
#######################################################
#                                                     #
#                        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 T0290AL242_3
# Molecule2: number of CA atoms  173 ( 1339),  selected  173 , name T0290
# PARAMETERS: T0290AL242_3.T0290  -4  -ie  -d:5  -o1  -sia  
# 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    E      21      R       1          2.522
LGA    L      22      P       2          2.809
LGA    F      23      R       3          3.652
LGA    S      24      C       4          4.417
LGA    -       -      F       5           -
LGA    -       -      F       6           -
LGA    -       -      D       7           -
LGA    -       -      I       8           -
LGA    -       -      A       9           -
LGA    -       -      I      10           -
LGA    -       -      N      11           -
LGA    -       -      N      12           -
LGA    -       -      Q      13           -
LGA    -       -      P      14           -
LGA    -       -      A      15           -
LGA    -       -      G      16           -
LGA    -       -      R      17           -
LGA    -       -      V      18           -
LGA    -       -      V      19           -
LGA    D      25      F      20          1.928
LGA    V      26      E      21           #
LGA    C      27      L      22          3.073
LGA    P      28      F      23          1.279
LGA    K      29      S      24          2.785
LGA    T      30      D      25          1.802
LGA    -       -      V      26           -
LGA    C      31      C      27          2.416
LGA    E      32      P      28          1.666
LGA    N      33      K      29          2.301
LGA    F      34      T      30          3.767
LGA    R      35      C      31           #
LGA    C      36      E      32          2.292
LGA    L      37      N      33          1.267
LGA    C      38      F      34          1.918
LGA    T      39      R      35          3.692
LGA    -       -      C      36           -
LGA    -       -      L      37           -
LGA    -       -      C      38           -
LGA    -       -      T      39           -
LGA    -       -      G      40           -
LGA    -       -      E      41           -
LGA    -       -      K      42           -
LGA    -       -      G      43           -
LGA    -       -      T      44           -
LGA    -       -      G      45           -
LGA    -       -      K      46           -
LGA    -       -      S      47           -
LGA    -       -      T      48           -
LGA    -       -      Q      49           -
LGA    -       -      K      50           -
LGA    -       -      P      51           -
LGA    -       -      L      52           -
LGA    G      40      H      53          3.602
LGA    E      41      Y      54          2.766
LGA    -       -      K      55           -
LGA    -       -      S      56           -
LGA    K      42      C      57          2.846
LGA    G      43      L      58          4.088
LGA    -       -      F      59           -
LGA    -       -      H      60           -
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    -       -      V      63           -
LGA    -       -      K      64           -
LGA    -       -      D      65           -
LGA    -       -      F      66           -
LGA    -       -      M      67           -
LGA    -       -      V      68           -
LGA    -       -      Q      69           -
LGA    -       -      G      70           -
LGA    T      44      G      71          3.214
LGA    G      45      D      72           -
LGA    K      46      F      73           -
LGA    S      47      S      74           -
LGA    -       -      E      75           -
LGA    -       -      G      76           -
LGA    -       -      N      77           -
LGA    -       -      G      78           -
LGA    -       -      R      79           -
LGA    -       -      G      80           -
LGA    -       -      G      81           -
LGA    -       -      E      82           -
LGA    -       -      S      83           -
