
#######################################################
#                                                     #
#                        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   34 (  140),  selected   34 , name T0353AL586_1
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353AL586_1.T0353.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    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      I       3           -
LGA    -       -      H       4           -
LGA    -       -      V       5           -
LGA    -       -      Y       6           -
LGA    -       -      D       7           -
LGA    -       -      T       8           -
LGA    -       -      Y       9           -
LGA    -       -      V      10           -
LGA    -       -      K      11           -
LGA    -       -      A      12           -
LGA    -       -      K      13           -
LGA    -       -      D      14           -
LGA    -       -      G      15           -
LGA    -       -      H      16           -
LGA    D       7      V      17          3.168
LGA    Y       9      M      18          4.571
LGA    V      10      H      19          5.760
LGA    K      11      F      20          4.542
LGA    A      12      D      21           #
LGA    V      17      -       -           -
LGA    V      22      V      22          3.484
LGA    F      23      F      23          4.394
LGA    -       -      T      24           -
LGA    -       -      D      25           -
LGA    -       -      V      26           -
LGA    -       -      R      27           -
LGA    -       -      D      28           -
LGA    A      32      D      29          2.989
LGA    -       -      K      30           -
LGA    -       -      K      31           -
LGA    -       -      A      32           -
LGA    F      35      I      33          2.913
LGA    A      36      E      34          3.931
LGA    Q      38      F      35          2.946
LGA    -       -      A      36           -
LGA    -       -      K      37           -
LGA    -       -      Q      38           -
LGA    L      40      W      39          3.433
LGA    -       -      L      40           -
LGA    -       -      S      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    G      44      E      45          3.197
LGA    E      45      E      46          3.281
LGA    -       -      G      47           -
LGA    -       -      A      48           -
LGA    -       -      T      49           -
LGA    G      47      V      50          1.697
LGA    -       -      T      51           -
LGA    -       -      S      52           -
LGA    -       -      E      53           -
LGA    A      48      E      54          3.768
LGA    T      49      C      55          2.703
LGA    V      50      R      56          3.345
LGA    S      52      -       -           -
LGA    E      54      -       -           -
LGA    R      56      F      57          2.132
LGA    F      57      C      58           #
LGA    -       -      H      59           -
LGA    -       -      S      60           -
LGA    -       -      Q      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      P      64           -
LGA    -       -      D      65           -
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    -       -      I      68           -
LGA    -       -      E      69           -
LGA    -       -      A      70           -
LGA    -       -      I      71           -
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    -       -      G      75           -
LGA    -       -      Y      76           -
LGA    -       -      F      77           -
LGA    C      58      I      78           #
LGA    H      59      -       -           -
LGA    S      60      -       -           -
LGA    Q      61      -       -           -
LGA    K      62      -       -           -
LGA    A      63      -       -           -
LGA    P      64      -       -           -
LGA    V      67      Y      79           #
LGA    I      71      K      80          2.001
LGA    K      72      M      81          0.918
LGA    C      84      E      82           -
LGA    -       -      G      83           -
LGA    -       -      C      84           -
LGA    -       -      N      85           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34   85    5.0     20    3.43    15.00     12.984     0.566

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.933167 * X  +  -0.358073 * Y  +   0.031359 * Z  +  -3.894221
  Y_new =   0.356832 * X  +   0.912355 * Y  +  -0.200697 * Z  +  -3.988867
  Z_new =   0.043253 * X  +   0.198474 * Y  +   0.979151 * Z  +   2.910264 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.199991   -2.941602  [ DEG:    11.4586   -168.5414 ]
  Theta =  -0.043267   -3.098326  [ DEG:    -2.4790   -177.5210 ]
  Phi   =   0.365232   -2.776361  [ DEG:    20.9263   -159.0737 ]
 
# 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: T0353AL586_1                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353AL586_1.T0353.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34   85   5.0   20   3.43   15.00  12.984
REMARK  ---------------------------------------------------------- 
