
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343TS393_1.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      -       -           -
LGA    R       4      T       2          1.295
LGA    E       5      -       -           -
LGA    I       6      W       3          4.372
LGA    L       7      -       -           -
LGA    R       8      -       -           -
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      -       -           -
LGA    Y      24      -       -           -
LGA    I      25      R       4          2.629
LGA    D      26      E       5          1.419
LGA    C      27      I       6           -
LGA    P      28      L       7           -
LGA    C      29      -       -           -
LGA    E      30      -       -           -
LGA    P      31      -       -           -
LGA    I      32      -       -           -
LGA    P      33      R       8           #
LGA    P      34      K       9          2.245
LGA    -       -      E      10           -
LGA    T      35      G      11          3.926
LGA    L      36      F      12          1.189
LGA    -       -      L      13           -
LGA    -       -      D      14           -
LGA    -       -      L      15           -
LGA    -       -      G      16           -
LGA    -       -      E      17           -
LGA    -       -      F      18           -
LGA    A      37      I      19          4.759
LGA    I      38      V      20           #
LGA    Y      39      E      21           -
LGA    D      40      L      22           -
LGA    K      41      -       -           -
LGA    K      42      -       -           -
LGA    G      43      -       -           -
LGA    D      44      -       -           -
LGA    E      45      -       -           -
LGA    W      46      -       -           -
LGA    Y      47      V      23           #
LGA    K      48      Y      24          4.321
LGA    V      49      I      25          3.909
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    E      50      P      34           #
LGA    E      51      -       -           -
LGA    A      52      -       -           -
LGA    P      53      -       -           -
LGA    N      54      -       -           -
LGA    V      55      -       -           -
LGA    Q      56      -       -           -
LGA    N      57      -       -           -
LGA    Y      58      -       -           -
LGA    R      59      -       -           -
LGA    E      60      -       -           -
LGA    A      61      -       -           -
LGA    V      62      T      35          4.226
LGA    E      63      -       -           -
LGA    W      64      L      36           #
LGA    A      65      A      37          2.138
LGA    I      66      I      38           -
LGA    E      67      Y      39           #
LGA    -       -      D      40           -
LGA    -       -      K      41           -
LGA    -       -      K      42           -
LGA    -       -      G      43           -
LGA    -       -      D      44           -
LGA    V      68      E      45          4.785
LGA    L      69      W      46          3.211
LGA    E      70      Y      47          5.097
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      -       -           -
LGA    L      80      -       -           -
LGA    V      81      K      48          4.508
LGA    S      82      V      49          0.570
LGA    L      83      E      50          2.963
LGA    D      84      E      51          1.283
LGA    G      85      A      52          1.482
LGA    P      86      P      53          2.291
LGA    A      87      N      54          2.415
LGA    P      88      V      55          3.602
LGA    P      89      Q      56           -
LGA    K      90      E      63           -
LGA    -       -      W      64           -
LGA    -       -      A      65           -
LGA    -       -      I      66           -
LGA    V      91      E      67          4.065
LGA    M      92      -       -           -
LGA    K      93      -       -           -
LGA    R      94      V      68           #
LGA    L      95      L      69          4.857
LGA    S      96      E      70          0.690
LGA    L      97      R      71          4.449
LGA    A      98      I      72          4.704
LGA    L      99      R      73          1.437
LGA    Q     100      D      74          2.150
LGA    K     101      G      75          2.806
LGA    L     102      E      76          1.712
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    T     103      M      92          4.267
LGA    E     104      K      93          3.812
