
#######################################################
#                                                     #
#                        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   19 (  149),  selected   19 , name T0382TS009_2_1
# Molecule2: number of CA atoms  121 (  929),  selected  121 , name T0382.pdb
# PARAMETERS: T0382TS009_2_1.T0382.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      K       3           -
LGA    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    -       -      T      11           -
LGA    -       -      Q      12           -
LGA    -       -      D      13           -
LGA    -       -      L      14           -
LGA    -       -      V      15           -
LGA    -       -      A      16           -
LGA    -       -      L      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      K      20           -
LGA    -       -      V      21           -
LGA    -       -      T      22           -
LGA    -       -      V      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      D      26           -
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    M       1      Q      33          1.243
LGA    S       2      I      34          0.898
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    K       3      F      37          1.454
LGA    L       4      N      38          3.693
LGA    D       5      R      39          2.505
LGA    L       6      L      40          1.798
LGA    H       7      F      41          1.626
LGA    Q       8      G      42          2.169
LGA    M       9      V      43          1.911
LGA    -       -      M      44           -
LGA    T      10      A      45          1.313
LGA    T      11      E      46          3.304
LGA    Q      12      I      47          3.465
LGA    D      13      A      48          1.561
LGA    -       -      D      49           -
LGA    L      14      E      50          0.370
LGA    V      15      L      51          2.128
LGA    -       -      K      52           -
LGA    A      16      A      53          2.196
LGA    L      17      R      54          2.324
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    F      18      D      57          3.622
LGA    A      19      Q      58          3.366
LGA    -       -      R      59           -
LGA    -       -      T      60           -
LGA    -       -      A      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      S      64           -
LGA    -       -      L      65           -
LGA    -       -      F      66           -
LGA    -       -      E      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      N      70           -
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    -       -      R      74           -
LGA    -       -      L      75           -
LGA    -       -      Q      76           -
LGA    -       -      A      77           -
LGA    -       -      A      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      T      81           -
LGA    -       -      L      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    -       -      V      87           -
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    -       -      R      90           -
LGA    -       -      E      91           -
LGA    -       -      Q      92           -
LGA    -       -      L      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    -       -      I      96           -
LGA    -       -      V      97           -
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
LGA    -       -      P     103           -
LGA    -       -      Q     104           -
LGA    -       -      A     105           -
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    -       -      C     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    -       -      P     122           -
LGA    -       -      K     123           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19  121    5.0     19    2.35    10.53     12.161     0.775

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.483449 * X  +  -0.818847 * Y  +  -0.309461 * Z  +  -5.935411
  Y_new =   0.494967 * X  +   0.547288 * Y  +  -0.674895 * Z  +  33.001148
