
#######################################################
#                                                     #
#                        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   29 (  116),  selected   29 , name T0343AL381_3
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343AL381_3.T0343.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T       2           -
LGA    -       -      W       3           -
LGA    -       -      R       4           -
LGA    -       -      E       5           -
LGA    -       -      I       6           -
LGA    -       -      L       7           -
LGA    -       -      R       8           -
LGA    -       -      K       9           -
LGA    -       -      E      10           -
LGA    K       9      G      11           #
LGA    E      10      F      12           -
LGA    G      11      L      13           -
LGA    F      12      D      14           -
LGA    L      13      L      15           -
LGA    D      14      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           -
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           -
LGA    -       -      T      35           -
LGA    -       -      L      36           -
LGA    -       -      A      37           -
LGA    -       -      I      38           -
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      49           -
LGA    -       -      E      50           -
LGA    -       -      E      51           -
LGA    -       -      A      52           -
LGA    -       -      P      53           -
LGA    -       -      N      54           -
LGA    -       -      V      55           -
LGA    L      15      Q      56          5.039
LGA    G      16      E      63          3.027
LGA    -       -      W      64           -
LGA    E      17      A      65          0.465
LGA    F      18      I      66          0.499
LGA    I      19      E      67          1.069
LGA    V      20      V      68          0.908
LGA    E      21      L      69          0.568
LGA    L      22      E      70          1.159
LGA    V      23      R      71          0.361
LGA    Y      24      I      72          1.259
LGA    I      25      R      73          1.326
LGA    D      26      D      74          1.406
LGA    C      27      G      75          0.295
LGA    P      28      E      76          0.766
LGA    C      29      N      77          1.404
LGA    E      30      V      78          1.454
LGA    P      31      K      79          3.660
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    -       -      M      92           -
LGA    -       -      K      93           -
LGA    -       -      R      94           -
LGA    I      32      L      95          4.519
LGA    P      33      S      96          2.168
LGA    -       -      L      97           -
LGA    P      34      A      98          4.458
LGA    T      35      L      99          4.781
LGA    L      36      Q     100           -
LGA    A      37      K     101           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   29   94    5.0     21    2.49     9.52     19.063     0.811

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.837915 * X  +   0.524346 * Y  +   0.151526 * Z  +  22.651934
  Y_new =  -0.540379 * X  +   0.836016 * Y  +   0.095229 * Z  +  21.535868
  Z_new =  -0.076745 * X  +  -0.161675 * Y  +   0.983855 * Z  +  31.900715 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.162872    2.978720  [ DEG:    -9.3319    170.6681 ]
  Theta =   0.076820    3.064772  [ DEG:     4.4015    175.5985 ]
  Phi   =  -0.572788    2.568805  [ DEG:   -32.8183    147.1817 ]
 
# 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: T0343AL381_3                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343AL381_3.T0343.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   29   94   5.0   21   2.49    9.52  19.063
REMARK  ---------------------------------------------------------- 
MOLECULE T0343AL381_3
REMARK Aligment from pdb entry: 1f8hA
ATOM      1  N   LYS     9      29.389  26.958  23.614  1.00  0.00              
ATOM      2  CA  LYS     9      29.890  26.273  24.843  1.00  0.00              
ATOM      3  C   LYS     9      30.066  27.288  25.976  1.00  0.00              
ATOM      4  O   LYS     9      31.062  27.289  26.672  1.00  0.00              
ATOM      5  N   GLU    10      29.109  28.151  26.163  1.00  0.00              
ATOM      6  CA  GLU    10      29.224  29.166  27.248  1.00  0.00              
