22      A      22          1.847
LGA    R      23      R      23          1.125
LGA    A      24      A      24          1.321
LGA    K      25      K      25          2.257
LGA    A      26      A      26          2.026
LGA    L      27      L      27          1.760
LGA    P      28      P      28          2.328
LGA    -       -      K      29           -
LGA    K      29      E      30          0.373
LGA    E      30      Y      31          1.444
LGA    -       -      H      32           -
LGA    -       -      H      33           -
LGA    Y      31      A      34          1.813
LGA    -       -      Y      35           -
LGA    -       -      K      36           -
LGA    -       -      A      37           -
LGA    -       -      I      38           -
LGA    -       -      Q      39           -
LGA    -       -      K      40           -
LGA    -       -      Y      41           -
LGA    -       -      M      42           -
LGA    -       -      W      43           -
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      T      49           -
LGA    -       -      D      50           -
LGA    -       -      W      51           -
LGA    -       -      Q      52           -
LGA    -       -      D      53           -
LGA    -       -      T      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    -       -      I      57           -
LGA    -       -      F      58           -
LGA    -       -      G      59           -
LGA    -       -      G      60           -
LGA    -       -      I      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      L      64           -
LGA    -       -      F      65           -
LGA    -       -      E      66           -
LGA    -       -      E      67           -
LGA    -       -      G      68           -
LGA    -       -      A      69           -
LGA    -       -      A      70           -
LGA    -       -      E      71           -
LGA    -       -      G      72           -
LGA    H      32      K      73           #
LGA    H      33      K      74          4.643
LGA    A      34      V      75          3.690
LGA    Y      35      T      76          2.243
LGA    K      36      D      77          2.374
LGA    A      37      L      78          1.300
LGA    I      38      T      79          1.179
LGA    Q      39      G      80          3.133
LGA    K      40      E      81           -
LGA    Y      41      D      82           -
LGA    M      42      V      83           -
LGA    W      43      A      84           -
LGA    T      44      A      85           -
LGA    S      45      -       -           -
LGA    G      46      -       -           -
LGA    G      47      -       -           -
LGA    P      48      -       -           -
LGA    T      49      -       -           -
LGA    D      50      -       -           -
LGA    W      51      -       -           -
LGA    Q      52      -       -           -
LGA    D      53      -       -           -
LGA    T      54      -       -           -
LGA    K      55      -       -           -
LGA    R      56      -       -           -
LGA    I      57      -       -           -
LGA    F      58      -       -           -
LGA    G      59      F      86          0.785
LGA    G      60      -       -           -
LGA    I      61      C      87          1.852
LGA    L      62      D      88           #
LGA    D      63      E      89           -
LGA    L      64      -       -           -
LGA    F      65      -       -           -
LGA    E      66      -       -           -
LGA    E      67      -       -           -
LGA    G      68      -       -           -
LGA    A      69      -       -           -
LGA    A      70      -       -           -
LGA    E      71      -       -           -
LGA    G      72      -       -           -
LGA    K      73      -       -           -
LGA    K      74      -       -           -
LGA    V      75      -       -           -
