
#######################################################
#                                                     #
#                        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   31 (  124),  selected   31 , name T0363AL333_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL333_4-D1.T0363_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    N      11      N      11           -
LGA    -       -      Q      12           -
LGA    -       -      I      13           -
LGA    -       -      N      14           -
LGA    -       -      I      15           -
LGA    -       -      E      16           -
LGA    -       -      I      17           -
LGA    -       -      A      18           -
LGA    -       -      Y      19           -
LGA    Q      12      A      20          3.550
LGA    I      13      F      21          1.871
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    N      14      Y      26          2.977
LGA    -       -      L      27           -
LGA    I      15      K      28           #
LGA    E      16      S      29           -
LGA    I      17      F      30           #
LGA    A      18      Q      31           -
LGA    Y      19      V      32           #
LGA    A      20      -       -           -
LGA    F      21      D      33           #
LGA    P      22      E      34          4.514
LGA    E      23      G      35          2.658
LGA    R      24      I      36          4.933
LGA    L      27      T      37          2.166
LGA    K      28      V      38          3.936
LGA    S      29      Q      39          2.300
LGA    -       -      T      40           -
LGA    -       -      A      41           -
LGA    F      30      I      42          2.472
LGA    Q      31      T      43          2.946
LGA    -       -      Q      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      I      47           -
LGA    V      32      L      48          0.922
LGA    D      33      S      49          1.999
LGA    E      34      Q      50          3.716
LGA    -       -      F      51           -
LGA    G      35      P      52          1.641
LGA    -       -      E      53           -
LGA    I      36      I      54          2.050
LGA    T      37      D      55          4.456
LGA    V      38      L      56          4.217
LGA    Q      39      -       -           -
LGA    T      40      -       -           -
LGA    A      41      -       -           -
LGA    I      42      -       -           -
LGA    T      43      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   31   46    5.0     18    3.16     5.56     25.155     0.551

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.531803 * X  +  -0.782693 * Y  +   0.323384 * Z  +  29.547606
  Y_new =   0.820564 * X  +   0.381804 * Y  +  -0.425325 * Z  +  12.552079
  Z_new =   0.209429 * X  +   0.491547 * Y  +   0.845294 * Z  +  -0.258538 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.526713   -2.614880  [ DEG:    30.1784   -149.8216 ]
  Theta =  -0.210991   -2.930601  [ DEG:   -12.0889   -167.9111 ]
  Phi   =   0.995762   -2.145831  [ DEG:    57.0529   -122.9471 ]
 
# 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: T0363AL333_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL333_4-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31   46   5.0   18   3.16    5.56  25.155
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL333_4-D1
REMARK Aligment from pdb entry: 1jt8_A
ATOM     41  N   ASN    11      26.098  26.815  -3.769  1.00  0.00              
ATOM     42  CA  ASN    11      26.722  28.170  -3.637  1.00  0.00              
ATOM     43  C   ASN    11      28.225  28.026  -3.362  1.00  0.00              
ATOM     44  O   ASN    11      29.041  28.624  -4.040  1.00  0.00              
ATOM     45  N   GLN    12      28.592  27.240  -2.375  1.00  0.00              
ATOM     46  CA  GLN    12      30.040  27.051  -2.048  1.00  0.00              
ATOM     47  C   GLN    12      30.458  25.596  -2.329  1.00  0.00              
ATOM     48  O   GLN    12      31.402  25.092  -1.744  1.00  0.00              
ATOM     49  N   ILE    13      29.765  24.920  -3.227  1.00  0.00              
ATOM     50  CA  ILE    13      30.112  23.499  -3.561  1.00  0.00              
ATOM     51  C   ILE    13      29.905  22.595  -2.333  1.00  0.00              
ATOM     52  O   ILE    13      29.597  23.058  -1.247  1.00  0.00              
ATOM     53  N   ASN    14      30.076  21.305  -2.505  1.00  0.00              
