
#######################################################
#                                                     #
#                        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   16 (   64),  selected   16 , name T0350AL509_1-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350AL509_1-D1.T0350_D1.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    V      12      -       -           -
LGA    W      13      M       1          3.826
LGA    D      14      N       2          2.782
LGA    R      15      I       3          2.389
LGA    Y      16      E       4          2.663
LGA    D      17      R       5          1.064
LGA    T      18      L       6          2.084
LGA    Q      19      T       7          2.710
LGA    I      20      T       8          4.132
LGA    H      21      L       9          4.721
LGA    S      36      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      Q      19           -
LGA    -       -      I      20           -
LGA    -       -      H      21           -
LGA    -       -      S      36           -
LGA    -       -      Y      37           -
LGA    -       -      T      38           -
LGA    -       -      N      39           -
LGA    -       -      L      40           -
LGA    -       -      A      41           -
LGA    -       -      E      42           -
LGA    Y      37      M      43          2.656
LGA    -       -      V      44           -
LGA    -       -      G      45           -
LGA    -       -      E      46           -
LGA    -       -      M      47           -
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      E      52           -
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    -       -      H      57           -
LGA    -       -      L      58           -
LGA    -       -      K      59           -
LGA    -       -      F      60           -
LGA    -       -      E      61           -
LGA    -       -      L      62           -
LGA    -       -      H      63           -
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    -       -      V      71           -
LGA    -       -      K      72           -
LGA    -       -      V      73           -
LGA    -       -      I      74           -
LGA    -       -      E      75           -
LGA    -       -      D      76           -
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    -       -      N      79           -
LGA    -       -      E      80           -
LGA    -       -      V      81           -
LGA    -       -      I      82           -
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    -       -      I      85           -
LGA    -       -      P      86           -
LGA    -       -      P      87           -
LGA    T      38      K      88          2.021
LGA    N      39      R      89          1.651
LGA    A      41      W      90          2.073
LGA    E      42      L      91          3.690
LGA    -       -      D      92           -
LGA    -       -      F      93           -
LGA    -       -      Y      94           -
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    -       -      T      98           -
LGA    -       -      E      99           -
LGA    -       -      F     100           -
LGA    -       -      L     101           -
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16   91    5.0     14    2.92     0.00     10.731     0.464

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.507751 * X  +  -0.347548 * Y  +  -0.788289 * Z  +  28.242222
  Y_new =   0.503751 * X  +   0.862058 * Y  +  -0.055597 * Z  + -66.971123
  Z_new =   0.698873 * X  +  -0.368872 * Y  +   0.612789 * Z  + -72.949501 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.541856    2.599736  [ DEG:   -31.0461    148.9539 ]
  Theta =  -0.773821   -2.367772  [ DEG:   -44.3367   -135.6633 ]
  Phi   =   0.781443   -2.360150  [ DEG:    44.7734   -135.2266 ]
 
# 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: T0350AL509_1-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350AL509_1-D1.T0350_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16   91   5.0   14   2.92    0.00  10.731
REMARK  ---------------------------------------------------------- 
MOLECULE T0350AL509_1-D1
REMARK Aligment from pdb entry: 1g8x_A
ATOM      1  N   VAL    12       1.363  -4.165  -0.442  1.00  0.00              
ATOM      2  CA  VAL    12       2.679  -3.642  -0.109  1.00  0.00              
ATOM      3  C   VAL    12       2.843  -2.189  -0.533  1.00  0.00              
ATOM      4  O   VAL    12       3.670  -1.471   0.015  1.00  0.00              
ATOM      5  N   TRP    13       2.054  -1.736  -1.497  1.00  0.00              
ATOM      6  CA  TRP    13       2.220  -0.367  -1.948  1.00  0.00              
