
#######################################################
#                                                     #
#                        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  104 (  104),  selected  104 , name T0343TS393_2
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343TS393_2.T0343.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    T       2      -       -           -
LGA    W       3      T       2          0.939
LGA    R       4      W       3          3.742
LGA    E       5      -       -           -
LGA    I       6      R       4           #
LGA    L       7      E       5           #
LGA    R       8      I       6           #
LGA    K       9      -       -           -
LGA    E      10      -       -           -
LGA    G      11      -       -           -
LGA    F      12      -       -           -
LGA    L      13      -       -           -
LGA    D      14      -       -           -
LGA    L      15      -       -           -
LGA    G      16      -       -           -
LGA    E      17      -       -           -
LGA    F      18      -       -           -
LGA    I      19      -       -           -
LGA    V      20      -       -           -
LGA    E      21      -       -           -
LGA    L      22      -       -           -
LGA    V      23      L       7          5.439
LGA    Y      24      R       8          5.049
LGA    I      25      K       9          2.532
LGA    D      26      -       -           -
LGA    C      27      -       -           -
LGA    P      28      -       -           -
LGA    C      29      -       -           -
LGA    E      30      -       -           -
LGA    P      31      -       -           -
LGA    I      32      -       -           -
LGA    P      33      -       -           -
LGA    P      34      E      10          2.198
LGA    T      35      G      11          2.592
LGA    L      36      F      12          1.514
LGA    A      37      L      13           -
LGA    -       -      D      14           -
LGA    -       -      L      15           -
LGA    -       -      G      16           -
LGA    -       -      E      17           -
LGA    -       -      F      18           -
LGA    I      38      I      19           #
LGA    Y      39      V      20           -
LGA    D      40      E      21           -
LGA    K      41      L      22           -
LGA    K      42      -       -           -
LGA    G      43      -       -           -
LGA    D      44      -       -           -
LGA    E      45      -       -           -
LGA    W      46      V      23          4.372
LGA    Y      47      Y      24          3.611
LGA    K      48      -       -           -
LGA    V      49      I      25          3.173
LGA    E      50      D      26          4.571
LGA    E      51      -       -           -
LGA    A      52      -       -           -
LGA    P      53      C      27          3.299
LGA    N      54      P      28          1.600
LGA    V      55      C      29          2.508
LGA    Q      56      E      30          4.305
LGA    N      57      P      31           #
LGA    Y      58      I      32          2.599
LGA    R      59      -       -           -
LGA    E      60      -       -           -
LGA    A      61      -       -           -
LGA    V      62      P      33          3.960
LGA    E      63      -       -           -
LGA    W      64      -       -           -
LGA    A      65      P      34           #
LGA    I      66      T      35           -
LGA    E      67      L      36           -
LGA    V      68      -       -           -
LGA    L      69      -       -           -
LGA    E      70      -       -           -
LGA    R      71      -       -           -
LGA    I      72      -       -           -
LGA    R      73      -       -           -
LGA    D      74      -       -           -
LGA    G      75      -       -           -
LGA    E      76      -       -           -
LGA    N      77      -       -           -
