
#######################################################
#                                                     #
#                        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   20 (   80),  selected   20 , name T0383AL242_2
# Molecule2: number of CA atoms  125 ( 1020),  selected  125 , name T0383.pdb
# PARAMETERS: T0383AL242_2.T0383.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    -       -      A       3           -
LGA    -       -      M       4           -
LGA    -       -      N       5           -
LGA    -       -      L       6           -
LGA    -       -      K       7           -
LGA    L       6      R       8          5.245
LGA    K       7      E       9           -
LGA    -       -      Q      10           -
LGA    -       -      E      11           -
LGA    -       -      F      12           -
LGA    -       -      V      13           -
LGA    -       -      S      14           -
LGA    -       -      Q      15           -
LGA    -       -      Y      16           -
LGA    -       -      H      17           -
LGA    -       -      F      18           -
LGA    -       -      D      19           -
LGA    -       -      A      20           -
LGA    -       -      R      21           -
LGA    -       -      N      22           -
LGA    -       -      F      23           -
LGA    -       -      E      24           -
LGA    -       -      W      25           -
LGA    -       -      E      26           -
LGA    -       -      N      27           -
LGA    -       -      E      28           -
LGA    -       -      N      29           -
LGA    -       -      G      30           -
LGA    -       -      A      31           -
LGA    -       -      P      32           -
LGA    -       -      E      33           -
LGA    -       -      T      34           -
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    -       -      D      37           -
LGA    R       8      V      38           #
LGA    E       9      N      39          4.099
LGA    Q      10      F      40          2.668
LGA    E      11      Q      41          1.419
LGA    F      12      L      42          1.320
LGA    V      13      L      43          2.432
LGA    S      14      Q      44          1.715
LGA    Q      15      H      45          2.395
LGA    Y      16      D      46          2.414
LGA    -       -      Q      47           -
LGA    -       -      E      48           -
LGA    -       -      N      49           -
LGA    -       -      Q      50           -
LGA    H      17      V      51          1.703
LGA    F      18      T      52          3.734
LGA    D      19      S      53          1.907
LGA    -       -      L      54           -
LGA    -       -      I      55           -
LGA    -       -      V      56           -
LGA    -       -      I      57           -
LGA    -       -      L      58           -
LGA    -       -      S      59           -
LGA    -       -      F      60           -
LGA    -       -      M      61           -
LGA    -       -      I      62           -
LGA    -       -      V      63           -
LGA    -       -      F      64           -
LGA    -       -      D      65           -
LGA    -       -      K      66           -
LGA    -       -      F      67           -
LGA    -       -      V      68           -
LGA    -       -      I      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      T      72           -
LGA    -       -      I      73           -
LGA    -       -      S      74           -
LGA    -       -      Q      75           -
LGA    -       -      V      76           -
LGA    -       -      N      77           -
LGA    -       -      H      78           -
LGA    -       -      I      79           -
LGA    -       -      D      80           -
LGA    -       -      G      81           -
LGA    -       -      R      82           -
LGA    -       -      I      83           -
LGA    A      20      V      84          3.525
LGA    R      21      N      85          3.918
LGA    N      22      E      86          4.307
LGA    F      23      P      87          2.671
LGA    E      24      S      88          3.360
LGA    -       -      E      89           -
LGA    W      25      L      90          2.051
LGA    -       -      N      91           -
LGA    -       -      Q      92           -
LGA    -       -      E      93           -
LGA    -       -      E      94           -
LGA    -       -      V      95           -