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     34    3.34     8.82     20.274     0.988

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.543103 * X  +  -0.288102 * Y  +  -0.788693 * Z  +  23.570948
  Y_new =  -0.593572 * X  +   0.796093 * Y  +   0.117935 * Z  +  20.448797
  Z_new =   0.593895 * X  +   0.532197 * Y  +  -0.603369 * Z  +  14.576689 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.418788   -0.722805  [ DEG:   138.5863    -41.4137 ]
  Theta =  -0.635892   -2.505701  [ DEG:   -36.4339   -143.5661 ]
  Phi   =  -2.311823    0.829770  [ DEG:  -132.4577     47.5423 ]
 
# 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_1                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343TS393_1.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   34   3.34    8.82  20.274
REMARK  ---------------------------------------------------------- 
MOLECULE T0343TS393_1
PFRMAT TS
TARGET T0343
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      24.393   8.889  35.151  1.00 25.00           C
ATOM      2  CA  THR     2      24.284  10.785  31.859  1.00 25.00           C
ATOM      3  CA  TRP     3      24.493  13.945  29.752  1.00 25.00           C
ATOM      4  CA  ARG     4      27.619  15.741  28.736  1.00 25.00           C
ATOM      5  CA  GLU     5      29.533  13.494  26.297  1.00 25.00           C
ATOM      6  CA  ILE     6      28.416  15.685  23.361  1.00 25.00           C
ATOM      7  CA  LEU     7      29.566  18.822  25.234  1.00 25.00           C
ATOM      8  CA  ARG     8      32.960  17.191  25.933  1.00 25.00           C
ATOM      9  CA  LYS     9      34.477  14.152  27.605  1.00 25.00           C
ATOM     10  CA  GLU    10      36.167  13.278  24.280  1.00 25.00           C
ATOM     11  CA  GLY    11      34.331   9.969  23.748  1.00 25.00           C
ATOM     12  CA  PHE    12      31.995   9.675  20.688  1.00 25.00           C
ATOM     13  CA  LEU    13      31.321  13.201  19.356  1.00 25.00           C
ATOM     14  CA  ASP    14      32.101  12.032  15.793  1.00 25.00           C
ATOM     15  CA  LEU    15      29.715   9.066  16.219  1.00 25.00           C
ATOM     16  CA  GLY    16      26.975  11.420  17.489  1.00 25.00           C
ATOM     17  CA  GLU    17      27.524  13.723  14.479  1.00 25.00           C
ATOM     18  CA  PHE    18      27.284  10.725  12.110  1.00 25.00           C
ATOM     19  CA  ILE    19      23.738  10.427  13.477  1.00 25.00           C
ATOM     20  CA  VAL    20      22.264  13.345  15.425  1.00 25.00           C
ATOM     21  CA  GLU    21      23.231  15.686  12.616  1.00 25.00           C
ATOM     22  CA  LEU    22      23.891  18.952  14.482  1.00 25.00           C
ATOM     23  CA  VAL    23      25.496  17.483  17.584  1.00 25.00           C
ATOM     24  CA  TYR    24      24.896  19.275  20.906  1.00 25.00           C
ATOM     25  CA  ILE    25      25.804  22.105  23.354  1.00 25.00           C
ATOM     26  CA  ASP    26      26.723  24.612  26.114  1.00 25.00           C
ATOM     27  CA  CYS    27      27.223  27.605  28.424  1.00 25.00           C
ATOM     28  CA  PRO    28      25.828  28.064  31.976  1.00 25.00           C
ATOM     29  CA  CYS    29      29.324  29.364  32.725  1.00 25.00           C
ATOM     30  CA  GLU    30      32.819  30.631  31.885  1.00 25.00           C
ATOM     31  CA  PRO    31      34.403  30.220  28.483  1.00 25.00           C
ATOM     32  CA  ILE    32      32.237  27.806  26.576  1.00 25.00           C
ATOM     33  CA  PRO    33      31.011  26.971  23.088  1.00 25.00           C
ATOM     34  CA  PRO    34      28.988  25.017  20.576  1.00 25.00           C
ATOM     35  CA  THR    35      29.633  21.331  19.700  1.00 25.00           C
ATOM     36  CA  LEU    36      28.710  21.431  15.976  1.00 25.00           C
ATOM     37  CA  ALA    37      29.261  18.371  13.783  1.00 25.00           C
ATOM     38  CA  ILE    38      30.497  16.211  10.870  1.00 25.00           C
ATOM     39  CA  TYR    39      31.471  18.617   8.081  1.00 25.00           C
ATOM     40  CA  ASP    40      34.286  17.708   5.734  1.00 25.00           C
ATOM     41  CA  LYS    41      36.501  20.006   3.576  1.00 25.00           C
ATOM     42  CA  LYS    42      34.923  23.089   2.017  1.00 25.00           C
ATOM     43  CA  GLY    43      31.932  24.694   0.291  1.00 25.00           C
ATOM     44  CA  ASP    44      28.224  23.644   0.393  1.00 25.00           C
ATOM     45  CA  GLU    45      24.498  24.275   0.883  1.00 25.00           C
ATOM     46  CA  TRP    46      23.264  26.226   3.884  1.00 25.00           C