ATOM     54  CA  ASN    14      29.899  20.352  -1.365  1.00  0.00              
ATOM     55  C   ASN    14      31.155  19.483  -1.217  1.00  0.00              
ATOM     56  O   ASN    14      32.056  19.527  -2.038  1.00  0.00              
ATOM     57  N   ILE    15      31.218  18.692  -0.173  1.00  0.00              
ATOM     58  CA  ILE    15      32.396  17.816   0.051  1.00  0.00              
ATOM     59  C   ILE    15      31.958  16.359  -0.182  1.00  0.00              
ATOM     60  O   ILE    15      30.772  16.069  -0.176  1.00  0.00              
ATOM     61  N   GLU    16      32.877  15.436  -0.406  1.00  0.00              
ATOM     62  CA  GLU    16      32.408  14.010  -0.658  1.00  0.00              
ATOM     63  C   GLU    16      33.095  13.073   0.323  1.00  0.00              
ATOM     64  O   GLU    16      34.304  13.021   0.352  1.00  0.00              
ATOM     65  N   ILE    17      31.002   7.175   4.893  1.00  0.00              
ATOM     66  CA  ILE    17      30.511   7.098   6.301  1.00  0.00              
ATOM     67  C   ILE    17      30.830   5.738   6.927  1.00  0.00              
ATOM     68  O   ILE    17      30.913   4.714   6.258  1.00  0.00              
ATOM     69  N   ALA    18      30.986   5.752   8.225  1.00  0.00              
ATOM     70  CA  ALA    18      31.282   4.514   8.999  1.00  0.00              
ATOM     71  C   ALA    18      30.564   4.577  10.356  1.00  0.00              
ATOM     72  O   ALA    18      30.551   5.615  11.012  1.00  0.00              
ATOM     73  N   TYR    19      29.989   3.470  10.783  1.00  0.00              
ATOM     74  CA  TYR    19      29.284   3.416  12.106  1.00  0.00              
ATOM     75  C   TYR    19      28.454   2.128  12.209  1.00  0.00              
ATOM     76  O   TYR    19      27.599   1.860  11.383  1.00  0.00              
ATOM     77  N   ALA    20      28.701   1.340  13.230  1.00  0.00              
ATOM     78  CA  ALA    20      27.934   0.069  13.423  1.00  0.00              
ATOM     79  C   ALA    20      26.999   0.209  14.635  1.00  0.00              
ATOM     80  O   ALA    20      25.949  -0.408  14.684  1.00  0.00              
ATOM     81  N   PHE    21      27.375   1.011  15.612  1.00  0.00              
ATOM     82  CA  PHE    21      26.518   1.194  16.829  1.00  0.00              
ATOM     83  C   PHE    21      25.114   1.652  16.410  1.00  0.00              
ATOM     84  O   PHE    21      24.127   1.016  16.734  1.00  0.00              
ATOM     85  N   PRO    22      25.021   2.746  15.687  1.00  0.00              
ATOM     86  CA  PRO    22      23.688   3.251  15.238  1.00  0.00              
ATOM     87  C   PRO    22      23.068   4.126  16.329  1.00  0.00              
ATOM     88  O   PRO    22      22.161   3.710  17.027  1.00  0.00              
ATOM     89  N   GLU    23      23.550   5.340  16.475  1.00  0.00              
ATOM     90  CA  GLU    23      22.996   6.262  17.515  1.00  0.00              
ATOM     91  C   GLU    23      22.438   7.524  16.834  1.00  0.00              
ATOM     92  O   GLU    23      22.562   8.624  17.347  1.00  0.00              
ATOM     93  N   ARG    24      21.828   7.365  15.675  1.00  0.00              
ATOM     94  CA  ARG    24      21.252   8.533  14.925  1.00  0.00              
ATOM     95  C   ARG    24      22.373   9.439  14.371  1.00  0.00              
ATOM     96  O   ARG    24      22.100  10.450  13.748  1.00  0.00              
ATOM     97  N   LEU    27      23.625   9.088  14.585  1.00  0.00              
ATOM     98  CA  LEU    27      24.754   9.925  14.068  1.00  0.00              
ATOM     99  C   LEU    27      25.879   9.010  13.555  1.00  0.00              
ATOM    100  O   LEU    27      26.005   7.870  13.968  1.00  0.00              
ATOM    101  N   LYS    28      26.686   9.505  12.650  1.00  0.00              
ATOM    102  CA  LYS    28      27.807   8.688  12.077  1.00  0.00              
ATOM    103  C   LYS    28      29.043   9.550  11.877  1.00  0.00              
ATOM    104  O   LYS    28      29.000  10.765  11.982  1.00  0.00              
ATOM    105  N   SER    29      30.146   8.923  11.585  1.00  0.00              
ATOM    106  CA  SER    29      31.423   9.699  11.366  1.00  0.00              
ATOM    107  C   SER    29      31.878   9.594   9.907  1.00  0.00              
ATOM    108  O   SER    29      31.988   8.509   9.360  1.00  0.00              
ATOM    109  N   PHE    30      32.136  10.720   9.270  1.00  0.00              
