
#######################################################
#                                                     #
#                        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 T0283TS168_4
# Molecule2: number of CA atoms  112 (  888),  selected  112 , name T0283
# PARAMETERS: T0283TS168_4.T0283  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           #
LGA    S       2      S       2          1.074
LGA    F       3      F       3          0.458
LGA    I       4      I       4          0.496
LGA    E       5      E       5          0.185
LGA    K       6      K       6          0.255
LGA    M       7      M       7          0.234
LGA    I       8      I       8          0.612
LGA    G       9      G       9          0.656
LGA    S      10      S      10          0.618
LGA    L      11      L      11          0.717
LGA    N      12      N      12          1.039
LGA    D      13      D      13          1.052
LGA    K      14      K      14          0.477
LGA    R      15      R      15          0.889
LGA    E      16      E      16          1.400
LGA    W      17      W      17          1.029
LGA    K      18      K      18          0.693
LGA    A      19      A      19          1.290
LGA    M      20      M      20          1.311
LGA    E      21      E      21          0.651
LGA    A      22      A      22          0.701
LGA    R      23      R      23          1.071
LGA    A      24      A      24          0.925
LGA    K      25      K      25          0.720
LGA    A      26      A      26          1.297
LGA    L      27      L      27          5.058
LGA    P      28      P      28           -
LGA    K      29      K      29           -
LGA    E      30      E      30           -
LGA    Y      31      Y      31           -
LGA    H      32      H      32           -
LGA    H      33      H      33           -
LGA    -       -      A      34           -
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    A      34      G      59          5.059
LGA    Y      35      -       -           -
LGA    K      36      -       -           -
LGA    A      37      -       -           -
LGA    I      38      G      60           #
LGA    Q      39      I      61           -
LGA    K      40      L      62           -
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      D      63          3.840
LGA    G      59      L      64           #
LGA    G      60      F      65          2.708
LGA    I      61      E      66          3.716
LGA    L      62      E      67           #
LGA    -       -      G      68           -
LGA    D      63      A      69          3.635
LGA    L      64      A      70           -
LGA    F      65      E      71           -
LGA    E      66      G      72           -
LGA    E      67      -       -           -
LGA    G      68      -       -           -
LGA    A      69      -       -           -
LGA    A      70      -       -           -
LGA    E      71      -       -           -
LGA    G      72      K      73           #
LGA    K      73      K      74          2.961
LGA    K      74      V      75          3.558
LGA    V      75      T      76          2.290
LGA    -       -      D      77           -
LGA    -       -      L      78           -
LGA    T      76      T      79          3.506
LGA    D      77      G      80          2.243
LGA    L      78      E      81          5.284
LGA    T      79      D      82           -
LGA    G      80      V      83           -
LGA    E      81      A      84           -
LGA    D      82      -       -           -
LGA    V      83      -       -           -
LGA    A      84      -       -           -
LGA    A      85      A      85           #
