
#######################################################
#                                                     #
#                        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   28 (  112),  selected   28 , name T0312AL381_2
# Molecule2: number of CA atoms  140 ( 1114),  selected  140 , name T0312.pdb
# PARAMETERS: T0312AL381_2.T0312.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      V       3           -
LGA    -       -      F       4           -
LGA    -       -      E       5           -
LGA    -       -      F       6           -
LGA    -       -      E       7           -
LGA    -       -      V       8           -
LGA    -       -      G       9           -
LGA    -       -      K      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      L      16           -
LGA    -       -      D      17           -
LGA    -       -      Y      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      L      22           -
LGA    -       -      V      23           -
LGA    -       -      R      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      E      27           -
LGA    -       -      E      28           -
LGA    -       -      F      29           -
LGA    -       -      L      30           -
LGA    -       -      E      31           -
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    -       -      G      34           -
LGA    -       -      I      35           -
LGA    -       -      H      36           -
LGA    -       -      A      37           -
LGA    -       -      A      38           -
LGA    -       -      H      39           -
LGA    -       -      I      40           -
LGA    -       -      S      41           -
LGA    -       -      A      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      A      45           -
LGA    -       -      V      46           -
LGA    -       -      R      47           -
LGA    -       -      S      48           -
LGA    -       -      A      49           -
LGA    -       -      V      50           -
LGA    -       -      I      51           -
LGA    -       -      G      52           -
LGA    -       -      Y      53           -
LGA    -       -      Y      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      57           -
LGA    -       -      K      58           -
LGA    -       -      K      59           -
LGA    -       -      E      60           -
LGA    -       -      Y      61           -
LGA    -       -      V      62           -
LGA    -       -      K      63           -
LGA    -       -      K      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      M      67           -
LGA    -       -      E      68           -
LGA    -       -      P      69           -
LGA    -       -      L      70           -
LGA    -       -      E      71           -
LGA    -       -      I      72           -
LGA    -       -      L      73           -
LGA    -       -      S      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    I      40      G      77          2.291
LGA    S      41      N      78          2.823
LGA    A      42      V      79          2.897
LGA    -       -      S      80           -
LGA    I      43      M      81          4.163
LGA    G      44      K      82          1.080
LGA    -       -      D      83           -
LGA    A      45      S      84          4.991
LGA    V      46      K      85          4.632
LGA    R      47      P      86          3.266
LGA    S      48      F      87          1.848
LGA    A      49      C      88          1.235
LGA    V      50      H      89          1.206
LGA    I      51      I      90          0.963
LGA    G      52      H      91          1.370
LGA    Y      53      V      92          1.044
LGA    Y      54      L      93          0.941
LGA    D      55      L      94          1.678
LGA    Q      56      G      95          2.285
LGA    E      57      K      96          2.426
LGA    K      58      D      97          3.159
LGA    K      59      G      98           #
LGA    E      60      E      99          3.721
LGA    Y      61      -       -           -
LGA    V      62      V     100          0.739
LGA    K      63      Y     101          4.530
LGA    K      64      G     102          2.219
LGA    E      65      -       -           -
LGA    L      66      G     103          1.450
LGA    M      67      H     104          1.506
LGA    -       -      L     105           -
LGA    -       -      F     106           -
LGA    -       -      S     107           -
LGA    -       -      A     108           -
LGA    -       -      E     109           -
LGA    -       -      V     110           -
LGA    -       -      F     111           -
LGA    -       -      A     112           -
LGA    -       -      C     113           -
LGA    -       -      E     114           -
LGA    -       -      V     115           -
LGA    -       -      F     116           -
LGA    -       -      V     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      L     120           -
LGA    -       -      S     121           -
LGA    -       -      G     122           -
LGA    -       -      E     123           -
LGA    -       -      A     124           -
LGA    -       -      P     125           -
LGA    -       -      E     126           -
LGA    -       -      R     127           -