ATOM     47  CA  TYR    47      21.485  28.543   6.301  1.00 25.00           C
ATOM     48  CA  LYS    48      22.679  31.502   8.349  1.00 25.00           C
ATOM     49  CA  VAL    49      20.671  30.596  11.423  1.00 25.00           C
ATOM     50  CA  GLU    50      20.792  33.449  13.949  1.00 25.00           C
ATOM     51  CA  GLU    51      21.234  37.052  12.908  1.00 25.00           C
ATOM     52  CA  ALA    52      24.528  37.197  14.899  1.00 25.00           C
ATOM     53  CA  PRO    53      27.172  38.173  12.364  1.00 25.00           C
ATOM     54  CA  ASN    54      30.618  36.848  13.430  1.00 25.00           C
ATOM     55  CA  VAL    55      28.759  33.561  14.155  1.00 25.00           C
ATOM     56  CA  GLN    56      31.377  31.173  12.704  1.00 25.00           C
ATOM     57  CA  ASN    57      30.047  28.337  14.909  1.00 25.00           C
ATOM     58  CA  TYR    58      26.475  29.073  13.743  1.00 25.00           C
ATOM     59  CA  ARG    59      27.628  29.015  10.091  1.00 25.00           C
ATOM     60  CA  GLU    60      29.384  25.661  10.673  1.00 25.00           C
ATOM     61  CA  ALA    61      26.203  24.246  12.271  1.00 25.00           C
ATOM     62  CA  VAL    62      24.136  25.452   9.282  1.00 25.00           C
ATOM     63  CA  GLU    63      26.617  23.810   6.871  1.00 25.00           C
ATOM     64  CA  TRP    64      26.407  20.535   8.844  1.00 25.00           C
ATOM     65  CA  ALA    65      22.582  20.676   8.718  1.00 25.00           C
ATOM     66  CA  ILE    66      22.705  21.263   4.936  1.00 25.00           C
ATOM     67  CA  GLU    67      25.070  18.280   4.525  1.00 25.00           C
ATOM     68  CA  VAL    68      22.709  16.090   6.597  1.00 25.00           C
ATOM     69  CA  LEU    69      19.748  17.196   4.437  1.00 25.00           C
ATOM     70  CA  GLU    70      21.721  16.364   1.262  1.00 25.00           C
ATOM     71  CA  ARG    71      22.581  12.909   2.674  1.00 25.00           C
ATOM     72  CA  ILE    72      18.892  12.304   3.506  1.00 25.00           C
ATOM     73  CA  ARG    73      17.896  13.330  -0.046  1.00 25.00           C
ATOM     74  CA  ASP    74      15.875  10.986  -2.201  1.00 25.00           C
ATOM     75  CA  GLY    75      19.109   9.182  -3.182  1.00 25.00           C
ATOM     76  CA  GLU    76      20.264   7.217  -0.179  1.00 25.00           C
ATOM     77  CA  ASN    77      18.777   6.548   3.240  1.00 25.00           C
ATOM     78  CA  VAL    78      19.876   8.236   6.486  1.00 25.00           C
ATOM     79  CA  LYS    79      19.070   9.949   9.821  1.00 25.00           C
ATOM     80  CA  LEU    80      19.023  13.778   9.895  1.00 25.00           C
ATOM     81  CA  VAL    81      18.755  17.406  11.018  1.00 25.00           C
ATOM     82  CA  SER    82      16.429  18.902   8.382  1.00 25.00           C
ATOM     83  CA  LEU    83      16.764  22.510   9.715  1.00 25.00           C
ATOM     84  CA  ASP    84      13.342  23.702   8.509  1.00 25.00           C
ATOM     85  CA  GLY    85      12.823  27.400   9.328  1.00 25.00           C
ATOM     86  CA  PRO    86      11.979  30.618  11.171  1.00 25.00           C
ATOM     87  CA  ALA    87      15.586  31.070  12.291  1.00 25.00           C
ATOM     88  CA  PRO    88      16.261  31.207  16.000  1.00 25.00           C
ATOM     89  CA  PRO    89      13.237  31.008  18.226  1.00 25.00           C
ATOM     90  CA  LYS    90      11.126  28.860  15.861  1.00 25.00           C
ATOM     91  CA  VAL    91      14.251  26.921  14.791  1.00 25.00           C
ATOM     92  CA  MET    92      15.183  26.350  18.463  1.00 25.00           C
ATOM     93  CA  LYS    93      11.639  25.093  19.190  1.00 25.00           C
ATOM     94  CA  ARG    94      11.844  22.708  16.202  1.00 25.00           C
ATOM     95  CA  LEU    95      15.221  21.400  17.445  1.00 25.00           C
ATOM     96  CA  SER    96      13.748  20.845  20.938  1.00 25.00           C
ATOM     97  CA  LEU    97      10.787  18.953  19.415  1.00 25.00           C
ATOM     98  CA  ALA    98      13.193  16.771  17.386  1.00 25.00           C
ATOM     99  CA  LEU    99      15.223  16.028  20.547  1.00 25.00           C
ATOM    100  CA  GLN   100      12.017  15.075  22.412  1.00 25.00           C
ATOM    101  CA  LYS   101      11.006  12.755  19.537  1.00 25.00           C
ATOM    102  CA  LEU   102      14.468  11.120  19.605  1.00 25.00           C
ATOM    103  CA  THR   103      13.811   9.935  15.999  1.00 25.00           C
ATOM    104  CA  GLU   104      12.050   6.696  16.994  1.00 25.00           C
TER
END
