
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0363AL316_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL316_3-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    -       -      I      13           -
LGA    N      11      N      14          5.263
LGA    Q      12      I      15          5.990
LGA    I      13      E      16          5.286
LGA    N      14      I      17          3.233
LGA    I      15      A      18          4.584
LGA    E      16      Y      19          2.402
LGA    I      17      -       -           -
LGA    A      18      A      20          3.715
LGA    Y      19      F      21           #
LGA    A      20      P      22          3.516
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    F      21      Y      25          2.893
LGA    P      22      Y      26          2.698
LGA    E      23      L      27          2.529
LGA    R      24      K      28          2.801
LGA    S      29      S      29          3.183
LGA    F      30      F      30          3.303
LGA    Q      31      Q      31          3.292
LGA    V      32      V      32           #
LGA    D      33      D      33          3.204
LGA    E      34      E      34          1.351
LGA    G      35      G      35          1.513
LGA    I      36      I      36          1.141
LGA    T      37      T      37          0.559
LGA    V      38      V      38          0.596
LGA    Q      39      Q      39          0.757
LGA    T      40      T      40          0.949
LGA    A      41      A      41          1.196
LGA    I      42      I      42          1.151
LGA    T      43      T      43          0.640
LGA    Q      44      Q      44          2.272
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    S      45      I      47          2.808
LGA    G      46      L      48          3.980
LGA    I      54      S      49           -
LGA    D      55      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    L      56      D      55          4.933
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35   46    5.0     30    3.11    56.67     47.927     0.933

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.618244 * X  +  -0.005759 * Y  +  -0.785965 * Z  +  22.021931
  Y_new =   0.758342 * X  +   0.258502 * Y  +  -0.598409 * Z  +   6.832987
  Z_new =   0.206620 * X  +  -0.965994 * Y  +  -0.155450 * Z  +   4.017629 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.730350    1.411242  [ DEG:   -99.1418     80.8582 ]
  Theta =  -0.208119   -2.933473  [ DEG:   -11.9244   -168.0756 ]
  Phi   =   2.254771   -0.886822  [ DEG:   129.1889    -50.8111 ]
 
# 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: T0363AL316_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL316_3-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35   46   5.0   30   3.11   56.67  47.927
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL316_3-D1
REMARK Aligment from pdb entry: 1rws_A
ATOM      1  N   ASN    11      21.966   4.803   6.575  1.00  0.00              
ATOM      2  CA  ASN    11      22.223   6.267   6.678  1.00  0.00              
ATOM      3  C   ASN    11      23.374   6.658   5.761  1.00  0.00              
ATOM      4  O   ASN    11      24.493   6.196   5.880  1.00  0.00              
ATOM      5  N   GLN    12      23.064   7.503   4.829  1.00  0.00              
ATOM      6  CA  GLN    12      24.071   7.964   3.841  1.00  0.00              
ATOM      7  C   GLN    12      24.318   9.457   4.051  1.00  0.00              
ATOM      8  O   GLN    12      23.552  10.148   4.691  1.00  0.00              
ATOM      9  N   ILE    13      25.446   9.919   3.604  1.00  0.00              
ATOM     10  CA  ILE    13      25.838  11.334   3.864  1.00  0.00              
ATOM     11  C   ILE    13      25.887  12.138   2.564  1.00  0.00              
ATOM     12  O   ILE    13      25.915  11.605   1.472  1.00  0.00              
ATOM     13  N   ASN    14      25.917  13.439   2.707  1.00  0.00              
ATOM     14  CA  ASN    14      25.989  14.381   1.551  1.00  0.00              
ATOM     15  C   ASN    14      26.985  15.447   1.948  1.00  0.00              
ATOM     16  O   ASN    14      27.140  15.770   3.103  1.00  0.00              
ATOM     17  N   ILE    15      27.761  15.877   1.005  1.00  0.00              
ATOM     18  CA  ILE    15      28.877  16.819   1.307  1.00  0.00              
ATOM     19  C   ILE    15      28.859  18.012   0.343  1.00  0.00              
ATOM     20  O   ILE    15      28.697  17.855  -0.850  1.00  0.00              
ATOM     21  N   GLU    16      29.070  19.203   0.851  1.00  0.00              
ATOM     22  CA  GLU    16      29.117  20.410  -0.026  1.00  0.00              
ATOM     23  C   GLU    16      30.185  21.372   0.495  1.00  0.00              