LGA    -       -      I      84           -
LGA    -       -      Y      85           -
LGA    -       -      G      86           -
LGA    -       -      G      87           -
LGA    -       -      F      88           -
LGA    -       -      F      89           -
LGA    -       -      E      90           -
LGA    -       -      D      91           -
LGA    -       -      E      92           -
LGA    -       -      S      93           -
LGA    -       -      F      94           -
LGA    -       -      A      95           -
LGA    -       -      V      96           -
LGA    -       -      K      97           -
LGA    -       -      H      98           -
LGA    -       -      N      99           -
LGA    -       -      A     100           -
LGA    -       -      A     101           -
LGA    T      48      F     102          5.087
LGA    Q      49      L     103          3.450
LGA    K      50      L     104          0.509
LGA    P      51      S     105          2.351
LGA    L      52      M     106          1.164
LGA    H      53      A     107          5.112
LGA    -       -      N     108           -
LGA    -       -      R     109           -
LGA    -       -      G     110           -
LGA    -       -      K     111           -
LGA    -       -      D     112           -
LGA    -       -      T     113           -
LGA    -       -      N     114           -
LGA    -       -      G     115           -
LGA    -       -      S     116           -
LGA    -       -      Q     117           -
LGA    -       -      F     118           -
LGA    -       -      F     119           -
LGA    -       -      I     120           -
LGA    -       -      T     121           -
LGA    -       -      T     122           -
LGA    -       -      K     123           -
LGA    -       -      P     124           -
LGA    -       -      T     125           -
LGA    -       -      P     126           -
LGA    -       -      H     127           -
LGA    -       -      L     128           -
LGA    -       -      D     129           -
LGA    -       -      G     130           -
LGA    -       -      H     131           -
LGA    Y      54      H     132           #
LGA    K      55      V     133          0.820
LGA    -       -      V     134           -
LGA    -       -      F     135           -
LGA    -       -      G     136           -
LGA    -       -      Q     137           -
LGA    -       -      V     138           -
LGA    -       -      I     139           -
LGA    -       -      S     140           -
LGA    -       -      G     141           -
LGA    -       -      Q     142           -
LGA    -       -      E     143           -
LGA    -       -      V     144           -
LGA    -       -      V     145           -
LGA    -       -      R     146           -
LGA    -       -      E     147           -
LGA    -       -      I     148           -
LGA    -       -      E     149           -
LGA    -       -      N     150           -
LGA    -       -      Q     151           -
LGA    -       -      K     152           -
LGA    -       -      T     153           -
LGA    -       -      D     154           -
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      S     157           -
LGA    -       -      K     158           -
LGA    -       -      P     159           -
LGA    -       -      F     160           -
LGA    -       -      A     161           -
LGA    -       -      E     162           -
LGA    -       -      V     163           -
LGA    -       -      R     164           -
LGA    -       -      I     165           -
LGA    -       -      L     166           -
LGA    -       -      S     167           -
LGA    -       -      C     168           -
LGA    -       -      G     169           -
LGA    -       -      E     170           -
LGA    -       -      L     171           -
LGA    -       -      I     172           -
LGA    -       -      P     173           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35  173    5.0     29    2.95     3.45     10.042     0.950

