
#######################################################
#                                                     #
#                        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   28 (  112),  selected   28 , name T0348TS550_3
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS550_3.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D       2           -
LGA    -       -      A       3           -
LGA    -       -      K       4           -
LGA    -       -      F       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      I       8           -
LGA    -       -      L       9           -
LGA    -       -      V      10           -
LGA    -       -      C      11           -
LGA    -       -      P      12           -
LGA    -       -      L      13           -
LGA    P      17      C      14          2.878
LGA    L      18      K      15          3.126
LGA    V      19      G      16          2.685
LGA    -       -      P      17           -
LGA    -       -      L      18           -
LGA    -       -      V      19           -
LGA    -       -      F      20           -
LGA    -       -      D      21           -
LGA    -       -      K      22           -
LGA    -       -      S      23           -
LGA    -       -      K      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      L      27           -
LGA    F      20      I      28          5.308
LGA    D      21      C      29          2.461
LGA    K      22      K      30           -
LGA    -       -      G      31           -
LGA    -       -      D      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      A      35           -
LGA    S      23      F      36          0.752
LGA    K      24      P      37          2.972
LGA    -       -      I      38           -
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    D      25      P      43          2.026
LGA    E      26      M      44          2.936
LGA    L      27      M      45          1.886
LGA    I      28      L      46          3.020
LGA    C      29      E      47          3.078
LGA    -       -      S      48           -
LGA    K      30      E      49          4.782
LGA    G      31      A      50          2.787
LGA    D      32      R      51          2.019
LGA    R      33      E      52          3.064
LGA    L      34      -       -           -
LGA    A      35      -       -           -
LGA    F      36      -       -           -
LGA    P      37      -       -           -
LGA    I      38      -       -           -
LGA    V      59      -       -           -
LGA    K      60      L      53          3.920
LGA    L      61      A      54          3.715
LGA    E      62      P      55           #
LGA    -       -      E      56           -
LGA    H      63      E      57          3.105
LGA    H      64      E      58           #
LGA    -       -      V      59           -
LGA    -       -      K      60           -
LGA    -       -      L      61           -
LGA    -       -      E      62           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   28   61    5.0     19    3.13     0.00     19.136     0.587

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.308674 * X  +  -0.594141 * Y  +   0.742776 * Z  +   7.024774
  Y_new =   0.924270 * X  +   0.371756 * Y  +  -0.086732 * Z  +  22.593010
  Z_new =  -0.224600 * X  +   0.713298 * Y  +   0.663898 * Z  +  50.917606 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.821253   -2.320340  [ DEG:    47.0543   -132.9457 ]
  Theta =   0.226533    2.915060  [ DEG:    12.9794    167.0206 ]
  Phi   =   1.248477   -1.893116  [ DEG:    71.5325   -108.4675 ]
 
# 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: T0348TS550_3                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS550_3.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   28   61   5.0   19   3.13    0.00  19.136
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS550_3