LGA    V      78      -       -           -
LGA    K      79      A      37           #
LGA    L      80      I      38          3.898
LGA    -       -      Y      39           -
LGA    -       -      D      40           -
LGA    -       -      K      41           -
LGA    -       -      K      42           -
LGA    -       -      G      43           -
LGA    -       -      D      44           -
LGA    -       -      E      45           -
LGA    -       -      W      46           -
LGA    -       -      Y      47           -
LGA    -       -      K      48           -
LGA    V      81      V      49          3.046
LGA    S      82      E      50          4.097
LGA    L      83      E      51           #
LGA    D      84      A      52          1.964
LGA    G      85      P      53          2.218
LGA    P      86      N      54          4.042
LGA    A      87      V      55          1.196
LGA    P      88      Q      56          2.989
LGA    P      89      -       -           -
LGA    K      90      E      63           #
LGA    V      91      W      64          4.800
LGA    M      92      A      65          4.681
LGA    K      93      I      66          3.552
LGA    R      94      E      67          3.505
LGA    L      95      V      68          2.476
LGA    S      96      L      69          1.432
LGA    L      97      E      70          1.860
LGA    A      98      R      71          2.255
LGA    L      99      I      72          2.162
LGA    Q     100      R      73          2.255
LGA    K     101      D      74          2.100
LGA    L     102      G      75          3.659
LGA    T     103      E      76          4.866
LGA    -       -      N      77           -
LGA    -       -      V      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      V      81           -
LGA    -       -      S      82           -
LGA    -       -      L      83           -
LGA    -       -      D      84           -
LGA    -       -      G      85           -
LGA    -       -      P      86           -
LGA    -       -      A      87           -
LGA    -       -      P      88           -
LGA    -       -      P      89           -
LGA    -       -      K      90           -
LGA    -       -      V      91           -
LGA    E     104      M      92          3.142
LGA    -       -      K      93           -
LGA    -       -      R      94           -
LGA    -       -      L      95           -
LGA    -       -      S      96           -
LGA    -       -      L      97           -
LGA    -       -      A      98           -
LGA    -       -      L      99           -
LGA    -       -      Q     100           -
LGA    -       -      K     101           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  104   94    5.0     40    3.31     5.00     24.737     1.173

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.741047 * X  +  -0.426853 * Y  +  -0.518311 * Z  +  23.595753
  Y_new =   0.662560 * X  +   0.339635 * Y  +   0.667580 * Z  +  23.598816
  Z_new =  -0.108922 * X  +  -0.838120 * Y  +   0.534501 * Z  +  12.766040 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.003089    2.138503  [ DEG:   -57.4728    122.5272 ]
  Theta =   0.109138    3.032454  [ DEG:     6.2532    173.7468 ]
  Phi   =   0.729538   -2.412055  [ DEG:    41.7994   -138.2006 ]
 
# 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: T0343TS393_2                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343TS393_2.T0343.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  104   94   5.0   40   3.31    5.00  24.737
REMARK  ---------------------------------------------------------- 
MOLECULE T0343TS393_2
PFRMAT TS
TARGET T0343
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      28.268  15.842  35.267  1.00 25.00           C
ATOM      2  CA  THR     2      28.664  15.144  31.524  1.00 25.00           C
ATOM      3  CA  TRP     3      26.682  15.603  28.258  1.00 25.00           C