LGA    -       -      E      96           -
LGA    -       -      T      97           -
LGA    -       -      L      98           -
LGA    -       -      A      99           -
LGA    -       -      R     100           -
LGA    -       -      P     101           -
LGA    -       -      C     102           -
LGA    -       -      L     103           -
LGA    -       -      N     104           -
LGA    -       -      M     105           -
LGA    -       -      L     106           -
LGA    -       -      N     107           -
LGA    -       -      R     108           -
LGA    -       -      L     109           -
LGA    -       -      T     110           -
LGA    -       -      Y     111           -
LGA    -       -      E     112           -
LGA    -       -      V     113           -
LGA    -       -      T     114           -
LGA    -       -      E     115           -
LGA    -       -      I     116           -
LGA    -       -      A     117           -
LGA    -       -      L     118           -
LGA    -       -      D     119           -
LGA    -       -      L     120           -
LGA    -       -      P     121           -
LGA    -       -      G     122           -
LGA    -       -      I     123           -
LGA    -       -      N     124           -
LGA    -       -      L     125           -
LGA    -       -      E     126           -
LGA    -       -      F     127           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   20  125    5.0     18    3.03     0.00      9.775     0.575

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.952351 * X  +  -0.101510 * Y  +   0.287615 * Z  +   7.884319
  Y_new =  -0.004227 * X  +   0.938508 * Y  +   0.345231 * Z  +  37.483006
  Z_new =  -0.304974 * X  +  -0.329997 * Y  +   0.893360 * Z  +  23.464336 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.353842    2.787750  [ DEG:   -20.2737    159.7263 ]
  Theta =   0.309911    2.831682  [ DEG:    17.7566    162.2434 ]
  Phi   =  -0.004438    3.137154  [ DEG:    -0.2543    179.7457 ]
 
# 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: T0383AL242_2                                  
REMARK     2: T0383.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0383AL242_2.T0383.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20  125   5.0   18   3.03    0.00   9.775
REMARK  ---------------------------------------------------------- 
MOLECULE T0383AL242_2
REMARK Aligment from pdb entry: 1f3k_A
ATOM      1  N   LEU     6      12.798  31.051  21.668  1.00  0.00              
ATOM      2  CA  LEU     6      12.104  32.358  21.850  1.00  0.00              
ATOM      3  C   LEU     6      10.772  32.359  21.089  1.00  0.00              
ATOM      4  O   LEU     6      10.147  31.328  20.935  1.00  0.00              
ATOM      5  N   LYS     7      10.327  33.494  20.602  1.00  0.00              
ATOM      6  CA  LYS     7       9.055  33.533  19.865  1.00  0.00              
ATOM      7  C   LYS     7       9.132  34.577  18.764  1.00  0.00              
ATOM      8  O   LYS     7       9.719  35.630  18.936  1.00  0.00              
ATOM      9  N   ARG     8       8.539  34.309  17.638  1.00  0.00              
ATOM     10  CA  ARG     8       8.578  35.308  16.548  1.00  0.00              
ATOM     11  C   ARG     8       7.515  36.369  16.796  1.00  0.00              
ATOM     12  O   ARG     8       6.479  36.110  17.375  1.00  0.00              
ATOM     13  N   GLU     9       7.784  37.556  16.369  1.00  0.00              
ATOM     14  CA  GLU     9       6.829  38.675  16.565  1.00  0.00              
ATOM     15  C   GLU     9       5.382  38.197  16.419  1.00  0.00              
ATOM     16  O   GLU     9       5.050  37.470  15.503  1.00  0.00              
ATOM     17  N   GLN    10       4.525  38.597  17.336  1.00  0.00              
ATOM     18  CA  GLN    10       3.086  38.183  17.299  1.00  0.00              
ATOM     19  C   GLN    10       2.926  36.791  17.907  1.00  0.00              
ATOM     20  O   GLN    10       1.934  36.123  17.699  1.00  0.00              
ATOM     21  N   GLU    11       3.894  36.351  18.665  1.00  0.00              
ATOM     22  CA  GLU    11       3.787  35.007  19.289  1.00  0.00              
ATOM     23  C   GLU    11       3.513  35.147  20.790  1.00  0.00              
ATOM     24  O   GLU    11       4.107  35.972  21.455  1.00  0.00              
ATOM     25  N   PHE    12       2.609  34.336  21.270  1.00  0.00              