ATOM     24  O   GLU    16      30.606  21.287   1.628  1.00  0.00              
ATOM     25  N   ILE    17      30.719  22.215  -0.351  1.00  0.00              
ATOM     26  CA  ILE    17      31.816  23.133   0.058  1.00  0.00              
ATOM     27  C   ILE    17      31.244  24.424   0.590  1.00  0.00              
ATOM     28  O   ILE    17      30.160  24.809   0.203  1.00  0.00              
ATOM     29  N   ALA    18      31.735  24.778   1.748  1.00  0.00              
ATOM     30  CA  ALA    18      30.877  25.707   2.564  1.00  0.00              
ATOM     31  C   ALA    18      29.895  26.388   1.598  1.00  0.00              
ATOM     32  O   ALA    18      30.326  26.949   0.610  1.00  0.00              
ATOM     33  N   TYR    19      28.609  26.467   1.889  1.00  0.00              
ATOM     34  CA  TYR    19      27.739  27.241   0.957  1.00  0.00              
ATOM     35  C   TYR    19      28.199  27.021  -0.483  1.00  0.00              
ATOM     36  O   TYR    19      28.413  27.951  -1.236  1.00  0.00              
ATOM     37  N   ALA    20      28.316  25.787  -0.872  1.00  0.00              
ATOM     38  CA  ALA    20      28.722  25.459  -2.269  1.00  0.00              
ATOM     39  C   ALA    20      27.512  25.014  -3.088  1.00  0.00              
ATOM     40  O   ALA    20      27.555  24.999  -4.302  1.00  0.00              
ATOM     41  N   PHE    21      26.408  24.719  -2.454  1.00  0.00              
ATOM     42  CA  PHE    21      25.160  24.358  -3.168  1.00  0.00              
ATOM     43  C   PHE    21      25.081  22.863  -3.444  1.00  0.00              
ATOM     44  O   PHE    21      24.968  22.460  -4.584  1.00  0.00              
ATOM     45  N   PRO    22      25.227  22.030  -2.457  1.00  0.00              
ATOM     46  CA  PRO    22      25.251  20.577  -2.792  1.00  0.00              
ATOM     47  C   PRO    22      24.207  19.770  -2.026  1.00  0.00              
ATOM     48  O   PRO    22      24.430  19.213  -0.970  1.00  0.00              
ATOM     49  N   GLU    23      23.079  19.676  -2.663  1.00  0.00              
ATOM     50  CA  GLU    23      21.880  18.898  -2.217  1.00  0.00              
ATOM     51  C   GLU    23      21.875  17.496  -2.812  1.00  0.00              
ATOM     52  O   GLU    23      22.068  17.312  -3.997  1.00  0.00              
ATOM     53  N   ARG    24      21.576  16.510  -2.006  1.00  0.00              
ATOM     54  CA  ARG    24      21.464  15.122  -2.519  1.00  0.00              
ATOM     55  C   ARG    24      20.674  14.343  -1.464  1.00  0.00              
ATOM     56  O   ARG    24      21.242  14.020  -0.441  1.00  0.00              
ATOM     57  N   SER    29      19.375  14.225  -1.541  1.00  0.00              
ATOM     58  CA  SER    29      18.657  13.650  -0.354  1.00  0.00              
ATOM     59  C   SER    29      19.486  12.512   0.248  1.00  0.00              
ATOM     60  O   SER    29      20.519  12.147  -0.275  1.00  0.00              
ATOM     61  N   PHE    30      19.138  12.043   1.431  1.00  0.00              
ATOM     62  CA  PHE    30      20.113  11.120   2.121  1.00  0.00              
ATOM     63  C   PHE    30      19.425  10.273   3.217  1.00  0.00              
ATOM     64  O   PHE    30      18.880  10.873   4.121  1.00  0.00              
ATOM     65  N   GLN    31      19.303   8.958   3.202  1.00  0.00              
ATOM     66  CA  GLN    31      18.512   8.245   4.262  1.00  0.00              
ATOM     67  C   GLN    31      19.053   8.622   5.651  1.00  0.00              
ATOM     68  O   GLN    31      19.349   9.767   5.931  1.00  0.00              
ATOM     69  N   VAL    32      19.180   7.657   6.520  1.00  0.00              
ATOM     70  CA  VAL    32      19.693   7.897   7.905  1.00  0.00              
ATOM     71  C   VAL    32      19.688   6.521   8.585  1.00  0.00              
ATOM     72  O   VAL    32      19.687   5.533   7.877  1.00  0.00              
ATOM     73  N   ASP    33      19.904   6.363   9.873  1.00  0.00              
ATOM     74  CA  ASP    33      20.173   4.951  10.297  1.00  0.00              
ATOM     75  C   ASP    33      19.979   4.654  11.804  1.00  0.00              
ATOM     76  O   ASP    33      18.868   4.778  12.282  1.00  0.00              
ATOM     77  N   GLU    34      20.958   4.201  12.583  1.00  0.00              
ATOM     78  CA  GLU    34      20.625   3.857  14.006  1.00  0.00              
ATOM     79  C   GLU    34      21.899   3.417  14.751  1.00  0.00              
ATOM     80  O   GLU    34      22.503   2.412  14.431  1.00  0.00              
ATOM     81  N   GLY    35      22.338   4.199  15.712  1.00  0.00              