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.161916 * X  +  -0.570778 * Y  +   0.804982 * Z  +  28.977322
  Y_new =   0.672597 * X  +  -0.660742 * Y  +  -0.333217 * Z  +  51.950718
  Z_new =   0.722078 * X  +   0.487475 * Y  +   0.490888 * Z  +  10.223663 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.781909   -2.359684  [ DEG:    44.8001   -135.1999 ]
  Theta =  -0.806802   -2.334791  [ DEG:   -46.2263   -133.7737 ]
  Phi   =   1.807034   -1.334559  [ DEG:   103.5354    -76.4646 ]
 
# 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: T0290AL242_3                                  
REMARK     2: T0290                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0290AL242_3.T0290 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35  173   5.0   29   2.95    3.45  10.042
REMARK  ---------------------------------------------------------- 
MOLECULE T0290AL242_3
REMARK Aligment from pdb entry: 1ji9_A
ATOM      1  N   GLU    21      35.606  42.957   9.885  1.00  0.00              
ATOM      2  CA  GLU    21      34.861  42.921  11.178  1.00  0.00              
ATOM      3  C   GLU    21      33.616  43.810  11.100  1.00  0.00              
ATOM      4  O   GLU    21      33.502  44.659  10.238  1.00  0.00              
ATOM      5  N   LEU    22      32.684  43.625  11.995  1.00  0.00              
ATOM      6  CA  LEU    22      31.451  44.464  11.972  1.00  0.00              
ATOM      7  C   LEU    22      31.825  45.944  11.991  1.00  0.00              
ATOM      8  O   LEU    22      31.049  46.798  11.616  1.00  0.00              
ATOM      9  N   PHE    23      33.016  46.234  12.425  1.00  0.00              
ATOM     10  CA  PHE    23      33.499  47.651  12.486  1.00  0.00              
ATOM     11  C   PHE    23      32.377  48.617  12.851  1.00  0.00              
ATOM     12  O   PHE    23      32.430  49.763  12.470  1.00  0.00              
ATOM     13  N   SER    24      31.353  48.191  13.546  1.00  0.00              
ATOM     14  CA  SER    24      30.256  49.158  13.836  1.00  0.00              
ATOM     15  C   SER    24      29.156  48.592  14.719  1.00  0.00              
ATOM     16  O   SER    24      28.928  47.400  14.797  1.00  0.00              
ATOM     17  N   ASP    25      28.421  49.484  15.309  1.00  0.00              
ATOM     18  CA  ASP    25      27.249  49.101  16.122  1.00  0.00              
ATOM     19  C   ASP    25      26.016  49.347  15.250  1.00  0.00              
ATOM     20  O   ASP    25      24.926  48.889  15.532  1.00  0.00              
ATOM     21  N   VAL    26      26.210  50.057  14.156  1.00  0.00              
ATOM     22  CA  VAL    26      25.075  50.327  13.216  1.00  0.00              
ATOM     23  C   VAL    26      25.220  49.475  11.954  1.00  0.00              
ATOM     24  O   VAL    26      24.402  49.517  11.056  1.00  0.00              
ATOM     25  N   CYS    27      26.269  48.717  11.887  1.00  0.00              
ATOM     26  CA  CYS    27      26.531  47.862  10.716  1.00  0.00              
ATOM     27  C   CYS    27      27.106  46.511  11.128  1.00  0.00              
ATOM     28  O   CYS    27      27.714  46.382  12.172  1.00  0.00              
ATOM     29  N   PRO    28      26.921  45.556  10.264  1.00  0.00              
ATOM     30  CA  PRO    28      27.448  44.207  10.491  1.00  0.00              
ATOM     31  C   PRO    28      28.832  44.115   9.848  1.00  0.00              
ATOM     32  O   PRO    28      29.371  45.101   9.387  1.00  0.00              
ATOM     33  N   LYS    29      29.409  42.954   9.795  1.00  0.00              
ATOM     34  CA  LYS    29      30.750  42.835   9.158  1.00  0.00              
ATOM     35  C   LYS    29      30.596  42.710   7.643  1.00  0.00              
ATOM     36  O   LYS    29      31.556  42.526   6.921  1.00  0.00              
ATOM     37  N   THR    30      29.389  42.794   7.158  1.00  0.00              
ATOM     38  CA  THR    30      29.165  42.665   5.693  1.00  0.00              
ATOM     39  C   THR    30      28.813  44.023   5.074  1.00  0.00              