ATOM      7  C   GLU    10      28.284  28.809  28.398  1.00  0.00              
ATOM      8  O   GLU    10      28.083  29.583  29.314  1.00  0.00              
ATOM      9  N   GLY    11      27.702  27.644  28.357  1.00  0.00              
ATOM     10  CA  GLY    11      26.774  27.242  29.444  1.00  0.00              
ATOM     11  C   GLY    11      25.408  27.893  29.210  1.00  0.00              
ATOM     12  O   GLY    11      24.639  28.081  30.132  1.00  0.00              
ATOM     13  N   PHE    12      25.092  28.226  27.985  1.00  0.00              
ATOM     14  CA  PHE    12      23.762  28.852  27.699  1.00  0.00              
ATOM     15  C   PHE    12      23.320  28.535  26.270  1.00  0.00              
ATOM     16  O   PHE    12      24.120  28.181  25.426  1.00  0.00              
ATOM     17  N   LEU    13      22.055  28.679  25.987  1.00  0.00              
ATOM     18  CA  LEU    13      21.564  28.405  24.608  1.00  0.00              
ATOM     19  C   LEU    13      20.999  29.691  23.995  1.00  0.00              
ATOM     20  O   LEU    13      19.904  30.109  24.311  1.00  0.00              
ATOM     21  N   ASP    14      21.734  30.321  23.119  1.00  0.00              
ATOM     22  CA  ASP    14      21.227  31.575  22.495  1.00  0.00              
ATOM     23  C   ASP    14      20.061  31.260  21.559  1.00  0.00              
ATOM     24  O   ASP    14      19.735  30.116  21.313  1.00  0.00              
ATOM     25  N   LEU    15      19.430  32.273  21.047  1.00  0.00              
ATOM     26  CA  LEU    15      18.272  32.049  20.135  1.00  0.00              
ATOM     27  C   LEU    15      18.631  31.048  19.033  1.00  0.00              
ATOM     28  O   LEU    15      17.794  30.299  18.570  1.00  0.00              
ATOM     29  N   GLY    16      19.862  31.024  18.610  1.00  0.00              
ATOM     30  CA  GLY    16      20.255  30.063  17.541  1.00  0.00              
ATOM     31  C   GLY    16      20.668  28.734  18.168  1.00  0.00              
ATOM     32  O   GLY    16      20.491  27.680  17.593  1.00  0.00              
ATOM     33  N   GLU    17      21.200  28.775  19.357  1.00  0.00              
ATOM     34  CA  GLU    17      21.603  27.512  20.031  1.00  0.00              
ATOM     35  C   GLU    17      20.364  26.849  20.619  1.00  0.00              
ATOM     36  O   GLU    17      20.189  25.650  20.546  1.00  0.00              
ATOM     37  N   PHE    18      19.490  27.633  21.188  1.00  0.00              
ATOM     38  CA  PHE    18      18.247  27.065  21.765  1.00  0.00              
ATOM     39  C   PHE    18      17.414  26.448  20.643  1.00  0.00              
ATOM     40  O   PHE    18      16.614  25.559  20.859  1.00  0.00              
ATOM     41  N   ILE    19      17.607  26.911  19.438  1.00  0.00              
ATOM     42  CA  ILE    19      16.834  26.349  18.294  1.00  0.00              
ATOM     43  C   ILE    19      17.302  24.925  17.998  1.00  0.00              
ATOM     44  O   ILE    19      16.518  23.996  17.914  1.00  0.00              
ATOM     45  N   VAL    20      18.584  24.752  17.838  1.00  0.00              
ATOM     46  CA  VAL    20      19.127  23.397  17.544  1.00  0.00              
ATOM     47  C   VAL    20      18.722  22.410  18.645  1.00  0.00              
ATOM     48  O   VAL    20      18.650  21.214  18.427  1.00  0.00              
ATOM     49  N   GLU    21      18.474  22.897  19.831  1.00  0.00              
ATOM     50  CA  GLU    21      18.096  21.981  20.948  1.00  0.00              
ATOM     51  C   GLU    21      16.578  21.759  21.010  1.00  0.00              
ATOM     52  O   GLU    21      16.097  20.971  21.798  1.00  0.00              
ATOM     53  N   LEU    22      15.819  22.439  20.193  1.00  0.00              
ATOM     54  CA  LEU    22      14.338  22.240  20.231  1.00  0.00              
ATOM     55  C   LEU    22      13.931  21.103  19.298  1.00  0.00              
ATOM     56  O   LEU    22      13.140  20.253  19.653  1.00  0.00              
ATOM     57  N   VAL    23      14.473  21.062  18.116  1.00  0.00              
ATOM     58  CA  VAL    23      14.110  19.951  17.193  1.00  0.00              
ATOM     59  C   VAL    23      14.872  18.700  17.627  1.00  0.00              
ATOM     60  O   VAL    23      14.476  17.583  17.355  1.00  0.00              
ATOM     61  N   TYR    24      15.955  18.889  18.336  1.00  0.00              