LGA    F      86      F      86          5.496
LGA    C      87      C      87          4.611
LGA    D      88      D      88          3.636
LGA    E      89      E      89          2.710
LGA    L      90      L      90          2.768
LGA    M      91      -       -           -
LGA    K      92      -       -           -
LGA    D      93      M      91          3.744
LGA    T      94      K      92           -
LGA    K      95      D      93           -
LGA    -       -      T      94           -
LGA    T      96      K      95           #
LGA    W      97      T      96           #
LGA    M      98      -       -           -
LGA    D      99      -       -           -
LGA    K     100      W      97          4.416
LGA    Y     101      M      98           -
LGA    R     102      D      99           -
LGA    -       -      K     100           -
LGA    T     103      Y     101           #
LGA    K     104      R     102           -
LGA    L     105      T     103           -
LGA    N     106      K     104           -
LGA    D     107      L     105           -
LGA    S     108      N     106           -
LGA    I     109      D     107           -
LGA    G     110      S     108           -
LGA    R     111      I     109           -
LGA    D     112      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     44    2.63    75.00     30.288     1.612

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.697188 * X  +   0.587864 * Y  +   0.410299 * Z  +  18.433748
  Y_new =   0.640532 * X  +   0.767842 * Y  +  -0.011737 * Z  +  24.319475
  Z_new =  -0.321945 * X  +   0.254627 * Y  +  -0.911875 * Z  +   0.345543 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.869294   -0.272299  [ DEG:   164.3984    -15.6016 ]
  Theta =   0.327783    2.813810  [ DEG:    18.7806    161.2194 ]
  Phi   =   2.398521   -0.743071  [ DEG:   137.4252    -42.5748 ]
 
# 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: T0283TS168_4                                  
REMARK     2: T0283                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS168_4.T0283 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  112  112   5.0   44   2.63   75.00  30.288
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS168_4
PFRMAT TS
TARGET T0283
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      24.444  11.825  24.103  1.00 25.00           C
ATOM      2  CA  SER     2      26.929  10.427  21.636  1.00 25.00           C
ATOM      3  CA  PHE     3      30.025   8.872  20.008  1.00 25.00           C
ATOM      4  CA  ILE     4      28.601   6.365  17.488  1.00 25.00           C
ATOM      5  CA  GLU     5      25.312   8.323  17.360  1.00 25.00           C
ATOM      6  CA  LYS     6      27.244  11.576  16.767  1.00 25.00           C
ATOM      7  CA  MET     7      29.228   9.914  13.945  1.00 25.00           C
ATOM      8  CA  ILE     8      25.973   8.663  12.361  1.00 25.00           C
ATOM      9  CA  GLY     9      24.486  12.185  12.577  1.00 25.00           C
ATOM     10  CA  SER    10      27.623  13.638  10.930  1.00 25.00           C
ATOM     11  CA  LEU    11      27.387  11.037   8.129  1.00 25.00           C
ATOM     12  CA  ASN    12      23.697  11.912   7.592  1.00 25.00           C
ATOM     13  CA  ASP    13      24.581  15.635   7.423  1.00 25.00           C
ATOM     14  CA  LYS    14      27.329  14.891   4.862  1.00 25.00           C
ATOM     15  CA  ARG    15      24.857  12.852   2.765  1.00 25.00           C
ATOM     16  CA  GLU    16      22.333  15.730   2.898  1.00 25.00           C
ATOM     17  CA  TRP    17      25.048  18.195   1.793  1.00 25.00           C
ATOM     18  CA  LYS    18      25.994  15.887  -1.113  1.00 25.00           C