ATOM     40  O   THR    30      28.744  44.153   3.868  1.00  0.00              
ATOM     41  N   CYS    31      28.587  45.039   5.868  1.00  0.00              
ATOM     42  CA  CYS    31      28.246  46.351   5.287  1.00  0.00              
ATOM     43  C   CYS    31      29.227  46.716   4.187  1.00  0.00              
ATOM     44  O   CYS    31      30.359  47.070   4.450  1.00  0.00              
ATOM     45  N   GLU    32      28.810  46.665   2.962  1.00  0.00              
ATOM     46  CA  GLU    32      29.742  47.048   1.882  1.00  0.00              
ATOM     47  C   GLU    32      29.873  48.560   1.860  1.00  0.00              
ATOM     48  O   GLU    32      30.707  49.129   1.185  1.00  0.00              
ATOM     49  N   ASN    33      29.084  49.200   2.650  1.00  0.00              
ATOM     50  CA  ASN    33      29.168  50.664   2.769  1.00  0.00              
ATOM     51  C   ASN    33      30.406  50.966   3.562  1.00  0.00              
ATOM     52  O   ASN    33      31.011  52.007   3.471  1.00  0.00              
ATOM     53  N   PHE    34      30.757  50.020   4.351  1.00  0.00              
ATOM     54  CA  PHE    34      31.942  50.163   5.224  1.00  0.00              
ATOM     55  C   PHE    34      33.077  49.336   4.667  1.00  0.00              
ATOM     56  O   PHE    34      34.190  49.343   5.155  1.00  0.00              
ATOM     57  N   ARG    35      32.776  48.613   3.648  1.00  0.00              
ATOM     58  CA  ARG    35      33.769  47.746   3.008  1.00  0.00              
ATOM     59  C   ARG    35      34.891  48.569   2.374  1.00  0.00              
ATOM     60  O   ARG    35      35.875  48.035   1.900  1.00  0.00              
ATOM     61  N   CYS    36      34.837  51.956   6.369  1.00  0.00              
ATOM     62  CA  CYS    36      33.825  52.349   7.391  1.00  0.00              
ATOM     63  C   CYS    36      33.294  53.745   7.063  1.00  0.00              
ATOM     64  O   CYS    36      33.812  54.746   7.517  1.00  0.00              
ATOM     65  N   LEU    37      32.273  53.812   6.256  1.00  0.00              
ATOM     66  CA  LEU    37      31.706  55.126   5.861  1.00  0.00              
ATOM     67  C   LEU    37      31.255  55.922   7.088  1.00  0.00              
ATOM     68  O   LEU    37      31.153  57.132   7.043  1.00  0.00              
ATOM     69  N   CYS    38      30.997  55.270   8.186  1.00  0.00              
ATOM     70  CA  CYS    38      30.573  56.035   9.397  1.00  0.00              
ATOM     71  C   CYS    38      31.749  56.190  10.365  1.00  0.00              
ATOM     72  O   CYS    38      31.575  56.568  11.506  1.00  0.00              
ATOM     73  N   THR    39      32.944  55.908   9.923  1.00  0.00              
ATOM     74  CA  THR    39      34.123  56.046  10.821  1.00  0.00              
ATOM     75  C   THR    39      34.027  57.327  11.641  1.00  0.00              
ATOM     76  O   THR    39      34.468  57.397  12.770  1.00  0.00              
ATOM     77  N   GLY    40      33.455  58.337  11.072  1.00  0.00              
ATOM     78  CA  GLY    40      33.321  59.631  11.798  1.00  0.00              
ATOM     79  C   GLY    40      32.550  59.412  13.099  1.00  0.00              
ATOM     80  O   GLY    40      31.343  59.268  13.098  1.00  0.00              
ATOM     81  N   GLU    41      33.233  59.389  14.211  1.00  0.00              
ATOM     82  CA  GLU    41      32.529  59.185  15.508  1.00  0.00              
ATOM     83  C   GLU    41      32.035  60.524  16.048  1.00  0.00              
ATOM     84  O   GLU    41      32.189  60.841  17.211  1.00  0.00              
ATOM     85  N   LYS    42      31.438  61.307  15.200  1.00  0.00              
ATOM     86  CA  LYS    42      30.914  62.629  15.624  1.00  0.00              
ATOM     87  C   LYS    42      29.434  62.504  15.989  1.00  0.00              
ATOM     88  O   LYS    42      29.085  62.063  17.066  1.00  0.00              
ATOM     89  N   GLY    43      28.561  62.868  15.094  1.00  0.00              
ATOM     90  CA  GLY    43      27.107  62.749  15.377  1.00  0.00              