LGA    T      76      -       -           -
LGA    D      77      -       -           -
LGA    L      78      -       -           -
LGA    T      79      -       -           -
LGA    G      80      -       -           -
LGA    E      81      -       -           -
LGA    D      82      -       -           -
LGA    V      83      -       -           -
LGA    A      84      -       -           -
LGA    A      85      -       -           -
LGA    F      86      -       -           -
LGA    C      87      -       -           -
LGA    D      88      L      90          5.178
LGA    E      89      -       -           -
LGA    L      90      -       -           -
LGA    M      91      -       -           -
LGA    K      92      -       -           -
LGA    D      93      M      91           #
LGA    T      94      K      92           -
LGA    -       -      D      93           -
LGA    K      95      T      94           #
LGA    T      96      K      95          1.807
LGA    W      97      T      96          1.670
LGA    M      98      W      97          3.847
LGA    D      99      M      98          3.793
LGA    K     100      D      99          1.927
LGA    Y     101      K     100          4.284
LGA    R     102      Y     101          4.670
LGA    T     103      R     102          1.116
LGA    K     104      T     103          4.507
LGA    L     105      K     104           #
LGA    N     106      -       -           -
LGA    D     107      -       -           -
LGA    S     108      L     105          3.403
LGA    I     109      N     106           -
LGA    G     110      D     107           -
LGA    R     111      S     108           -
LGA    D     112      I     109           -
LGA    -       -      G     110           -
LGA    -       -      R     111           -
LGA    -       -      D     112           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  112  112    5.0     51    2.61    54.90     35.423     1.884

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.042800 * X  +  -0.075901 * Y  +   0.996196 * Z  +  19.013268
  Y_new =   0.909101 * X  +   0.410595 * Y  +   0.070342 * Z  +  28.698248
  Z_new =  -0.414372 * X  +   0.908653 * Y  +   0.051428 * Z  +   2.217782 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.514259   -1.627334  [ DEG:    86.7607    -93.2393 ]
  Theta =   0.427253    2.714340  [ DEG:    24.4798    155.5202 ]
  Phi   =   1.617841   -1.523751  [ DEG:    92.6955    -87.3045 ]
 
# 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: T0283TS393_2                                  
REMARK     2: T0283                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS393_2.T0283 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  112  112   5.0   51   2.61   54.90  35.423
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS393_2
PFRMAT TS
TARGET T0283
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      31.476   8.689  23.209  1.00 25.00           C
ATOM      2  CA  SER     2      30.035   5.494  21.833  1.00 25.00           C
ATOM      3  CA  PHE     3      27.394   7.646  20.181  1.00 25.00           C
ATOM      4  CA  ILE     4      27.524   5.285  17.168  1.00 25.00           C
ATOM      5  CA  GLU     5      23.898   6.159  16.295  1.00 25.00           C
ATOM      6  CA  LYS     6      24.716   9.893  16.531  1.00 25.00           C
ATOM      7  CA  MET     7      27.746   9.400  14.241  1.00 25.00           C
ATOM      8  CA  ILE     8      25.564   7.514  11.720  1.00 25.00           C
ATOM      9  CA  GLY     9      22.980  10.339  11.806  1.00 25.00           C
ATOM     10  CA  SER    10      25.747  12.921  11.217  1.00 25.00           C
ATOM     11  CA  LEU    11      27.058  10.876   8.256  1.00 25.00           C
ATOM     12  CA  ASN    12      23.523  10.681   6.793  1.00 25.00           C
ATOM     13  CA  ASP    13      23.127  14.471   7.181  1.00 25.00           C