ATOM      7  C   TRP    13       1.359   0.698  -1.304  1.00  0.00              
ATOM      8  O   TRP    13       1.647   1.880  -1.459  1.00  0.00              
ATOM      9  N   ASP    14       5.713   5.710  -0.239  1.00  0.00              
ATOM     10  CA  ASP    14       6.114   6.830  -1.092  1.00  0.00              
ATOM     11  C   ASP    14       7.023   6.388  -2.238  1.00  0.00              
ATOM     12  O   ASP    14       7.786   5.435  -2.104  1.00  0.00              
ATOM     13  N   ARG    15       6.947   7.103  -3.356  1.00  0.00              
ATOM     14  CA  ARG    15       7.729   6.779  -4.545  1.00  0.00              
ATOM     15  C   ARG    15       9.133   6.260  -4.286  1.00  0.00              
ATOM     16  O   ARG    15       9.539   5.244  -4.866  1.00  0.00              
ATOM     17  N   TYR    16       9.874   6.930  -3.413  1.00  0.00              
ATOM     18  CA  TYR    16      11.241   6.508  -3.131  1.00  0.00              
ATOM     19  C   TYR    16      11.391   5.557  -1.936  1.00  0.00              
ATOM     20  O   TYR    16      12.501   5.276  -1.500  1.00  0.00              
ATOM     21  N   ASP    17      10.273   5.070  -1.407  1.00  0.00              
ATOM     22  CA  ASP    17      10.291   4.131  -0.283  1.00  0.00              
ATOM     23  C   ASP    17      10.081   2.703  -0.786  1.00  0.00              
ATOM     24  O   ASP    17      10.270   1.732  -0.042  1.00  0.00              
ATOM     25  N   THR    18       9.668   2.576  -2.043  1.00  0.00              
ATOM     26  CA  THR    18       9.464   1.270  -2.632  1.00  0.00              
ATOM     27  C   THR    18      10.054   1.215  -4.017  1.00  0.00              
ATOM     28  O   THR    18      10.389   2.239  -4.593  1.00  0.00              
ATOM     29  N   GLN    19      10.177   0.000  -4.537  1.00  0.00              
ATOM     30  CA  GLN    19      10.710  -0.259  -5.865  1.00  0.00              
ATOM     31  C   GLN    19       9.786   0.347  -6.920  1.00  0.00              
ATOM     32  O   GLN    19       8.604   0.541  -6.670  1.00  0.00              
ATOM     33  N   ILE    20      10.319   0.672  -8.109  1.00  0.00              
ATOM     34  CA  ILE    20       9.489   1.253  -9.178  1.00  0.00              
ATOM     35  C   ILE    20       8.365   0.275  -9.517  1.00  0.00              
ATOM     36  O   ILE    20       8.583  -0.933  -9.519  1.00  0.00              
ATOM     37  N   HIS    21       7.173   0.787  -9.810  1.00  0.00              
ATOM     38  CA  HIS    21       6.041  -0.084 -10.121  1.00  0.00              
ATOM     39  C   HIS    21       4.821   0.713 -10.562  1.00  0.00              
ATOM     40  O   HIS    21       4.610   1.826 -10.081  1.00  0.00              
ATOM     77  N   SER    36      -0.880   9.922 -17.490  1.00  0.00              
ATOM     78  CA  SER    36      -0.684   9.918 -18.940  1.00  0.00              
ATOM     79  C   SER    36       0.250   8.785 -19.341  1.00  0.00              
ATOM     80  O   SER    36       1.456   8.864 -19.118  1.00  0.00              
ATOM     81  N   TYR    37      -0.324   7.736 -19.934  1.00  0.00              
ATOM     82  CA  TYR    37       0.414   6.536 -20.362  1.00  0.00              
ATOM     83  C   TYR    37       0.586   6.426 -21.879  1.00  0.00              
ATOM     84  O   TYR    37      -0.344   6.048 -22.575  1.00  0.00              
ATOM     85  N   THR    38       2.724   1.051 -30.403  1.00  0.00              
ATOM     86  CA  THR    38       1.715   0.014 -30.428  1.00  0.00              
ATOM     87  C   THR    38       2.321  -1.308 -29.959  1.00  0.00              
ATOM     88  O   THR    38       3.247  -1.823 -30.573  1.00  0.00              
ATOM     89  N   ASN    39       1.797  -1.873 -28.885  1.00  0.00              
ATOM     90  CA  ASN    39       2.336  -3.129 -28.402  1.00  0.00              
ATOM     91  C   ASN    39       3.356  -2.923 -27.297  1.00  0.00              
ATOM     92  O   ASN    39       3.991  -3.861 -26.821  1.00  0.00              
ATOM     93  N   ALA    41       3.517  -1.686 -26.870  1.00  0.00              
ATOM     94  CA  ALA    41       4.473  -1.399 -25.818  1.00  0.00              
ATOM     95  C   ALA    41       3.978  -1.787 -24.417  1.00  0.00              
ATOM     96  O   ALA    41       4.789  -1.965 -23.511  1.00  0.00              
ATOM     97  N   GLU    42       2.656  -1.887 -24.245  1.00  0.00              
ATOM     98  CA  GLU    42       2.080  -2.267 -22.960  1.00  0.00              
ATOM     99  C   GLU    42       1.216  -1.213 -22.281  1.00  0.00              
ATOM    100  O   GLU    42       0.949  -1.307 -21.079  1.00  0.00              
END
