
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0363AL242_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL242_5-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      14           -
LGA    -       -      I      15           -
LGA    -       -      E      16           -
LGA    -       -      I      17           -
LGA    -       -      A      18           -
LGA    -       -      Y      19           -
LGA    -       -      A      20           -
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    -       -      Y      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      S      29           -
LGA    N      11      F      30          2.390
LGA    Q      12      Q      31          2.061
LGA    D      33      V      32          1.447
LGA    E      34      D      33          2.881
LGA    G      35      E      34          2.572
LGA    -       -      G      35           -
LGA    I      36      I      36          1.370
LGA    T      37      T      37          1.615
LGA    V      38      V      38          2.089
LGA    Q      39      Q      39          1.968
LGA    T      40      T      40          1.621
LGA    A      41      A      41          1.761
LGA    I      42      I      42          2.055
LGA    T      43      T      43          2.180
LGA    Q      44      Q      44          2.640
LGA    -       -      S      45           -
LGA    S      45      G      46          2.202
LGA    G      46      I      47          4.143
LGA    I      47      L      48          0.812
LGA    L      48      S      49           #
LGA    S      49      Q      50           -
LGA    -       -      F      51           -
LGA    Q      50      P      52          2.610
LGA    F      51      E      53          3.411
LGA    P      52      I      54          1.478
LGA    E      53      D      55          5.328
LGA    I      54      L      56           -
LGA    D      55      -       -           -
LGA    L      56      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   26   46    5.0     21    2.52    47.62     36.683     0.802

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.644936 * X  +   0.692390 * Y  +   0.323503 * Z  +  52.543381
  Y_new =   0.292658 * X  +   0.167280 * Y  +  -0.941472 * Z  +  64.517357
  Z_new =  -0.705981 * X  +   0.701864 * Y  +  -0.094748 * Z  + -16.785917 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.704980   -1.436612  [ DEG:    97.6882    -82.3118 ]
  Theta =   0.783807    2.357785  [ DEG:    44.9088    135.0912 ]
  Phi   =   0.425992   -2.715601  [ DEG:    24.4075   -155.5925 ]
 
# 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: T0363AL242_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL242_5-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26   46   5.0   21   2.52   47.62  36.683
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL242_5-D1
REMARK Aligment from pdb entry: 1tyg_B
ATOM     41  N   ASN    11      20.087   9.084   3.887  1.00  0.00              
ATOM     42  CA  ASN    11      21.291   8.557   4.580  1.00  0.00              
ATOM     43  C   ASN    11      21.311   7.047   4.873  1.00  0.00              
ATOM     44  O   ASN    11      20.515   6.563   5.667  1.00  0.00              
ATOM     45  N   GLN    12      22.270   6.320   4.309  1.00  0.00              
ATOM     46  CA  GLN    12      22.139   4.864   4.184  1.00  0.00              
ATOM     47  C   GLN    12      21.404   4.100   5.296  1.00  0.00              
ATOM     48  O   GLN    12      20.457   3.351   4.989  1.00  0.00              
ATOM     49  N   ASP    33      21.820   4.270   6.557  1.00  0.00              
ATOM     50  CA  ASP    33      21.348   3.388   7.645  1.00  0.00              
ATOM     51  C   ASP    33      20.611   4.052   8.835  1.00  0.00              