ATOM     62  CA  TYR    24      16.738  17.728  18.835  1.00  0.00              
ATOM     63  C   TYR    24      15.984  17.091  20.002  1.00  0.00              
ATOM     64  O   TYR    24      16.135  15.923  20.295  1.00  0.00              
ATOM     65  N   ILE    25      15.160  17.862  20.661  1.00  0.00              
ATOM     66  CA  ILE    25      14.371  17.320  21.802  1.00  0.00              
ATOM     67  C   ILE    25      13.019  16.806  21.309  1.00  0.00              
ATOM     68  O   ILE    25      12.538  15.778  21.740  1.00  0.00              
ATOM     69  N   ASP    26      12.397  17.523  20.414  1.00  0.00              
ATOM     70  CA  ASP    26      11.069  17.082  19.901  1.00  0.00              
ATOM     71  C   ASP    26      11.220  15.864  18.990  1.00  0.00              
ATOM     72  O   ASP    26      10.291  15.103  18.797  1.00  0.00              
ATOM     73  N   CYS    27      12.380  15.666  18.432  1.00  0.00              
ATOM     74  CA  CYS    27      12.575  14.491  17.543  1.00  0.00              
ATOM     75  C   CYS    27      12.887  13.252  18.382  1.00  0.00              
ATOM     76  O   CYS    27      12.709  12.132  17.945  1.00  0.00              
ATOM     77  N   PRO    28      13.340  13.443  19.591  1.00  0.00              
ATOM     78  CA  PRO    28      13.646  12.274  20.459  1.00  0.00              
ATOM     79  C   PRO    28      12.354  11.751  21.076  1.00  0.00              
ATOM     80  O   PRO    28      12.304  10.674  21.636  1.00  0.00              
ATOM     81  N   CYS    29      11.303  12.515  20.976  1.00  0.00              
ATOM     82  CA  CYS    29      10.005  12.079  21.552  1.00  0.00              
ATOM     83  C   CYS    29       9.181  11.319  20.515  1.00  0.00              
ATOM     84  O   CYS    29       8.533  10.337  20.820  1.00  0.00              
ATOM     85  N   GLU    30       9.175  11.783  19.296  1.00  0.00              
ATOM     86  CA  GLU    30       8.362  11.103  18.250  1.00  0.00              
ATOM     87  C   GLU    30       9.212  10.723  17.025  1.00  0.00              
ATOM     88  O   GLU    30       8.748  10.026  16.143  1.00  0.00              
ATOM     89  N   PRO    31      10.433  11.172  16.942  1.00  0.00              
ATOM     90  CA  PRO    31      11.255  10.815  15.743  1.00  0.00              
ATOM     91  C   PRO    31      12.390   9.853  16.103  1.00  0.00              
ATOM     92  O   PRO    31      12.232   8.649  16.047  1.00  0.00              
ATOM     93  N   ILE    32      13.536  10.368  16.456  1.00  0.00              
ATOM     94  CA  ILE    32      14.679   9.470  16.796  1.00  0.00              
ATOM     95  C   ILE    32      15.542  10.087  17.898  1.00  0.00              
ATOM     96  O   ILE    32      15.344  11.219  18.281  1.00  0.00              
ATOM     97  N   PRO    33      16.480   9.310  18.368  1.00  0.00              
ATOM     98  CA  PRO    33      17.391   9.776  19.444  1.00  0.00              
ATOM     99  C   PRO    33      18.306  10.890  18.930  1.00  0.00              
ATOM    100  O   PRO    33      18.106  11.426  17.858  1.00  0.00              
ATOM    101  N   PRO    34      19.301  11.251  19.692  1.00  0.00              
ATOM    102  CA  PRO    34      20.220  12.338  19.256  1.00  0.00              
ATOM    103  C   PRO    34      21.677  11.879  19.343  1.00  0.00              
ATOM    104  O   PRO    34      22.072  11.257  20.309  1.00  0.00              
ATOM    105  N   THR    35      22.436  12.219  18.336  1.00  0.00              
ATOM    106  CA  THR    35      23.863  11.856  18.314  1.00  0.00              
ATOM    107  C   THR    35      24.644  12.912  19.094  1.00  0.00              
ATOM    108  O   THR    35      24.081  13.888  19.539  1.00  0.00              
ATOM    109  N   LEU    36      25.919  12.739  19.279  1.00  0.00              
ATOM    110  CA  LEU    36      26.684  13.765  20.043  1.00  0.00              
ATOM    111  C   LEU    36      27.592  14.555  19.112  1.00  0.00              
ATOM    112  O   LEU    36      28.544  15.174  19.544  1.00  0.00              
ATOM    113  N   ALA    37      27.340  14.520  17.842  1.00  0.00              
ATOM    114  CA  ALA    37      28.243  15.257  16.923  1.00  0.00              
ATOM    115  C   ALA    37      27.552  16.437  16.256  1.00  0.00              
ATOM    116  O   ALA    37      26.853  16.300  15.271  1.00  0.00              
END