ATOM    110  CA  PHE    30      32.571  10.699   7.850  1.00  0.00              
ATOM    111  C   PHE    30      33.940  11.346   7.652  1.00  0.00              
ATOM    112  O   PHE    30      34.309  12.318   8.292  1.00  0.00              
ATOM    113  N   GLN    31      34.636  10.832   6.682  1.00  0.00              
ATOM    114  CA  GLN    31      35.965  11.383   6.266  1.00  0.00              
ATOM    115  C   GLN    31      35.772  11.764   4.806  1.00  0.00              
ATOM    116  O   GLN    31      35.133  11.029   4.070  1.00  0.00              
ATOM    117  N   VAL    32      36.218  12.914   4.376  1.00  0.00              
ATOM    118  CA  VAL    32      35.911  13.290   2.970  1.00  0.00              
ATOM    119  C   VAL    32      37.058  13.975   2.234  1.00  0.00              
ATOM    120  O   VAL    32      37.950  14.578   2.811  1.00  0.00              
ATOM    121  N   ASP    33      36.948  13.938   0.931  1.00  0.00              
ATOM    122  CA  ASP    33      37.888  14.605   0.041  1.00  0.00              
ATOM    123  C   ASP    33      37.288  15.975  -0.250  1.00  0.00              
ATOM    124  O   ASP    33      36.227  16.342   0.293  1.00  0.00              
ATOM    125  N   GLU    34      37.988  16.749  -1.033  1.00  0.00              
ATOM    126  CA  GLU    34      37.595  18.157  -1.261  1.00  0.00              
ATOM    127  C   GLU    34      38.010  18.880   0.047  1.00  0.00              
ATOM    128  O   GLU    34      37.546  19.958   0.369  1.00  0.00              
ATOM    129  N   GLY    35      38.966  18.263   0.759  1.00  0.00              
ATOM    130  CA  GLY    35      39.553  18.833   2.016  1.00  0.00              
ATOM    131  C   GLY    35      38.563  18.914   3.185  1.00  0.00              
ATOM    132  O   GLY    35      38.393  19.983   3.744  1.00  0.00              
ATOM    133  N   ILE    36      37.926  17.829   3.603  1.00  0.00              
ATOM    134  CA  ILE    36      37.004  17.971   4.775  1.00  0.00              
ATOM    135  C   ILE    36      36.973  16.736   5.677  1.00  0.00              
ATOM    136  O   ILE    36      37.167  15.612   5.251  1.00  0.00              
ATOM    137  N   THR    37      36.637  16.973   6.916  1.00  0.00              
ATOM    138  CA  THR    37      36.461  15.878   7.927  1.00  0.00              
ATOM    139  C   THR    37      35.263  16.306   8.771  1.00  0.00              
ATOM    140  O   THR    37      35.267  17.378   9.369  1.00  0.00              
ATOM    141  N   VAL    38      34.205  15.538   8.763  1.00  0.00              
ATOM    142  CA  VAL    38      32.989  15.985   9.498  1.00  0.00              
ATOM    143  C   VAL    38      32.194  14.835  10.100  1.00  0.00              
ATOM    144  O   VAL    38      32.323  13.689   9.711  1.00  0.00              
ATOM    145  N   GLN    39      31.307  15.174  11.000  1.00  0.00              
ATOM    146  CA  GLN    39      30.395  14.153  11.592  1.00  0.00              
ATOM    147  C   GLN    39      29.091  14.283  10.793  1.00  0.00              
ATOM    148  O   GLN    39      28.564  15.372  10.641  1.00  0.00              
ATOM    149  N   THR    40      28.604  13.218  10.214  1.00  0.00              
ATOM    150  CA  THR    40      27.387  13.331   9.353  1.00  0.00              
ATOM    151  C   THR    40      26.111  12.994  10.116  1.00  0.00              
ATOM    152  O   THR    40      26.076  12.105  10.949  1.00  0.00              
ATOM    153  N   ALA    41      25.056  13.716   9.808  1.00  0.00              
ATOM    154  CA  ALA    41      23.744  13.485  10.471  1.00  0.00              
ATOM    155  C   ALA    41      22.683  13.146   9.417  1.00  0.00              
ATOM    156  O   ALA    41      22.747  13.596   8.284  1.00  0.00              
ATOM    157  N   ILE    42      21.709  12.353   9.788  1.00  0.00              
ATOM    158  CA  ILE    42      20.630  11.964   8.830  1.00  0.00              
ATOM    159  C   ILE    42      19.254  12.277   9.461  1.00  0.00              
ATOM    160  O   ILE    42      19.137  12.353  10.671  1.00  0.00              
ATOM    161  N   THR    43      18.255  12.452   8.618  1.00  0.00              
ATOM    162  CA  THR    43      16.877  12.761   9.067  1.00  0.00              
ATOM    163  C   THR    43      16.194  11.517   9.659  1.00  0.00              
ATOM    164  O   THR    43      16.684  10.411   9.531  1.00  0.00              
END