ATOM      4  CA  ARG     4      28.702  18.206  26.414  1.00 25.00           C
ATOM      5  CA  GLU     5      30.064  15.165  24.524  1.00 25.00           C
ATOM      6  CA  ILE     6      30.065  17.165  21.258  1.00 25.00           C
ATOM      7  CA  LEU     7      31.933  20.028  22.983  1.00 25.00           C
ATOM      8  CA  ARG     8      34.515  17.551  24.350  1.00 25.00           C
ATOM      9  CA  LYS     9      36.399  14.279  23.549  1.00 25.00           C
ATOM     10  CA  GLU    10      36.335  13.603  19.775  1.00 25.00           C
ATOM     11  CA  GLY    11      35.009  10.136  20.297  1.00 25.00           C
ATOM     12  CA  PHE    12      32.259  11.181  17.818  1.00 25.00           C
ATOM     13  CA  LEU    13      33.016  14.502  16.070  1.00 25.00           C
ATOM     14  CA  ASP    14      31.936  13.010  12.713  1.00 25.00           C
ATOM     15  CA  LEU    15      28.684  11.748  14.292  1.00 25.00           C
ATOM     16  CA  GLY    16      28.023  15.221  15.766  1.00 25.00           C
ATOM     17  CA  GLU    17      28.634  16.819  12.339  1.00 25.00           C
ATOM     18  CA  PHE    18      26.212  14.332  10.721  1.00 25.00           C
ATOM     19  CA  ILE    19      22.412  14.466  10.674  1.00 25.00           C
ATOM     20  CA  VAL    20      21.405  17.392  12.888  1.00 25.00           C
ATOM     21  CA  GLU    21      23.950  19.114  15.031  1.00 25.00           C
ATOM     22  CA  LEU    22      24.213  21.760  12.338  1.00 25.00           C
ATOM     23  CA  VAL    23      25.223  24.179  15.131  1.00 25.00           C
ATOM     24  CA  TYR    24      27.688  26.680  16.640  1.00 25.00           C
ATOM     25  CA  ILE    25      28.859  27.885  20.116  1.00 25.00           C
ATOM     26  CA  ASP    26      31.095  29.430  22.789  1.00 25.00           C
ATOM     27  CA  CYS    27      32.699  31.184  25.762  1.00 25.00           C
ATOM     28  CA  PRO    28      36.390  31.999  25.615  1.00 25.00           C
ATOM     29  CA  CYS    29      38.943  29.527  24.221  1.00 25.00           C
ATOM     30  CA  GLU    30      41.521  31.628  22.403  1.00 25.00           C
ATOM     31  CA  PRO    31      41.549  29.132  19.510  1.00 25.00           C
ATOM     32  CA  ILE    32      37.767  29.536  18.900  1.00 25.00           C
ATOM     33  CA  PRO    33      34.311  27.865  18.955  1.00 25.00           C
ATOM     34  CA  PRO    34      32.281  24.915  17.644  1.00 25.00           C
ATOM     35  CA  THR    35      29.600  22.405  18.779  1.00 25.00           C
ATOM     36  CA  LEU    36      29.287  21.106  15.218  1.00 25.00           C
ATOM     37  CA  ALA    37      29.667  22.089  11.555  1.00 25.00           C
ATOM     38  CA  ILE    38      28.739  20.293   8.368  1.00 25.00           C
ATOM     39  CA  TYR    39      30.572  19.055   5.323  1.00 25.00           C
ATOM     40  CA  ASP    40      30.719  18.598   1.564  1.00 25.00           C
ATOM     41  CA  LYS    41      34.159  20.116   1.267  1.00 25.00           C
ATOM     42  CA  LYS    42      37.501  21.903   1.906  1.00 25.00           C
ATOM     43  CA  GLY    43      35.788  25.268   2.596  1.00 25.00           C
ATOM     44  CA  ASP    44      32.029  25.343   3.172  1.00 25.00           C
ATOM     45  CA  GLU    45      28.793  23.632   4.307  1.00 25.00           C
ATOM     46  CA  TRP    46      27.184  24.998   7.480  1.00 25.00           C
ATOM     47  CA  TYR    47      25.779  27.855   9.509  1.00 25.00           C
ATOM     48  CA  LYS    48      25.678  31.631  10.268  1.00 25.00           C
ATOM     49  CA  VAL    49      22.893  30.885  12.739  1.00 25.00           C
ATOM     50  CA  GLU    50      21.649  34.458  13.161  1.00 25.00           C
ATOM     51  CA  GLU    51      21.413  38.238  12.439  1.00 25.00           C
ATOM     52  CA  ALA    52      25.035  39.121  13.225  1.00 25.00           C
ATOM     53  CA  PRO    53      27.288  40.534  10.529  1.00 25.00           C
ATOM     54  CA  ASN    54      25.258  42.535   8.030  1.00 25.00           C