ATOM     26  CA  PHE    12       2.238  34.367  22.706  1.00  0.00              
ATOM     27  C   PHE    12       3.344  33.767  23.571  1.00  0.00              
ATOM     28  O   PHE    12       3.925  32.752  23.239  1.00  0.00              
ATOM     29  N   VAL    13       3.633  34.382  24.683  1.00  0.00              
ATOM     30  CA  VAL    13       4.696  33.838  25.573  1.00  0.00              
ATOM     31  C   VAL    13       4.552  34.388  26.992  1.00  0.00              
ATOM     32  O   VAL    13       3.696  35.201  27.278  1.00  0.00              
ATOM     33  N   SER    14       5.393  33.945  27.880  1.00  0.00              
ATOM     34  CA  SER    14       5.328  34.434  29.284  1.00  0.00              
ATOM     35  C   SER    14       6.145  35.721  29.416  1.00  0.00              
ATOM     36  O   SER    14       7.276  35.797  28.977  1.00  0.00              
ATOM     37  N   GLN    15       5.585  36.732  30.014  1.00  0.00              
ATOM     38  CA  GLN    15       6.333  38.009  30.172  1.00  0.00              
ATOM     39  C   GLN    15       7.120  37.988  31.482  1.00  0.00              
ATOM     40  O   GLN    15       6.924  38.821  32.344  1.00  0.00              
ATOM     41  N   TYR    16       8.002  37.040  31.647  1.00  0.00              
ATOM     42  CA  TYR    16       8.780  36.980  32.918  1.00  0.00              
ATOM     43  C   TYR    16      10.231  36.577  32.643  1.00  0.00              
ATOM     44  O   TYR    16      11.146  37.052  33.285  1.00  0.00              
ATOM     45  N   HIS    17      10.450  35.700  31.706  1.00  0.00              
ATOM     46  CA  HIS    17      11.845  35.270  31.415  1.00  0.00              
ATOM     47  C   HIS    17      12.092  35.226  29.911  1.00  0.00              
ATOM     48  O   HIS    17      12.764  36.072  29.354  1.00  0.00              
ATOM     49  N   PHE    18      11.567  34.237  29.251  1.00  0.00              
ATOM     50  CA  PHE    18      11.784  34.129  27.784  1.00  0.00              
ATOM     51  C   PHE    18      10.473  34.305  27.015  1.00  0.00              
ATOM     52  O   PHE    18       9.414  33.918  27.468  1.00  0.00              
ATOM     53  N   ASP    19      10.546  34.861  25.844  1.00  0.00              
ATOM     54  CA  ASP    19       9.320  35.035  25.014  1.00  0.00              
ATOM     55  C   ASP    19       9.726  35.295  23.574  1.00  0.00              
ATOM     56  O   ASP    19       9.824  34.392  22.771  1.00  0.00              
ATOM     57  N   ALA    20       4.440  41.313  26.043  1.00  0.00              
ATOM     58  CA  ALA    20       3.248  42.032  26.571  1.00  0.00              
ATOM     59  C   ALA    20       2.041  41.545  25.777  1.00  0.00              
ATOM     60  O   ALA    20       1.438  42.271  25.013  1.00  0.00              
ATOM     61  N   ARG    21       1.739  40.285  25.916  1.00  0.00              
ATOM     62  CA  ARG    21       0.631  39.673  25.141  1.00  0.00              
ATOM     63  C   ARG    21       1.293  38.816  24.065  1.00  0.00              
ATOM     64  O   ARG    21       1.028  37.639  23.924  1.00  0.00              
ATOM     65  N   ASN    22       2.193  39.416  23.333  1.00  0.00              
ATOM     66  CA  ASN    22       2.947  38.690  22.278  1.00  0.00              
ATOM     67  C   ASN    22       4.190  39.509  21.932  1.00  0.00              
ATOM     68  O   ASN    22       4.243  40.695  22.190  1.00  0.00              
ATOM     69  N   PHE    23       5.186  38.904  21.358  1.00  0.00              
ATOM     70  CA  PHE    23       6.409  39.680  21.008  1.00  0.00              
ATOM     71  C   PHE    23       6.015  41.022  20.381  1.00  0.00              
ATOM     72  O   PHE    23       5.430  41.063  19.316  1.00  0.00              
ATOM     73  N   GLU    24       6.319  42.121  21.027  1.00  0.00              
ATOM     74  CA  GLU    24       5.941  43.447  20.447  1.00  0.00              
ATOM     75  C   GLU    24       7.101  44.037  19.655  1.00  0.00              
ATOM     76  O   GLU    24       7.347  45.227  19.655  1.00  0.00              
ATOM     77  N   TRP    25       7.794  43.194  18.969  1.00  0.00              
ATOM     78  CA  TRP    25       8.944  43.631  18.136  1.00  0.00              
ATOM     79  C   TRP    25       9.235  42.586  17.056  1.00  0.00              
ATOM     80  O   TRP    25       9.976  41.660  17.340  1.00  0.00              
END