  Z_new =   0.722000 * X  +   0.173104 * Y  +   0.669889 * Z  +  15.596538 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.252876   -2.888717  [ DEG:    14.4887   -165.5113 ]
  Theta =  -0.806689   -2.334904  [ DEG:   -46.2199   -133.7802 ]
  Phi   =   0.797170   -2.344423  [ DEG:    45.6745   -134.3255 ]
 
# 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: T0382TS009_2_1                                
REMARK     2: T0382.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_2_1.T0382.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19  121   5.0   19   2.35   10.53  12.161
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_2_1
REMARK PARENT number 1
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                      
ATOM      1  N   MET     1      -5.935  33.001  15.597  1.00  0.00              
ATOM      2  CA  MET     1      -4.654  32.835  14.852  1.00  0.00              
ATOM      3  C   MET     1      -4.453  33.962  13.844  1.00  0.00              
ATOM      4  O   MET     1      -4.311  33.718  12.646  1.00  0.00              
ATOM      5  CB  MET     1      -3.474  32.781  15.824  1.00  0.00              
ATOM      6  CG  MET     1      -2.324  31.904  15.355  1.00  0.00              
ATOM      7  SD  MET     1      -1.001  31.779  16.574  1.00  0.00              
ATOM      8  CE  MET     1      -0.026  30.446  15.880  1.00  0.00              
ATOM      9  N   SER     2      -4.440  35.196  14.338  1.00  0.00              
ATOM     10  CA  SER     2      -4.256  36.362  13.482  1.00  0.00              
ATOM     11  C   SER     2      -4.927  36.163  12.127  1.00  0.00              
ATOM     12  O   SER     2      -5.997  35.561  12.035  1.00  0.00              
ATOM     13  CB  SER     2      -4.807  37.618  14.162  1.00  0.00              
ATOM     14  OG  SER     2      -3.785  38.309  14.860  1.00  0.00              
ATOM     15  N   LYS     3      -4.290  36.672  11.077  1.00  0.00              
ATOM     16  CA  LYS     3      -4.823  36.551   9.726  1.00  0.00              
ATOM     17  C   LYS     3      -3.841  35.832   8.807  1.00  0.00              
ATOM     18  O   LYS     3      -2.757  35.434   9.232  1.00  0.00              
ATOM     19  CB  LYS     3      -6.163  35.813   9.742  1.00  0.00              
ATOM     20  CG  LYS     3      -7.320  36.614   9.167  1.00  0.00              
ATOM     21  CD  LYS     3      -8.568  35.757   9.023  1.00  0.00              
ATOM     22  CE  LYS     3      -9.716  36.551   8.420  1.00  0.00              
ATOM     23  NZ  LYS     3     -10.965  35.744   8.338  1.00  0.00              
ATOM     24  N   LEU     4      -4.227  35.670   7.546  1.00  0.00              
ATOM     25  CA  LEU     4      -3.381  35.000   6.566  1.00  0.00              
ATOM     26  C   LEU     4      -3.627  35.542   5.162  1.00  0.00              
ATOM     27  O   LEU     4      -3.124  36.606   4.801  1.00  0.00              
ATOM     28  CB  LEU     4      -1.905  35.152   6.938  1.00  0.00              
ATOM     29  CG  LEU     4      -1.157  33.863   7.287  1.00  0.00              
ATOM     30  CD1 LEU     4       0.321  33.994   6.955  1.00  0.00              
ATOM     31  CD2 LEU     4      -1.771  32.673   6.565  1.00  0.00              
ATOM     32  N   ASP     5      -4.404  34.806   4.375  1.00  0.00              
ATOM     33  CA  ASP     5      -4.718  35.212   3.011  1.00  0.00              
ATOM     34  C   ASP     5      -5.743  36.340   2.993  1.00  0.00              
ATOM     35  O   ASP     5      -5.391  37.513   3.119  1.00  0.00              
ATOM     36  CB  ASP     5      -3.447  35.643   2.275  1.00  0.00              
ATOM     37  CG  ASP     5      -2.958  34.596   1.294  1.00  0.00              
ATOM     38  OD1 ASP     5      -2.991  34.863   0.074  1.00  0.00              
ATOM     39  OD2 ASP     5      -2.542  33.508   1.745  1.00  0.00              
ATOM     40  N   LEU     6      -7.012  35.977   2.835  1.00  0.00              
ATOM     41  CA  LEU     6      -8.090  36.959   2.801  1.00  0.00              
ATOM     42  C   LEU     6      -7.736  38.196   3.619  1.00  0.00              
ATOM     43  O   LEU     6      -8.292  39.273   3.404  1.00  0.00              
ATOM     44  CB  LEU     6      -8.407  37.355   1.357  1.00  0.00              