ATOM     52  O   ASP    33      20.496   5.269   8.910  1.00  0.00              
ATOM     53  N   GLU    34      20.136   3.206   9.746  1.00  0.00              
ATOM     54  CA  GLU    34      19.397   3.545  10.970  1.00  0.00              
ATOM     55  C   GLU    34      20.068   4.543  11.926  1.00  0.00              
ATOM     56  O   GLU    34      19.419   5.472  12.424  1.00  0.00              
ATOM     57  N   GLY    35      21.342   4.307  12.236  1.00  0.00              
ATOM     58  CA  GLY    35      22.101   5.186  13.127  1.00  0.00              
ATOM     59  C   GLY    35      23.379   5.692  12.466  1.00  0.00              
ATOM     60  O   GLY    35      23.802   5.177  11.425  1.00  0.00              
ATOM     61  N   ILE    36      23.999   6.697  13.078  1.00  0.00              
ATOM     62  CA  ILE    36      25.249   7.217  12.550  1.00  0.00              
ATOM     63  C   ILE    36      25.847   8.377  13.309  1.00  0.00              
ATOM     64  O   ILE    36      25.189   8.948  14.174  1.00  0.00              
ATOM     65  N   THR    37      27.103   8.692  12.975  1.00  0.00              
ATOM     66  CA  THR    37      27.881   9.784  13.587  1.00  0.00              
ATOM     67  C   THR    37      28.522  10.694  12.537  1.00  0.00              
ATOM     68  O   THR    37      28.887  10.237  11.455  1.00  0.00              
ATOM     69  N   VAL    38      28.687  11.974  12.856  1.00  0.00              
ATOM     70  CA  VAL    38      29.339  12.888  11.916  1.00  0.00              
ATOM     71  C   VAL    38      30.543  12.252  11.192  1.00  0.00              
ATOM     72  O   VAL    38      30.785  12.521  10.004  1.00  0.00              
ATOM     73  N   GLN    39      31.291  11.409  11.896  1.00  0.00              
ATOM     74  CA  GLN    39      32.398  10.742  11.248  1.00  0.00              
ATOM     75  C   GLN    39      31.899   9.774  10.162  1.00  0.00              
ATOM     76  O   GLN    39      32.276   9.940   8.996  1.00  0.00              
ATOM     77  N   THR    40      31.006   8.838  10.515  1.00  0.00              
ATOM     78  CA  THR    40      30.412   7.869   9.548  1.00  0.00              
ATOM     79  C   THR    40      30.026   8.534   8.234  1.00  0.00              
ATOM     80  O   THR    40      30.184   7.949   7.142  1.00  0.00              
ATOM     81  N   ALA    41      29.496   9.753   8.385  1.00  0.00              
ATOM     82  CA  ALA    41      28.959  10.544   7.297  1.00  0.00              
ATOM     83  C   ALA    41      30.084  11.035   6.388  1.00  0.00              
ATOM     84  O   ALA    41      30.016  10.809   5.183  1.00  0.00              
ATOM     85  N   ILE    42      31.113  11.671   6.957  1.00  0.00              
ATOM     86  CA  ILE    42      32.280  12.118   6.184  1.00  0.00              
ATOM     87  C   ILE    42      32.958  10.961   5.449  1.00  0.00              
ATOM     88  O   ILE    42      33.331  11.077   4.283  1.00  0.00              
ATOM     89  N   THR    43      33.106   9.845   6.144  1.00  0.00              
ATOM     90  CA  THR    43      33.538   8.609   5.520  1.00  0.00              
ATOM     91  C   THR    43      32.759   8.256   4.225  1.00  0.00              
ATOM     92  O   THR    43      33.330   8.250   3.130  1.00  0.00              
ATOM     93  N   GLN    44      31.466   7.974   4.336  1.00  0.00              
ATOM     94  CA  GLN    44      30.664   7.636   3.161  1.00  0.00              
ATOM     95  C   GLN    44      30.794   8.585   1.953  1.00  0.00              
ATOM     96  O   GLN    44      30.537   8.178   0.824  1.00  0.00              
ATOM     97  N   SER    45      31.174   9.842   2.193  1.00  0.00              