LGA    -       -      A     128           -
LGA    -       -      F     129           -
LGA    -       -      D     130           -
LGA    -       -      E     131           -
LGA    -       -      Q     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    -       -      L     135           -
LGA    -       -      F     136           -
LGA    -       -      L     137           -
LGA    -       -      W     138           -
LGA    -       -      L     139           -
LGA    -       -      E     140           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   28  140    5.0     25    2.66    12.00     12.300     0.907

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.575026 * X  +  -0.811207 * Y  +  -0.106248 * Z  + 101.399986
  Y_new =  -0.747514 * X  +  -0.468158 * Y  +  -0.471223 * Z  +  79.485641
  Z_new =   0.332518 * X  +   0.350387 * Y  +  -0.875592 * Z  + -15.490377 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.760938   -0.380654  [ DEG:   158.1901    -21.8099 ]
  Theta =  -0.338973   -2.802620  [ DEG:   -19.4217   -160.5783 ]
  Phi   =  -0.915088    2.226505  [ DEG:   -52.4307    127.5693 ]
 
# 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: T0312AL381_2                                  
REMARK     2: T0312.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312AL381_2.T0312.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   28  140   5.0   25   2.66   12.00  12.300
REMARK  ---------------------------------------------------------- 
MOLECULE T0312AL381_2
REMARK Aligment from pdb entry: 1yh6A
ATOM      1  N   ILE    40      57.572   7.425  22.989  1.00  0.00              
ATOM      2  CA  ILE    40      58.709   6.807  22.313  1.00  0.00              
ATOM      3  C   ILE    40      59.534   5.826  23.173  1.00  0.00              
ATOM      4  O   ILE    40      59.960   6.175  24.279  1.00  0.00              
ATOM      5  N   SER    41      59.793   4.631  22.625  1.00  0.00              
ATOM      6  CA  SER    41      60.720   3.633  23.181  1.00  0.00              
ATOM      7  C   SER    41      61.950   3.492  22.274  1.00  0.00              
ATOM      8  O   SER    41      61.828   3.252  21.064  1.00  0.00              
ATOM      9  N   ALA    42      63.135   3.653  22.872  1.00  0.00              
ATOM     10  CA  ALA    42      64.381   3.688  22.121  1.00  0.00              
ATOM     11  C   ALA    42      64.893   2.288  22.138  1.00  0.00              
ATOM     12  O   ALA    42      64.856   1.666  23.192  1.00  0.00              
ATOM     13  N   ILE    43      65.330   1.769  20.985  1.00  0.00              
ATOM     14  CA  ILE    43      65.843   0.388  20.913  1.00  0.00              
ATOM     15  C   ILE    43      67.374   0.327  21.066  1.00  0.00              
ATOM     16  O   ILE    43      67.884   0.608  22.149  1.00  0.00              
ATOM     17  N   GLY    44      68.104   0.002  20.005  1.00  0.00              
ATOM     18  CA  GLY    44      69.583   0.033  20.037  1.00  0.00              
ATOM     19  C   GLY    44      70.231   1.400  20.258  1.00  0.00              
ATOM     20  O   GLY    44      71.344   1.496  20.781  1.00  0.00              
ATOM     21  N   ALA    45      69.537   2.460  19.885  1.00  0.00              
ATOM     22  CA  ALA    45      70.077   3.804  19.968  1.00  0.00              
ATOM     23  C   ALA    45      69.065   4.702  19.283  1.00  0.00              
ATOM     24  O   ALA    45      67.981   4.254  18.949  1.00  0.00              
ATOM     25  N   VAL    46      69.427   5.948  19.032  1.00  0.00              
ATOM     26  CA  VAL    46      68.455   6.903  18.458  1.00  0.00              
ATOM     27  C   VAL    46      68.076   6.651  16.990  1.00  0.00              
ATOM     28  O   VAL    46      67.110   7.213  16.504  1.00  0.00              
ATOM     29  N   ARG    47      68.807   5.786  16.303  1.00  0.00              
ATOM     30  CA  ARG    47      68.396   5.355  14.960  1.00  0.00              
ATOM     31  C   ARG    47      67.347   4.243  14.931  1.00  0.00              
ATOM     32  O   ARG    47      67.013   3.773  13.868  1.00  0.00              
ATOM     33  N   SER    48      66.827   3.815  16.086  1.00  0.00              
ATOM     34  CA  SER    48      65.731   2.828  16.100  1.00  0.00              
ATOM     35  C   SER    48      64.876   3.060  17.298  1.00  0.00              
ATOM     36  O   SER    48      65.348   2.990  18.418  1.00  0.00              
ATOM     37  N   ALA    49      63.612   3.334  17.071  1.00  0.00              
ATOM     38  CA  ALA    49      62.704   3.589  18.172  1.00  0.00              
ATOM     39  C   ALA    49      61.326   3.104  17.763  1.00  0.00              
ATOM     40  O   ALA    49      61.077   2.864  16.582  1.00  0.00              
ATOM     41  N   VAL    50      60.435   2.988  18.738  1.00  0.00              
ATOM     42  CA  VAL    50      59.095   2.526  18.514  1.00  0.00              
ATOM     43  C   VAL    50      58.202   3.551  19.172  1.00  0.00              
ATOM     44  O   VAL    50      58.510   4.045  20.261  1.00  0.00              
ATOM     45  N   ILE    51      57.098   3.866  18.504  1.00  0.00              
ATOM     46  CA  ILE    51      56.139   4.833  18.969  1.00  0.00              