ATOM     91  C   GLY    43      26.605  61.413  14.829  1.00  0.00              
ATOM     92  O   GLY    43      25.466  61.037  15.022  1.00  0.00              
ATOM     93  N   THR    44      27.452  60.694  14.139  1.00  0.00              
ATOM     94  CA  THR    44      27.042  59.387  13.569  1.00  0.00              
ATOM     95  C   THR    44      27.270  58.268  14.573  1.00  0.00              
ATOM     96  O   THR    44      27.705  57.182  14.242  1.00  0.00              
ATOM     97  N   GLY    45      26.978  58.542  15.792  1.00  0.00              
ATOM     98  CA  GLY    45      27.157  57.541  16.873  1.00  0.00              
ATOM     99  C   GLY    45      26.766  56.139  16.392  1.00  0.00              
ATOM    100  O   GLY    45      25.725  55.944  15.794  1.00  0.00              
ATOM    101  N   LYS    46      27.593  55.163  16.654  1.00  0.00              
ATOM    102  CA  LYS    46      27.270  53.772  16.220  1.00  0.00              
ATOM    103  C   LYS    46      26.386  53.097  17.260  1.00  0.00              
ATOM    104  O   LYS    46      25.509  52.317  16.943  1.00  0.00              
ATOM    105  N   SER    47      26.610  53.412  18.497  1.00  0.00              
ATOM    106  CA  SER    47      25.795  52.827  19.596  1.00  0.00              
ATOM    107  C   SER    47      24.348  52.769  19.169  1.00  0.00              
ATOM    108  O   SER    47      23.604  51.871  19.505  1.00  0.00              
ATOM    109  N   THR    48      23.975  53.730  18.404  1.00  0.00              
ATOM    110  CA  THR    48      22.587  53.801  17.872  1.00  0.00              
ATOM    111  C   THR    48      22.082  52.406  17.502  1.00  0.00              
ATOM    112  O   THR    48      20.896  52.165  17.467  1.00  0.00              
ATOM    113  N   GLN    49      23.004  51.516  17.193  1.00  0.00              
ATOM    114  CA  GLN    49      22.689  50.117  16.774  1.00  0.00              
ATOM    115  C   GLN    49      22.525  50.064  15.271  1.00  0.00              
ATOM    116  O   GLN    49      22.650  49.029  14.646  1.00  0.00              
ATOM    117  N   LYS    50      22.257  51.183  14.695  1.00  0.00              
ATOM    118  CA  LYS    50      22.091  51.270  13.238  1.00  0.00              
ATOM    119  C   LYS    50      22.324  52.712  12.798  1.00  0.00              
ATOM    120  O   LYS    50      22.174  53.639  13.567  1.00  0.00              
ATOM    121  N   PRO    51      22.703  52.909  11.580  1.00  0.00              
ATOM    122  CA  PRO    51      22.947  54.308  11.105  1.00  0.00              
ATOM    123  C   PRO    51      22.010  54.678   9.956  1.00  0.00              
ATOM    124  O   PRO    51      21.024  54.016   9.701  1.00  0.00              
ATOM    125  N   LEU    52      22.308  55.752   9.273  1.00  0.00              
ATOM    126  CA  LEU    52      21.436  56.197   8.153  1.00  0.00              
ATOM    127  C   LEU    52      22.271  56.545   6.918  1.00  0.00              
ATOM    128  O   LEU    52      21.825  57.258   6.042  1.00  0.00              
ATOM    129  N   HIS    53      23.473  56.044   6.828  1.00  0.00              
ATOM    130  CA  HIS    53      24.310  56.357   5.623  1.00  0.00              
ATOM    131  C   HIS    53      24.399  55.138   4.725  1.00  0.00              
ATOM    132  O   HIS    53      24.293  55.215   3.516  1.00  0.00              
ATOM    133  N   TYR    54      24.603  54.019   5.322  1.00  0.00              
ATOM    134  CA  TYR    54      24.719  52.756   4.561  1.00  0.00              
ATOM    135  C   TYR    54      23.343  52.259   4.149  1.00  0.00              
ATOM    136  O   TYR    54      23.133  51.784   3.050  1.00  0.00              
ATOM    137  N   LYS    55      22.418  52.367   5.041  1.00  0.00              
ATOM    138  CA  LYS    55      21.028  51.913   4.766  1.00  0.00              
ATOM    139  C   LYS    55      20.638  52.219   3.317  1.00  0.00              
ATOM    140  O   LYS    55      20.771  51.332   2.490  1.00  0.00              
END