ATOM     55  CA  VAL    55      21.902  40.812   7.645  1.00 25.00           C
ATOM     56  CA  GLN    56      23.381  39.741   4.278  1.00 25.00           C
ATOM     57  CA  ASN    57      24.994  36.686   5.930  1.00 25.00           C
ATOM     58  CA  TYR    58      21.649  35.765   7.551  1.00 25.00           C
ATOM     59  CA  ARG    59      19.891  36.089   4.164  1.00 25.00           C
ATOM     60  CA  GLU    60      22.540  33.844   2.548  1.00 25.00           C
ATOM     61  CA  ALA    61      22.071  31.248   5.324  1.00 25.00           C
ATOM     62  CA  VAL    62      18.278  31.342   4.804  1.00 25.00           C
ATOM     63  CA  GLU    63      18.758  30.853   1.036  1.00 25.00           C
ATOM     64  CA  TRP    64      21.077  27.878   1.693  1.00 25.00           C
ATOM     65  CA  ALA    65      18.486  26.347   4.060  1.00 25.00           C
ATOM     66  CA  ILE    66      15.760  26.803   1.409  1.00 25.00           C
ATOM     67  CA  GLU    67      17.992  25.122  -1.210  1.00 25.00           C
ATOM     68  CA  VAL    68      18.636  22.198   1.179  1.00 25.00           C
ATOM     69  CA  LEU    69      14.873  21.842   1.796  1.00 25.00           C
ATOM     70  CA  GLU    70      14.230  21.837  -1.979  1.00 25.00           C
ATOM     71  CA  ARG    71      16.909  19.143  -2.458  1.00 25.00           C
ATOM     72  CA  ILE    72      15.316  17.031   0.311  1.00 25.00           C
ATOM     73  CA  ARG    73      11.883  17.406  -1.344  1.00 25.00           C
ATOM     74  CA  ASP    74      13.412  15.665  -4.332  1.00 25.00           C
ATOM     75  CA  GLY    75      15.390  12.731  -2.910  1.00 25.00           C
ATOM     76  CA  GLU    76      13.313  12.323   0.217  1.00 25.00           C
ATOM     77  CA  ASN    77      16.048  12.673   2.908  1.00 25.00           C
ATOM     78  CA  VAL    78      17.129  14.065   6.262  1.00 25.00           C
ATOM     79  CA  LYS    79      19.433  16.303   4.154  1.00 25.00           C
ATOM     80  CA  LEU    80      21.360  17.919   7.062  1.00 25.00           C
ATOM     81  CA  VAL    81      19.490  20.413   9.185  1.00 25.00           C
ATOM     82  CA  SER    82      17.468  23.289  10.707  1.00 25.00           C
ATOM     83  CA  LEU    83      15.974  26.584  11.770  1.00 25.00           C
ATOM     84  CA  ASP    84      12.242  27.201  11.953  1.00 25.00           C
ATOM     85  CA  GLY    85      11.162  30.708  13.014  1.00 25.00           C
ATOM     86  CA  PRO    86      11.261  33.750  15.349  1.00 25.00           C
ATOM     87  CA  ALA    87      15.026  33.666  14.656  1.00 25.00           C
ATOM     88  CA  PRO    88      17.252  33.326  17.727  1.00 25.00           C
ATOM     89  CA  PRO    89      15.754  32.875  21.212  1.00 25.00           C
ATOM     90  CA  LYS    90      12.466  31.140  20.295  1.00 25.00           C
ATOM     91  CA  VAL    91      14.193  29.354  17.380  1.00 25.00           C
ATOM     92  CA  MET    92      17.008  28.215  19.714  1.00 25.00           C
ATOM     93  CA  LYS    93      14.430  26.900  22.222  1.00 25.00           C
ATOM     94  CA  ARG    94      12.637  25.001  19.421  1.00 25.00           C
ATOM     95  CA  LEU    95      15.964  23.480  18.289  1.00 25.00           C
ATOM     96  CA  SER    96      16.728  22.412  21.887  1.00 25.00           C
ATOM     97  CA  LEU    97      13.262  20.809  22.173  1.00 25.00           C
ATOM     98  CA  ALA    98      13.828  18.938  18.880  1.00 25.00           C
ATOM     99  CA  LEU    99      17.224  17.696  20.142  1.00 25.00           C
ATOM    100  CA  GLN   100      15.604  16.503  23.401  1.00 25.00           C
ATOM    101  CA  LYS   101      12.898  14.664  21.411  1.00 25.00           C
ATOM    102  CA  LEU   102      15.584  13.000  19.247  1.00 25.00           C
ATOM    103  CA  THR   103      13.839  14.152  16.002  1.00 25.00           C
ATOM    104  CA  GLU   104      14.494  10.773  14.434  1.00 25.00           C
TER
END