ATOM     45  CG  LEU     6      -9.879  37.280   0.942  1.00  0.00              
ATOM     46  CD1 LEU     6     -10.201  38.350  -0.090  1.00  0.00              
ATOM     47  CD2 LEU     6     -10.787  37.409   2.156  1.00  0.00              
ATOM     48  N   HIS     7      -6.808  38.034   4.556  1.00  0.00              
ATOM     49  CA  HIS     7      -6.378  39.138   5.406  1.00  0.00              
ATOM     50  C   HIS     7      -6.175  40.413   4.595  1.00  0.00              
ATOM     51  O   HIS     7      -7.028  41.300   4.593  1.00  0.00              
ATOM     52  CB  HIS     7      -7.395  39.381   6.523  1.00  0.00              
ATOM     53  CG  HIS     7      -6.784  39.472   7.887  1.00  0.00              
ATOM     54  ND1 HIS     7      -5.573  38.893   8.201  1.00  0.00              
ATOM     55  CD2 HIS     7      -7.218  40.073   9.020  1.00  0.00              
ATOM     56  CE1 HIS     7      -5.288  39.136   9.468  1.00  0.00              
ATOM     57  NE2 HIS     7      -6.269  39.849   9.988  1.00  0.00              
ATOM     58  N   GLN     8      -5.041  40.498   3.908  1.00  0.00              
ATOM     59  CA  GLN     8      -4.724  41.663   3.093  1.00  0.00              
ATOM     60  C   GLN     8      -5.331  41.543   1.699  1.00  0.00              
ATOM     61  O   GLN     8      -5.927  42.490   1.187  1.00  0.00              
ATOM     62  CB  GLN     8      -5.217  42.943   3.772  1.00  0.00              
ATOM     63  CG  GLN     8      -4.203  44.076   3.774  1.00  0.00              
ATOM     64  CD  GLN     8      -4.799  45.391   4.237  1.00  0.00              
ATOM     65  OE1 GLN     8      -4.160  46.438   4.146  1.00  0.00              
ATOM     66  NE2 GLN     8      -6.029  45.339   4.734  1.00  0.00              
ATOM     67  N   MET     9      -5.174  40.372   1.090  1.00  0.00              
ATOM     68  CA  MET     9      -5.705  40.126  -0.245  1.00  0.00              
ATOM     69  C   MET     9      -6.438  41.351  -0.782  1.00  0.00              
ATOM     70  O   MET     9      -6.376  41.649  -1.975  1.00  0.00              
ATOM     71  CB  MET     9      -4.582  39.722  -1.202  1.00  0.00              
ATOM     72  CG  MET     9      -4.365  38.221  -1.308  1.00  0.00              
ATOM     73  SD  MET     9      -2.730  37.797  -1.938  1.00  0.00              
ATOM     74  CE  MET     9      -2.795  36.009  -1.871  1.00  0.00              
ATOM     75  N   THR    10      -7.129  42.057   0.106  1.00  0.00              
ATOM     76  CA  THR    10      -7.891  43.277  -0.285  1.00  0.00              
ATOM     77  C   THR    10      -7.186  44.031  -1.408  1.00  0.00              
ATOM     78  O   THR    10      -7.832  44.611  -2.281  1.00  0.00              
ATOM     79  CB  THR    10      -9.323  42.930  -0.734  1.00  0.00              
ATOM     80  OG1 THR    10      -9.452  41.509  -0.871  1.00  0.00              
ATOM     81  CG2 THR    10     -10.336  43.431   0.284  1.00  0.00              
ATOM     82  N   THR    11      -5.858  44.019  -1.379  1.00  0.00              
ATOM     83  CA  THR    11      -5.044  44.717  -2.416  1.00  0.00             
ATOM     84  C   THR    11      -5.507  44.346  -3.820  1.00  0.00             
ATOM     85  O   THR    11      -5.664  45.212  -4.682  1.00  0.00             
ATOM     86  CB  THR    11      -5.111  46.246  -2.251  1.00  0.00             
ATOM     87  OG1 THR    11      -6.153  46.586  -1.327  1.00  0.00             
ATOM     88  CG2 THR    11      -3.786  46.784  -1.733  1.00  0.00             
ATOM     89  N   GLN    12      -5.726  43.054  -4.045  1.00  0.00             
ATOM     90  CA  GLN    12      -6.171  42.567  -5.345  1.00  0.00             
ATOM     91  C   GLN    12      -7.295  43.433  -5.903  1.00  0.00             
ATOM     92  O   GLN    12      -7.495  43.503  -7.115  1.00  0.00             
ATOM     93  CB  GLN    12      -5.001  42.524  -6.330  1.00  0.00             
ATOM     94  CG  GLN    12      -4.987  41.294  -7.223  1.00  0.00             
ATOM     95  CD  GLN    12      -3.741  41.212  -8.082  1.00  0.00             
ATOM     96  OE1 GLN    12      -3.418  40.154  -8.624  1.00  0.00             