PFRMAT TS
TARGET T0348
MODEL 3
PARENT 1wee_A
ATOM      1  N   PRO    17       4.119  26.512  63.628  1.00  0.00
ATOM      2  CA  PRO    17       5.568  26.594  63.644  1.00  0.00
ATOM      3  C   PRO    17       6.060  27.576  62.574  1.00  0.00
ATOM      4  O   PRO    17       6.018  27.278  61.377  1.00  0.00
ATOM      5  N   LEU    18       6.520  28.740  63.010  1.00  0.00
ATOM      6  CA  LEU    18       7.023  29.757  62.098  1.00  0.00
ATOM      7  C   LEU    18       8.527  29.940  62.247  1.00  0.00
ATOM      8  O   LEU    18       8.990  30.676  63.105  1.00  0.00
ATOM      9  N   VAL    19       9.319  28.709  62.717  1.00  0.00
ATOM     10  CA  VAL    19      10.774  28.655  62.548  1.00  0.00
ATOM     11  C   VAL    19      11.349  27.315  62.089  1.00  0.00
ATOM     12  O   VAL    19      12.567  27.113  62.188  1.00  0.00
ATOM     13  N   PHE    20      10.508  26.409  61.588  1.00  0.00
ATOM     14  CA  PHE    20      10.997  25.097  61.156  1.00  0.00
ATOM     15  C   PHE    20      11.388  25.056  59.688  1.00  0.00
ATOM     16  O   PHE    20      12.568  25.131  59.340  1.00  0.00
ATOM     17  N   ASP    21      10.389  24.919  58.829  1.00  0.00
ATOM     18  CA  ASP    21      10.620  24.873  57.394  1.00  0.00
ATOM     19  C   ASP    21       9.580  25.737  56.701  1.00  0.00
ATOM     20  O   ASP    21       8.430  25.825  57.148  1.00  0.00
ATOM     21  N   LYS    22       9.993  26.373  55.608  1.00  0.00
ATOM     22  CA  LYS    22       9.115  27.249  54.845  1.00  0.00
ATOM     23  C   LYS    22       8.743  26.657  53.498  1.00  0.00
ATOM     24  O   LYS    22       9.556  26.633  52.576  1.00  0.00
ATOM     25  N   SER    23       7.513  26.161  53.404  1.00  0.00
ATOM     26  CA  SER    23       7.019  25.609  52.159  1.00  0.00
ATOM     27  C   SER    23       6.322  26.772  51.486  1.00  0.00
ATOM     28  O   SER    23       6.688  27.928  51.719  1.00  0.00
ATOM     29  N   LYS    24       5.318  26.487  50.665  1.00  0.00
ATOM     30  CA  LYS    24       4.566  27.540  49.977  1.00  0.00
ATOM     31  C   LYS    24       4.528  28.881  50.740  1.00  0.00
ATOM     32  O   LYS    24       3.866  29.001  51.775  1.00  0.00
ATOM     33  N   ASP    25       5.275  29.893  50.257  1.00  0.00
ATOM     34  CA  ASP    25       5.267  31.192  50.937  1.00  0.00
ATOM     35  C   ASP    25       3.952  32.009  50.898  1.00  0.00
ATOM     36  O   ASP    25       3.819  33.009  50.172  1.00  0.00
ATOM     37  N   GLU    26       2.990  31.536  51.696  1.00  0.00
ATOM     38  CA  GLU    26       1.681  32.162  51.910  1.00  0.00
ATOM     39  C   GLU    26       1.978  32.927  53.209  1.00  0.00
ATOM     40  O   GLU    26       1.085  33.384  53.925  1.00  0.00
ATOM     41  N   LEU    27       3.315  33.837  54.066  1.00  0.00
ATOM     42  CA  LEU    27       4.000  32.593  54.388  1.00  0.00
ATOM     43  C   LEU    27       3.155  31.393  53.987  1.00  0.00
ATOM     44  O   LEU    27       1.984  31.528  53.642  1.00  0.00
ATOM     45  N   ILE    28       3.758  30.200  54.045  1.00  0.00
ATOM     46  CA  ILE    28       3.055  28.975  53.692  1.00  0.00
ATOM     47  C   ILE    28       3.558  27.798  54.528  1.00  0.00
ATOM     48  O   ILE    28       4.750  27.673  54.759  1.00  0.00
ATOM     49  N   CYS    29       2.638  26.945  54.963  1.00  0.00
ATOM     50  CA  CYS    29       2.989  25.788  55.760  1.00  0.00
ATOM     51  C   CYS    29       3.459  24.637  54.873  1.00  0.00
ATOM     52  O   CYS    29       2.885  24.386  53.811  1.00  0.00
ATOM     53  N   LYS    30       4.492  24.263  55.078  1.00  0.00
ATOM     54  CA  LYS    30       5.144  23.117  54.434  1.00  0.00
ATOM     55  C   LYS    30       4.180  21.954  54.433  1.00  0.00