ATOM     19  CA  ALA    19      22.317  15.649  -2.155  1.00 25.00           C
ATOM     20  CA  MET    20      22.012  19.465  -2.044  1.00 25.00           C
ATOM     21  CA  GLU    21      25.162  19.803  -4.197  1.00 25.00           C
ATOM     22  CA  ALA    22      23.738  17.295  -6.717  1.00 25.00           C
ATOM     23  CA  ARG    23      20.449  19.254  -6.845  1.00 25.00           C
ATOM     24  CA  ALA    24      22.382  22.507  -7.437  1.00 25.00           C
ATOM     25  CA  LYS    25      24.364  20.843 -10.260  1.00 25.00           C
ATOM     26  CA  ALA    26      21.109  19.593 -11.844  1.00 25.00           C
ATOM     27  CA  LEU    27      17.461  18.789 -11.154  1.00 25.00           C
ATOM     28  CA  PRO    28      16.141  15.608  -9.456  1.00 25.00           C
ATOM     29  CA  LYS    29      15.675  12.676  -7.056  1.00 25.00           C
ATOM     30  CA  GLU    30      16.943  13.911  -3.659  1.00 25.00           C
ATOM     31  CA  TYR    31      16.252  17.533  -4.692  1.00 25.00           C
ATOM     32  CA  HIS    32      12.713  16.571  -5.794  1.00 25.00           C
ATOM     33  CA  HIS    33      12.121  14.812  -2.443  1.00 25.00           C
ATOM     34  CA  ALA    34      13.354  17.917  -0.569  1.00 25.00           C
ATOM     35  CA  TYR    35      11.005  20.127  -2.635  1.00 25.00           C
ATOM     36  CA  LYS    36       8.077  17.785  -1.856  1.00 25.00           C
ATOM     37  CA  ALA    37       8.931  17.919   1.876  1.00 25.00           C
ATOM     38  CA  ILE    38       9.052  21.745   1.736  1.00 25.00           C
ATOM     39  CA  GLN    39       5.644  21.813  -0.011  1.00 25.00           C
ATOM     40  CA  LYS    40       4.195  19.495   2.671  1.00 25.00           C
ATOM     41  CA  TYR    41       5.594  21.762   5.422  1.00 25.00           C
ATOM     42  CA  MET    42       4.046  24.823   3.721  1.00 25.00           C
ATOM     43  CA  TRP    43       0.673  23.023   3.496  1.00 25.00           C
ATOM     44  CA  THR    44       0.882  22.117   7.211  1.00 25.00           C
ATOM     45  CA  SER    45       1.728  25.693   8.184  1.00 25.00           C
ATOM     46  CA  GLY    46       0.709  28.161   5.542  1.00 25.00           C
ATOM     47  CA  GLY    47      -0.965  28.616   2.198  1.00 25.00           C
ATOM     48  CA  PRO    48       1.127  27.129  -0.612  1.00 25.00           C
ATOM     49  CA  THR    49      -0.800  25.883  -3.648  1.00 25.00           C
ATOM     50  CA  ASP    50       0.676  22.451  -3.269  1.00 25.00           C
ATOM     51  CA  TRP    51       2.103  20.189  -6.032  1.00 25.00           C
ATOM     52  CA  GLN    52       2.060  23.393  -8.129  1.00 25.00           C
ATOM     53  CA  ASP    53       4.244  25.156  -5.525  1.00 25.00           C
ATOM     54  CA  THR    54       6.706  22.223  -5.566  1.00 25.00           C
ATOM     55  CA  LYS    55       6.844  22.361  -9.391  1.00 25.00           C
ATOM     56  CA  ARG    56       7.511  26.131  -9.255  1.00 25.00           C
ATOM     57  CA  ILE    57      10.318  25.567  -6.711  1.00 25.00           C
ATOM     58  CA  PHE    58      11.854  22.877  -8.964  1.00 25.00           C
ATOM     59  CA  GLY    59      11.690  25.258 -11.960  1.00 25.00           C
ATOM     60  CA  GLY    60      13.389  28.004  -9.900  1.00 25.00           C
ATOM     61  CA  ILE    61      16.140  25.553  -8.854  1.00 25.00           C
ATOM     62  CA  LEU    62      16.663  24.542 -12.511  1.00 25.00           C
ATOM     63  CA  ASP    63      16.908  28.227 -13.520  1.00 25.00           C
ATOM     64  CA  LEU    64      19.477  28.842 -10.747  1.00 25.00           C
ATOM     65  CA  PHE    65      21.516  25.826 -11.934  1.00 25.00           C