ATOM     82  CA  GLY    35      23.604   3.861  16.439  1.00  0.00              
ATOM     83  C   GLY    35      24.736   4.802  15.990  1.00  0.00              
ATOM     84  O   GLY    35      25.690   5.053  16.702  1.00  0.00              
ATOM     85  N   ILE    36      24.622   5.287  14.790  1.00  0.00              
ATOM     86  CA  ILE    36      25.687   6.198  14.223  1.00  0.00              
ATOM     87  C   ILE    36      25.412   7.561  14.851  1.00  0.00              
ATOM     88  O   ILE    36      24.983   7.713  15.978  1.00  0.00              
ATOM     89  N   THR    37      26.150   8.407  14.265  1.00  0.00              
ATOM     90  CA  THR    37      26.547   9.735  14.786  1.00  0.00              
ATOM     91  C   THR    37      26.673  10.752  13.632  1.00  0.00              
ATOM     92  O   THR    37      27.095  10.378  12.556  1.00  0.00              
ATOM     93  N   VAL    38      26.638  12.047  13.898  1.00  0.00              
ATOM     94  CA  VAL    38      27.159  13.033  12.895  1.00  0.00              
ATOM     95  C   VAL    38      28.523  12.597  12.369  1.00  0.00              
ATOM     96  O   VAL    38      28.742  12.514  11.177  1.00  0.00              
ATOM     97  N   GLN    39      29.486  12.506  13.244  1.00  0.00              
ATOM     98  CA  GLN    39      30.886  12.296  12.807  1.00  0.00              
ATOM     99  C   GLN    39      30.903  11.293  11.656  1.00  0.00              
ATOM    100  O   GLN    39      31.250  11.617  10.538  1.00  0.00              
ATOM    101  N   THR    40      30.480  10.085  11.915  1.00  0.00              
ATOM    102  CA  THR    40      30.432   9.093  10.780  1.00  0.00              
ATOM    103  C   THR    40      29.881   9.732   9.502  1.00  0.00              
ATOM    104  O   THR    40      30.570   9.763   8.502  1.00  0.00              
ATOM    105  N   ALA    41      28.639  10.132   9.445  1.00  0.00              
ATOM    106  CA  ALA    41      28.131  10.620   8.127  1.00  0.00              
ATOM    107  C   ALA    41      29.219  11.491   7.489  1.00  0.00              
ATOM    108  O   ALA    41      29.508  11.413   6.311  1.00  0.00              
ATOM    109  N   ILE    42      29.861  12.254   8.308  1.00  0.00              
ATOM    110  CA  ILE    42      31.005  13.102   7.854  1.00  0.00              
ATOM    111  C   ILE    42      32.174  12.189   7.469  1.00  0.00              
ATOM    112  O   ILE    42      32.809  12.366   6.448  1.00  0.00              
ATOM    113  N   THR    43      32.327  11.114   8.188  1.00  0.00              
ATOM    114  CA  THR    43      33.298  10.052   7.785  1.00  0.00              
ATOM    115  C   THR    43      32.991   9.559   6.369  1.00  0.00              
ATOM    116  O   THR    43      33.888   9.219   5.625  1.00  0.00              
ATOM    117  N   GLN    44      31.745   9.536   5.966  1.00  0.00              
ATOM    118  CA  GLN    44      31.466   9.075   4.555  1.00  0.00              
ATOM    119  C   GLN    44      32.139  10.074   3.611  1.00  0.00              
ATOM    120  O   GLN    44      32.440   9.795   2.469  1.00  0.00              
ATOM    121  N   SER    45      32.501  11.179   4.177  1.00  0.00              
ATOM    122  CA  SER    45      33.306  12.148   3.392  1.00  0.00              
ATOM    123  C   SER    45      34.777  11.793   3.604  1.00  0.00              
ATOM    124  O   SER    45      35.654  12.392   3.014  1.00  0.00              
ATOM    125  N   GLY    46      35.067  10.940   4.555  1.00  0.00              
ATOM    126  CA  GLY    46      36.489  10.705   4.915  1.00  0.00              
ATOM    127  C   GLY    46      36.896  11.940   5.705  1.00  0.00              
ATOM    128  O   GLY    46      37.995  12.446   5.591  1.00  0.00              
ATOM    129  N   ILE    54      35.923  12.527   6.360  1.00  0.00              
ATOM    130  CA  ILE    54      36.105  13.855   7.022  1.00  0.00              
ATOM    131  C   ILE    54      35.152  13.901   8.230  1.00  0.00              
ATOM    132  O   ILE    54      34.046  14.383   8.098  1.00  0.00              
ATOM    133  N   ASP    55      35.631  13.697   9.428  1.00  0.00              
ATOM    134  CA  ASP    55      34.835  14.144  10.615  1.00  0.00              
ATOM    135  C   ASP    55      34.652  15.665  10.533  1.00  0.00              
ATOM    136  O   ASP    55      35.033  16.405  11.418  1.00  0.00              
ATOM    137  N   LEU    56      34.278  16.121   9.369  1.00  0.00              
ATOM    138  CA  LEU    56      34.315  17.605   9.130  1.00  0.00              
ATOM    139  C   LEU    56      35.699  18.139   9.508  1.00  0.00              
ATOM    140  O   LEU    56      35.836  18.596  10.627  1.00  0.00              
END