ATOM     56  O   LYS    30       3.582  21.647  55.460  1.00  0.00
ATOM     57  N   GLY    31       4.008  21.319  53.277  1.00  0.00
ATOM     58  CA  GLY    31       3.079  20.206  53.155  1.00  0.00
ATOM     59  C   GLY    31       3.483  19.005  53.990  1.00  0.00
ATOM     60  O   GLY    31       2.639  18.212  54.414  1.00  0.00
ATOM     61  N   ASP    32       4.773  18.853  54.221  1.00  0.00
ATOM     62  CA  ASP    32       5.250  17.716  55.002  1.00  0.00
ATOM     63  C   ASP    32       5.369  17.941  56.522  1.00  0.00
ATOM     64  O   ASP    32       4.857  17.144  57.305  1.00  0.00
ATOM     65  N   ARG    33       6.034  19.018  56.933  1.00  0.00
ATOM     66  CA  ARG    33       6.233  19.231  58.361  1.00  0.00
ATOM     67  C   ARG    33       5.409  20.397  58.977  1.00  0.00
ATOM     68  O   ARG    33       5.587  20.760  60.150  1.00  0.00
ATOM     69  N   LEU    34       4.526  20.988  58.156  1.00  0.00
ATOM     70  CA  LEU    34       3.615  22.058  58.594  1.00  0.00
ATOM     71  C   LEU    34       4.275  23.335  59.166  1.00  0.00
ATOM     72  O   LEU    34       3.618  24.124  59.826  1.00  0.00
ATOM     73  N   ALA    35       5.339  23.631  58.618  1.00  0.00
ATOM     74  CA  ALA    35       6.057  24.803  59.082  1.00  0.00
ATOM     75  C   ALA    35       5.896  25.964  58.118  1.00  0.00
ATOM     76  O   ALA    35       6.108  25.817  56.913  1.00  0.00
ATOM     77  N   PHE    36       5.512  27.120  58.654  1.00  0.00
ATOM     78  CA  PHE    36       5.323  28.315  57.832  1.00  0.00
ATOM     79  C   PHE    36       6.659  28.916  57.425  1.00  0.00
ATOM     80  O   PHE    36       7.534  29.132  58.266  1.00  0.00
ATOM     81  N   PRO    37       6.810  29.190  56.132  1.00  0.00
ATOM     82  CA  PRO    37       8.040  29.779  55.616  1.00  0.00
ATOM     83  C   PRO    37       7.744  31.014  54.768  1.00  0.00
ATOM     84  O   PRO    37       6.609  31.222  54.332  1.00  0.00
ATOM     85  N   ILE    38       8.770  31.827  54.540  1.00  0.00
ATOM     86  CA  ILE    38       8.618  33.039  53.754  1.00  0.00
ATOM     87  C   ILE    38       8.494  32.709  52.267  1.00  0.00
ATOM     88  O   ILE    38       9.447  32.260  51.640  1.00  0.00
ATOM     89  N   VAL    59      13.417  21.155  53.248  1.00  0.00
ATOM     90  CA  VAL    59      14.635  20.356  53.151  1.00  0.00
ATOM     91  C   VAL    59      14.612  19.217  54.174  1.00  0.00
ATOM     92  O   VAL    59      15.085  18.118  53.907  1.00  0.00
ATOM     93  N   LYS    60      14.068  19.511  55.348  1.00  0.00
ATOM     94  CA  LYS    60      13.989  18.510  56.421  1.00  0.00
ATOM     95  C   LYS    60      13.083  17.352  56.017  1.00  0.00
ATOM     96  O   LYS    60      13.306  16.216  56.417  1.00  0.00
ATOM     97  N   LEU    61      12.061  17.663  55.228  1.00  0.00
ATOM     98  CA  LEU    61      11.112  16.647  54.771  1.00  0.00
ATOM     99  C   LEU    61      11.777  15.705  53.769  1.00  0.00
ATOM    100  O   LEU    61      11.593  14.486  53.845  1.00  0.00
ATOM    101  N   GLU    62      12.529  16.277  52.836  1.00  0.00
ATOM    102  CA  GLU    62      13.209  15.489  51.822  1.00  0.00
ATOM    103  C   GLU    62      13.658  14.144  52.379  1.00  0.00
ATOM    104  O   GLU    62      13.501  13.100  51.740  1.00  0.00
ATOM    105  N   HIS    63      14.219  14.165  53.592  1.00  0.00
ATOM    106  CA  HIS    63      14.684  12.944  54.237  1.00  0.00
ATOM    107  C   HIS    63      13.619  12.377  55.159  1.00  0.00
ATOM    108  O   HIS    63      13.540  11.165  55.361  1.00  0.00
ATOM    109  N   HIS    64      12.804  13.254  55.734  1.00  0.00
ATOM    110  CA  HIS    64      11.739  12.843  56.631  1.00  0.00
ATOM    111  C   HIS    64      10.804  11.846  55.965  1.00  0.00
ATOM    112  O   HIS    64      10.430  10.826  56.551  1.00  0.00
TER
END