ATOM     97  NE2 GLN    12      -3.035  42.330  -8.207  1.00  0.00             
ATOM     98  N   ASP    13      -8.026  44.092  -5.010  1.00  0.00             
ATOM     99  CA  ASP    13      -9.132  44.955  -5.411  1.00  0.00             
ATOM    100  C   ASP    13      -9.309  44.955  -6.926  1.00  0.00             
ATOM    101  O   ASP    13     -10.141  45.685  -7.463  1.00  0.00             
ATOM    102  CB  ASP    13     -10.429  44.516  -4.730  1.00  0.00             
ATOM    103  CG  ASP    13     -10.985  45.574  -3.798  1.00  0.00             
ATOM    104  OD1 ASP    13     -12.211  45.810  -3.831  1.00  0.00             
ATOM    105  OD2 ASP    13     -10.195  46.169  -3.035  1.00  0.00             
ATOM    106  N   LEU    14      -8.522  44.131  -7.609  1.00  0.00             
ATOM    107  CA  LEU    14      -8.590  44.034  -9.062  1.00  0.00             
ATOM    108  C   LEU    14      -9.716  44.899  -9.620  1.00  0.00             
ATOM    109  O   LEU    14     -10.528  44.437 -10.422  1.00  0.00             
ATOM    110  CB  LEU    14      -7.255  44.440  -9.690  1.00  0.00             
ATOM    111  CG  LEU    14      -6.307  43.298 -10.065  1.00  0.00             
ATOM    112  CD1 LEU    14      -5.861  43.424 -11.513  1.00  0.00             
ATOM    113  CD2 LEU    14      -6.966  41.950  -9.818  1.00  0.00             
ATOM    114  N   VAL    15      -9.758  46.156  -9.190  1.00  0.00             
ATOM    115  CA  VAL    15     -10.807  47.108  -9.656  1.00  0.00             
ATOM    116  C   VAL    15     -10.925  47.097 -11.176  1.00  0.00             
ATOM    117  O   VAL    15     -12.022  47.214 -11.724  1.00  0.00             
ATOM    118  CB  VAL    15     -12.181  46.778  -9.042  1.00  0.00             
ATOM    119  CG1 VAL    15     -12.484  47.715  -7.882  1.00  0.00             
ATOM    120  CG2 VAL    15     -12.228  45.327  -8.590  1.00  0.00             
ATOM    121  N   ALA    16      -9.789  46.958 -11.851  1.00  0.00             
ATOM    122  CA  ALA    16      -9.763  46.934 -13.309  1.00  0.00             
ATOM    123  C   ALA    16     -11.173  47.005 -13.888  1.00  0.00             
ATOM    124  O   ALA    16     -11.590  48.042 -14.404  1.00  0.00             
ATOM    125  CB  ALA    16      -8.918  48.079 -13.844  1.00  0.00             
ATOM    126  N   LEU    17     -11.901  45.897 -13.798  1.00  0.00             
ATOM    127  CA  LEU    17     -13.264  45.833 -14.311  1.00  0.00             
ATOM    128  C   LEU    17     -14.107  46.986 -13.782  1.00  0.00             
ATOM    129  O   LEU    17     -14.360  47.960 -14.492  1.00  0.00             
ATOM    130  CB  LEU    17     -13.260  45.841 -15.842  1.00  0.00             
ATOM    131  CG  LEU    17     -13.977  44.677 -16.528  1.00  0.00             
ATOM    132  CD1 LEU    17     -14.529  45.106 -17.879  1.00  0.00             
ATOM    133  CD2 LEU    17     -15.086  44.130 -15.640  1.00  0.00             
ATOM    134  N   PHE    18     -14.542  46.871 -12.531  1.00  0.00             
ATOM    135  CA  PHE    18     -15.358  47.903 -11.904  1.00  0.00             
ATOM    136  C   PHE    18     -14.496  49.055 -11.396  1.00  0.00             
ATOM    137  O   PHE    18     -13.437  49.343 -11.953  1.00  0.00             
ATOM    138  CB  PHE    18     -16.407  48.426 -12.888  1.00  0.00             
ATOM    139  CG  PHE    18     -17.823  48.155 -12.464  1.00  0.00             
ATOM    140  CD1 PHE    18     -18.114  47.795 -11.159  1.00  0.00             
ATOM    141  CD2 PHE    18     -18.863  48.259 -13.370  1.00  0.00             
ATOM    142  CE1 PHE    18     -19.416  47.545 -10.770  1.00  0.00             
ATOM    143  CE2 PHE    18     -20.165  48.007 -12.981  1.00  0.00             
ATOM    144  CZ  PHE    18     -20.444  47.652 -11.687  1.00  0.00             
ATOM    145  N   ALA    19     -14.958  49.709 -10.335  1.00  0.00             
ATOM    146  CA  ALA    19     -14.231  50.829  -9.750  1.00  0.00             
ATOM    147  C   ALA    19     -14.030  50.632  -8.251  1.00  0.00             
ATOM    148  O   ALA    19     -14.675  49.787  -7.633  1.00  0.00             
ATOM    149  CB  ALA    19     -12.887  51.008 -10.440  1.00  0.00             
TER
END