ATOM     66  CA  GLU    66      21.417  27.142 -15.529  1.00 25.00           C
ATOM     67  CA  GLU    67      22.589  30.585 -14.327  1.00 25.00           C
ATOM     68  CA  GLY    68      25.459  28.956 -12.383  1.00 25.00           C
ATOM     69  CA  ALA    69      26.467  26.963 -15.494  1.00 25.00           C
ATOM     70  CA  ALA    70      26.424  30.167 -17.592  1.00 25.00           C
ATOM     71  CA  GLU    71      23.606  31.895 -19.525  1.00 25.00           C
ATOM     72  CA  GLY    72      19.989  33.184 -19.760  1.00 25.00           C
ATOM     73  CA  LYS    73      18.616  33.609 -16.269  1.00 25.00           C
ATOM     74  CA  LYS    74      16.262  35.481 -13.851  1.00 25.00           C
ATOM     75  CA  VAL    75      16.907  34.335 -10.247  1.00 25.00           C
ATOM     76  CA  THR    76      17.676  35.833  -6.807  1.00 25.00           C
ATOM     77  CA  ASP    77      16.330  39.229  -7.958  1.00 25.00           C
ATOM     78  CA  LEU    78      13.139  37.554  -9.254  1.00 25.00           C
ATOM     79  CA  THR    79       9.637  36.224  -9.352  1.00 25.00           C
ATOM     80  CA  GLY    80       6.204  37.137  -7.876  1.00 25.00           C
ATOM     81  CA  GLU    81       7.086  39.705  -5.174  1.00 25.00           C
ATOM     82  CA  ASP    82       6.101  37.207  -2.444  1.00 25.00           C
ATOM     83  CA  VAL    83       8.278  34.516  -4.084  1.00 25.00           C
ATOM     84  CA  ALA    84      11.225  36.958  -4.237  1.00 25.00           C
ATOM     85  CA  ALA    85      10.741  37.811  -0.535  1.00 25.00           C
ATOM     86  CA  PHE    86      10.680  34.083   0.341  1.00 25.00           C
ATOM     87  CA  CYS    87      13.901  33.536  -1.657  1.00 25.00           C
ATOM     88  CA  ASP    88      15.561  36.463   0.171  1.00 25.00           C
ATOM     89  CA  GLU    89      14.480  35.003   3.542  1.00 25.00           C
ATOM     90  CA  LEU    90      15.912  31.592   2.553  1.00 25.00           C
ATOM     91  CA  MET    91      19.212  33.247   1.534  1.00 25.00           C
ATOM     92  CA  LYS    92      19.351  35.094   4.886  1.00 25.00           C
ATOM     93  CA  ASP    93      18.719  31.809   6.750  1.00 25.00           C
ATOM     94  CA  THR    94      21.517  30.113   4.760  1.00 25.00           C
ATOM     95  CA  LYS    95      23.894  32.997   5.596  1.00 25.00           C
ATOM     96  CA  THR    96      22.987  32.701   9.305  1.00 25.00           C
ATOM     97  CA  TRP    97      23.643  28.930   9.189  1.00 25.00           C
ATOM     98  CA  MET    98      27.038  29.546   7.529  1.00 25.00           C
ATOM     99  CA  ASP    99      27.920  32.113  10.230  1.00 25.00           C
ATOM    100  CA  LYS   100      26.935  29.615  12.961  1.00 25.00           C
ATOM    101  CA  TYR   101      29.112  26.925  11.320  1.00 25.00           C
ATOM    102  CA  ARG   102      32.058  29.367  11.168  1.00 25.00           C
ATOM    103  CA  THR   103      31.575  30.220  14.871  1.00 25.00           C
ATOM    104  CA  LYS   104      31.514  26.491  15.746  1.00 25.00           C
ATOM    105  CA  LEU   105      34.735  25.944  13.748  1.00 25.00           C
ATOM    106  CA  ASN   106      36.395  28.873  15.576  1.00 25.00           C
ATOM    107  CA  ASP   107      35.314  27.413  18.947  1.00 25.00           C
ATOM    108  CA  SER   108      36.746  24.002  17.958  1.00 25.00           C
ATOM    109  CA  ILE   109      40.047  25.656  16.939  1.00 25.00           C
ATOM    110  CA  GLY   110      41.886  24.109  13.992  1.00 25.00           C
ATOM    111  CA  ARG   111      44.158  21.098  14.487  1.00 25.00           C
ATOM    112  CA  ASP   112      41.811  19.039  12.395  1.00 25.00           C
TER
END