ATOM     14  CA  LYS    14      26.487  15.026   5.429  1.00 25.00           C
ATOM     15  CA  ARG    15      25.404  12.721   2.569  1.00 25.00           C
ATOM     16  CA  GLU    16      22.109  14.643   2.235  1.00 25.00           C
ATOM     17  CA  TRP    17      24.024  17.958   2.131  1.00 25.00           C
ATOM     18  CA  LYS    18      26.343  16.562  -0.579  1.00 25.00           C
ATOM     19  CA  ALA    19      23.310  15.409  -2.614  1.00 25.00           C
ATOM     20  CA  MET    20      21.733  18.882  -2.278  1.00 25.00           C
ATOM     21  CA  GLU    21      25.001  20.506  -3.440  1.00 25.00           C
ATOM     22  CA  ALA    22      25.132  18.145  -6.453  1.00 25.00           C
ATOM     23  CA  ARG    23      21.506  19.019  -7.324  1.00 25.00           C
ATOM     24  CA  ALA    24      22.323  22.753  -7.089  1.00 25.00           C
ATOM     25  CA  LYS    25      25.353  22.260  -9.379  1.00 25.00           C
ATOM     26  CA  ALA    26      23.172  20.374 -11.899  1.00 25.00           C
ATOM     27  CA  LEU    27      21.523  23.735 -12.382  1.00 25.00           C
ATOM     28  CA  PRO    28      21.008  26.592 -14.894  1.00 25.00           C
ATOM     29  CA  LYS    29      23.536  29.463 -14.388  1.00 25.00           C
ATOM     30  CA  GLU    30      22.333  28.442 -10.899  1.00 25.00           C
ATOM     31  CA  TYR    31      22.565  32.079  -9.726  1.00 25.00           C
ATOM     32  CA  HIS    32      20.560  33.219 -12.783  1.00 25.00           C
ATOM     33  CA  HIS    33      17.896  30.566 -12.056  1.00 25.00           C
ATOM     34  CA  ALA    34      17.698  31.729  -8.411  1.00 25.00           C
ATOM     35  CA  TYR    35      17.302  35.358  -9.566  1.00 25.00           C
ATOM     36  CA  LYS    36      14.509  34.316 -11.970  1.00 25.00           C
ATOM     37  CA  ALA    37      12.746  32.429  -9.141  1.00 25.00           C
ATOM     38  CA  ILE    38      13.023  35.508  -6.881  1.00 25.00           C
ATOM     39  CA  GLN    39      11.562  37.706  -9.655  1.00 25.00           C
ATOM     40  CA  LYS    40       8.663  35.245 -10.112  1.00 25.00           C
ATOM     41  CA  TYR    41       8.004  35.282  -6.340  1.00 25.00           C
ATOM     42  CA  MET    42       8.003  39.112  -6.354  1.00 25.00           C
ATOM     43  CA  TRP    43       5.535  39.125  -9.282  1.00 25.00           C
ATOM     44  CA  THR    44       3.265  36.672  -7.412  1.00 25.00           C
ATOM     45  CA  SER    45       3.372  33.240  -5.685  1.00 25.00           C
ATOM     46  CA  GLY    46       5.420  32.479  -2.537  1.00 25.00           C
ATOM     47  CA  GLY    47       3.941  33.941   0.623  1.00 25.00           C
ATOM     48  CA  PRO    48       4.587  32.918   4.236  1.00 25.00           C
ATOM     49  CA  THR    49       3.910  36.398   5.679  1.00 25.00           C
ATOM     50  CA  ASP    50       1.845  38.425   3.218  1.00 25.00           C
ATOM     51  CA  TRP    51       2.261  38.588  -0.597  1.00 25.00           C
ATOM     52  CA  GLN    52       4.752  40.855  -2.419  1.00 25.00           C
ATOM     53  CA  ASP    53       6.453  41.698   0.907  1.00 25.00           C
ATOM     54  CA  THR    54       6.689  37.972   1.761  1.00 25.00           C
ATOM     55  CA  LYS    55       8.222  37.257  -1.675  1.00 25.00           C
ATOM     56  CA  ARG    56      10.772  40.067  -1.149  1.00 25.00           C
ATOM     57  CA  ILE    57      11.670  38.641   2.291  1.00 25.00           C
ATOM     58  CA  PHE    58      12.126  35.161   0.756  1.00 25.00           C
ATOM     59  CA  GLY    59      14.387  36.629  -1.964  1.00 25.00           C
ATOM     60  CA  GLY    60      16.463  38.434   0.701  1.00 25.00           C
ATOM     61  CA  ILE    61      16.798  35.172   2.682  1.00 25.00           C
ATOM     62  CA  LEU    62      17.923  33.336  -0.485  1.00 25.00           C
ATOM     63  CA  ASP    63      20.514  36.069  -1.179  1.00 25.00           C