ATOM     98  CA  SER    45      31.317  10.852   1.132  1.00  0.00              
ATOM     99  C   SER    45      32.773  11.160   0.821  1.00  0.00              
ATOM    100  O   SER    45      33.052  12.064   0.019  1.00  0.00              
ATOM    101  N   GLY    46      33.671  10.422   1.485  1.00  0.00              
ATOM    102  CA  GLY    46      35.130  10.401   1.243  1.00  0.00              
ATOM    103  C   GLY    46      35.904  11.616   1.714  1.00  0.00              
ATOM    104  O   GLY    46      36.897  11.979   1.103  1.00  0.00              
ATOM    105  N   ILE    47      35.447  12.218   2.809  1.00  0.00              
ATOM    106  CA  ILE    47      35.979  13.498   3.317  1.00  0.00              
ATOM    107  C   ILE    47      36.777  13.353   4.617  1.00  0.00              
ATOM    108  O   ILE    47      37.079  14.335   5.300  1.00  0.00              
ATOM    109  N   LEU    48      37.111  12.108   4.937  1.00  0.00              
ATOM    110  CA  LEU    48      37.811  11.762   6.155  1.00  0.00              
ATOM    111  C   LEU    48      39.220  12.336   6.111  1.00  0.00              
ATOM    112  O   LEU    48      39.727  12.797   7.135  1.00  0.00              
ATOM    113  N   SER    49      39.833  12.351   4.924  1.00  0.00              
ATOM    114  CA  SER    49      41.194  12.881   4.769  1.00  0.00              
ATOM    115  C   SER    49      41.289  14.301   4.143  1.00  0.00              
ATOM    116  O   SER    49      42.231  14.629   3.405  1.00  0.00              
ATOM    117  N   GLN    50      40.316  15.142   4.481  1.00  0.00              
ATOM    118  CA  GLN    50      40.164  16.461   3.886  1.00  0.00              
ATOM    119  C   GLN    50      39.793  17.416   4.988  1.00  0.00              
ATOM    120  O   GLN    50      38.994  17.071   5.862  1.00  0.00              
ATOM    121  N   PHE    51      40.351  18.620   4.950  1.00  0.00              
ATOM    122  CA  PHE    51      40.033  19.626   5.941  1.00  0.00              
ATOM    123  C   PHE    51      38.688  20.063   5.531  1.00  0.00              
ATOM    124  O   PHE    51      38.529  20.432   4.379  1.00  0.00              
ATOM    125  N   PRO    52      37.711  19.971   6.433  1.00  0.00              
ATOM    126  CA  PRO    52      36.356  20.536   6.221  1.00  0.00              
ATOM    127  C   PRO    52      35.855  20.994   7.561  1.00  0.00              
ATOM    128  O   PRO    52      36.333  20.534   8.577  1.00  0.00              
ATOM    129  N   GLU    53      34.905  21.903   7.593  1.00  0.00              
ATOM    130  CA  GLU    53      34.279  22.280   8.876  1.00  0.00              
ATOM    131  C   GLU    53      32.846  21.770   8.800  1.00  0.00              
ATOM    132  O   GLU    53      32.227  21.892   7.742  1.00  0.00              
ATOM    133  N   ILE    54      32.302  21.196   9.874  1.00  0.00              
ATOM    134  CA  ILE    54      30.908  20.672   9.803  1.00  0.00              
ATOM    135  C   ILE    54      29.938  21.336  10.760  1.00  0.00              
ATOM    136  O   ILE    54      30.189  21.373  11.965  1.00  0.00              
ATOM    137  N   ASP    55      28.826  21.860  10.254  1.00  0.00              
ATOM    138  CA  ASP    55      27.797  22.332  11.195  1.00  0.00              
ATOM    139  C   ASP    55      26.518  21.505  11.121  1.00  0.00              
ATOM    140  O   ASP    55      26.162  21.019  10.042  1.00  0.00              
ATOM    141  N   LEU    56      25.856  21.322  12.266  1.00  0.00              
ATOM    142  CA  LEU    56      24.716  20.407  12.393  1.00  0.00              
ATOM    143  C   LEU    56      23.657  21.137  13.176  1.00  0.00              
ATOM    144  O   LEU    56      23.857  21.428  14.360  1.00  0.00              
END