ATOM     47  C   ILE    51      54.764   4.164  19.055  1.00  0.00              
ATOM     48  O   ILE    51      54.340   3.472  18.130  1.00  0.00              
ATOM     49  N   GLY    52      54.058   4.401  20.157  1.00  0.00              
ATOM     50  CA  GLY    52      52.659   4.013  20.262  1.00  0.00              
ATOM     51  C   GLY    52      51.816   4.926  19.387  1.00  0.00              
ATOM     52  O   GLY    52      51.879   6.134  19.496  1.00  0.00              
ATOM     53  N   TYR    53      51.034   4.330  18.509  1.00  0.00              
ATOM     54  CA  TYR    53      50.253   5.063  17.533  1.00  0.00              
ATOM     55  C   TYR    53      48.808   4.584  17.610  1.00  0.00              
ATOM     56  O   TYR    53      48.523   3.367  17.632  1.00  0.00              
ATOM     57  N   TYR    54      47.907   5.552  17.623  1.00  0.00              
ATOM     58  CA  TYR    54      46.481   5.328  17.772  1.00  0.00              
ATOM     59  C   TYR    54      45.766   5.543  16.447  1.00  0.00              
ATOM     60  O   TYR    54      46.004   6.553  15.770  1.00  0.00              
ATOM     61  N   ASP    55      44.881   4.612  16.079  1.00  0.00              
ATOM     62  CA  ASP    55      44.160   4.712  14.795  1.00  0.00              
ATOM     63  C   ASP    55      43.392   6.024  14.688  1.00  0.00              
ATOM     64  O   ASP    55      42.816   6.462  15.669  1.00  0.00              
ATOM     65  N   GLN    56      43.446   6.701  13.526  1.00  0.00              
ATOM     66  CA  GLN    56      42.764   8.002  13.403  1.00  0.00              
ATOM     67  C   GLN    56      41.232   7.916  13.484  1.00  0.00              
ATOM     68  O   GLN    56      40.612   6.981  12.948  1.00  0.00              
ATOM     69  N   GLU    57      40.649   8.893  14.176  1.00  0.00              
ATOM     70  CA  GLU    57      39.217   8.947  14.423  1.00  0.00              
ATOM     71  C   GLU    57      38.506   9.080  13.111  1.00  0.00              
ATOM     72  O   GLU    57      39.013   9.735  12.204  1.00  0.00              
ATOM     73  N   LYS    58      37.371   8.395  12.999  1.00  0.00              
ATOM     74  CA  LYS    58      36.530   8.468  11.816  1.00  0.00              
ATOM     75  C   LYS    58      37.075   7.663  10.656  1.00  0.00              
ATOM     76  O   LYS    58      36.762   7.956   9.504  1.00  0.00              
ATOM     77  N   LYS    59      37.926   6.683  10.962  1.00  0.00              
ATOM     78  CA  LYS    59      38.439   5.746   9.984  1.00  0.00              
ATOM     79  C   LYS    59      38.138   4.370  10.565  1.00  0.00              
ATOM     80  O   LYS    59      37.879   4.253  11.767  1.00  0.00              
ATOM     81  N   GLU    60      38.179   3.316   9.731  1.00  0.00              
ATOM     82  CA  GLU    60      38.009   1.976  10.285  1.00  0.00              
ATOM     83  C   GLU    60      39.086   1.571  11.312  1.00  0.00              
ATOM     84  O   GLU    60      38.841   0.686  12.125  1.00  0.00              
ATOM     85  N   TYR    61      40.250   2.241  11.283  1.00  0.00              
ATOM     86  CA  TYR    61      41.338   2.080  12.290  1.00  0.00              
ATOM     87  C   TYR    61      41.075   2.693  13.680  1.00  0.00              
ATOM     88  O   TYR    61      41.823   2.461  14.630  1.00  0.00              
ATOM     89  N   VAL    62      40.028   3.491  13.797  1.00  0.00              
ATOM     90  CA  VAL    62      39.732   4.121  15.064  1.00  0.00              
ATOM     91  C   VAL    62      39.586   3.043  16.137  1.00  0.00              
ATOM     92  O   VAL    62      38.991   1.992  15.896  1.00  0.00              
ATOM     93  N   LYS    63      40.192   3.273  17.298  1.00  0.00              
ATOM     94  CA  LYS    63      40.160   2.284  18.355  1.00  0.00              
ATOM     95  C   LYS    63      41.393   1.399  18.355  1.00  0.00              
ATOM     96  O   LYS    63      41.687   0.759  19.357  1.00  0.00              
ATOM     97  N   LYS    64      42.126   1.331  17.241  1.00  0.00              
ATOM     98  CA  LYS    64      43.306   0.478  17.204  1.00  0.00              
ATOM     99  C   LYS    64      44.502   1.134  17.878  1.00  0.00              
ATOM    100  O   LYS    64      44.619   2.371  17.922  1.00  0.00              
ATOM    101  N   GLU    65      45.399   0.299  18.398  1.00  0.00              
ATOM    102  CA  GLU    65      46.671   0.769  18.971  1.00  0.00              
ATOM    103  C   GLU    65      47.791  -0.074  18.371  1.00  0.00              
ATOM    104  O   GLU    65      47.676  -1.296  18.246  1.00  0.00              
ATOM    105  N   LEU    66      48.844   0.599  17.924  1.00  0.00              
ATOM    106  CA  LEU    66      49.942  -0.085  17.244  1.00  0.00              
ATOM    107  C   LEU    66      51.263   0.371  17.807  1.00  0.00              
ATOM    108  O   LEU    66      51.393   1.509  18.302  1.00  0.00              
ATOM    109  N   MET    67      52.237  -0.527  17.700  1.00  0.00              
ATOM    110  CA  MET    67      53.610  -0.214  17.967  1.00  0.00              
ATOM    111  C   MET    67      54.288  -0.070  16.611  1.00  0.00              
ATOM    112  O   MET    67      54.346  -0.996  15.813  1.00  0.00              
END