ATOM     64  CA  LEU    64      21.807  35.791   2.416  1.00 25.00           C
ATOM     65  CA  PHE    65      22.083  31.989   2.047  1.00 25.00           C
ATOM     66  CA  GLU    66      24.012  32.422  -1.233  1.00 25.00           C
ATOM     67  CA  GLU    67      26.383  34.908   0.461  1.00 25.00           C
ATOM     68  CA  GLY    68      26.948  32.446   3.340  1.00 25.00           C
ATOM     69  CA  ALA    69      27.698  29.650   0.833  1.00 25.00           C
ATOM     70  CA  ALA    70      30.189  31.916  -0.989  1.00 25.00           C
ATOM     71  CA  GLU    71      29.356  34.100  -4.009  1.00 25.00           C
ATOM     72  CA  GLY    72      27.831  33.419  -7.423  1.00 25.00           C
ATOM     73  CA  LYS    73      24.633  34.681  -5.907  1.00 25.00           C
ATOM     74  CA  LYS    74      21.399  32.901  -5.158  1.00 25.00           C
ATOM     75  CA  VAL    75      20.672  29.175  -4.881  1.00 25.00           C
ATOM     76  CA  THR    76      20.093  25.988  -2.838  1.00 25.00           C
ATOM     77  CA  ASP    77      18.235  24.405  -5.790  1.00 25.00           C
ATOM     78  CA  LEU    78      15.141  26.048  -7.275  1.00 25.00           C
ATOM     79  CA  THR    79      12.717  23.463  -8.518  1.00 25.00           C
ATOM     80  CA  GLY    80      10.010  20.750  -8.197  1.00 25.00           C
ATOM     81  CA  GLU    81       7.613  22.066  -5.516  1.00 25.00           C
ATOM     82  CA  ASP    82       9.349  19.909  -2.871  1.00 25.00           C
ATOM     83  CA  VAL    83      12.761  21.242  -3.988  1.00 25.00           C
ATOM     84  CA  ALA    84      11.459  24.837  -3.762  1.00 25.00           C
ATOM     85  CA  ALA    85      10.117  24.155  -0.240  1.00 25.00           C
ATOM     86  CA  PHE    86      13.505  22.698   0.794  1.00 25.00           C
ATOM     87  CA  CYS    87      15.288  25.786  -0.604  1.00 25.00           C
ATOM     88  CA  ASP    88      12.900  28.071   1.330  1.00 25.00           C
ATOM     89  CA  GLU    89      13.565  26.090   4.540  1.00 25.00           C
ATOM     90  CA  LEU    90      17.341  26.393   3.974  1.00 25.00           C
ATOM     91  CA  MET    91      16.983  30.169   3.444  1.00 25.00           C
ATOM     92  CA  LYS    92      14.950  30.455   6.677  1.00 25.00           C
ATOM     93  CA  ASP    93      17.632  28.480   8.567  1.00 25.00           C
ATOM     94  CA  THR    94      20.352  30.780   7.161  1.00 25.00           C
ATOM     95  CA  LYS    95      18.344  33.857   8.242  1.00 25.00           C
ATOM     96  CA  THR    96      17.940  32.388  11.757  1.00 25.00           C
ATOM     97  CA  TRP    97      21.707  31.722  11.938  1.00 25.00           C
ATOM     98  CA  MET    98      22.422  35.323  10.844  1.00 25.00           C
ATOM     99  CA  ASP    99      20.025  36.639  13.525  1.00 25.00           C
ATOM    100  CA  LYS   100      21.761  34.482  16.171  1.00 25.00           C
ATOM    101  CA  TYR   101      25.173  35.816  15.053  1.00 25.00           C
ATOM    102  CA  ARG   102      23.871  39.409  15.280  1.00 25.00           C
ATOM    103  CA  THR   103      22.529  38.728  18.801  1.00 25.00           C
ATOM    104  CA  LYS   104      25.916  37.271  19.835  1.00 25.00           C
ATOM    105  CA  LEU   105      27.700  40.359  18.437  1.00 25.00           C
ATOM    106  CA  ASN   106      25.312  42.644  20.372  1.00 25.00           C
ATOM    107  CA  ASP   107      25.976  40.663  23.581  1.00 25.00           C
ATOM    108  CA  SER   108      29.753  40.966  23.016  1.00 25.00           C
ATOM    109  CA  ILE   109      29.395  44.742  22.486  1.00 25.00           C
ATOM    110  CA  GLY   110      33.190  45.225  22.309  1.00 25.00           C
ATOM    111  CA  ARG   111      35.182  42.299  20.802  1.00 25.00           C
ATOM    112  CA  ASP   112      35.750  39.009  18.903  1.00 25.00           C
TER
END