MOLECULE T0353AL586_1
REMARK Aligment from pdb entry: 1aho
ATOM      1  N   ASP     7      -6.136  -2.053  13.285  1.00  0.00              
ATOM      2  CA  ASP     7      -6.148  -1.042  12.254  1.00  0.00              
ATOM      3  C   ASP     7      -4.731  -0.544  11.977  1.00  0.00              
ATOM      4  O   ASP     7      -3.905  -0.598  12.922  1.00  0.00              
ATOM      5  N   TYR     9      -1.527   1.187   8.949  1.00  0.00              
ATOM      6  CA  TYR     9      -0.952   1.342   7.610  1.00  0.00              
ATOM      7  C   TYR     9      -0.376   0.034   7.154  1.00  0.00              
ATOM      8  O   TYR     9       0.591  -0.474   7.751  1.00  0.00              
ATOM      9  N   VAL    10      -0.900  -0.524   6.071  1.00  0.00              
ATOM     10  CA  VAL    10      -0.402  -1.795   5.535  1.00  0.00              
ATOM     11  C   VAL    10       0.965  -1.572   4.899  1.00  0.00              
ATOM     12  O   VAL    10       1.272  -0.549   4.335  1.00  0.00              
ATOM     13  N   LYS    11       1.796  -2.628   4.995  1.00  0.00              
ATOM     14  CA  LYS    11       3.140  -2.590   4.408  1.00  0.00              
ATOM     15  C   LYS    11       3.469  -3.884   3.699  1.00  0.00              
ATOM     16  O   LYS    11       2.808  -4.912   3.904  1.00  0.00              
ATOM     17  N   ALA    12       4.471  -3.850   2.826  1.00  0.00              
ATOM     18  CA  ALA    12       5.043  -5.024   2.159  1.00  0.00              
ATOM     19  C   ALA    12       5.939  -5.717   3.210  1.00  0.00              
ATOM     20  O   ALA    12       5.996  -5.403   4.397  1.00  0.00              
ATOM     21  N   VAL    17       9.058  -5.603   3.568  1.00  0.00              
ATOM     22  CA  VAL    17      10.233  -4.872   4.020  1.00  0.00              
ATOM     23  C   VAL    17       9.848  -3.517   4.653  1.00  0.00              
ATOM     24  O   VAL    17      10.579  -2.608   4.688  1.00  0.00              
ATOM     25  N   VAL    22       5.154   1.237   2.967  1.00  0.00              
ATOM     26  CA  VAL    22       3.716   1.533   2.813  1.00  0.00              
ATOM     27  C   VAL    22       3.286   1.549   1.362  1.00  0.00              
ATOM     28  O   VAL    22       4.084   1.625   0.422  1.00  0.00              
ATOM     29  N   PHE    23       1.958   1.473   1.163  1.00  0.00              
ATOM     30  CA  PHE    23       1.317   1.456  -0.143  1.00  0.00              
ATOM     31  C   PHE    23       0.971   2.880  -0.587  1.00  0.00              
ATOM     32  O   PHE    23       0.074   3.519  -0.000  1.00  0.00              
ATOM     33  N   ALA    32      -0.763   5.776  -2.677  1.00  0.00              
ATOM     34  CA  ALA    32      -2.108   5.858  -3.198  1.00  0.00              
ATOM     35  C   ALA    32      -2.453   7.304  -3.556  1.00  0.00              
ATOM     36  O   ALA    32      -1.855   8.232  -3.079  1.00  0.00              
ATOM     37  N   PHE    35      -9.028   2.721  -4.273  1.00  0.00              
ATOM     38  CA  PHE    35      -7.866   1.848  -4.474  1.00  0.00              
ATOM     39  C   PHE    35      -7.471   1.238  -3.155  1.00  0.00              
ATOM     40  O   PHE    35      -7.239   0.010  -3.041  1.00  0.00              
ATOM     41  N   ALA    36      -7.361   2.038  -2.082  1.00  0.00              
ATOM     42  CA  ALA    36      -6.989   1.483  -0.797  1.00  0.00              
ATOM     43  C   ALA    36      -8.058   0.568  -0.236  1.00  0.00              
ATOM     44  O   ALA    36      -7.736  -0.432   0.398  1.00  0.00              
ATOM     45  N   GLN    38      -7.275  -2.713  -1.792  1.00  0.00              
ATOM     46  CA  GLN    38      -6.076  -3.341  -1.288  1.00  0.00              
ATOM     47  C   GLN    38      -6.298  -3.854   0.124  1.00  0.00              
ATOM     48  O   GLN    38      -5.781  -4.926   0.527  1.00  0.00              
ATOM     49  N   LEU    40      -6.478  -8.135   1.659  1.00  0.00              
ATOM     50  CA  LEU    40      -5.821  -8.616   2.861  1.00  0.00              
ATOM     51  C   LEU    40      -6.791  -9.024   3.951  1.00  0.00              
ATOM     52  O   LEU    40      -6.359  -9.357   5.080  1.00  0.00              
ATOM     53  N   GLY    44     -11.585  -4.964   6.741  1.00  0.00              
ATOM     54  CA  GLY    44     -12.948  -4.496   6.542  1.00  0.00              
ATOM     55  C   GLY    44     -13.069  -3.488   5.420  1.00  0.00              
ATOM     56  O   GLY    44     -13.925  -3.566   4.542  1.00  0.00              
ATOM     57  N   GLU    45     -12.188  -2.462   5.437  1.00  0.00              
ATOM     58  CA  GLU    45     -12.276  -1.310   4.556  1.00  0.00              
ATOM     59  C   GLU    45     -11.011  -0.501   4.731  1.00  0.00              
ATOM     60  O   GLU    45     -10.167  -0.829   5.586  1.00  0.00              
ATOM     61  N   GLY    47      -8.814   3.499   3.308  1.00  0.00              
ATOM     62  CA  GLY    47      -8.837   4.732   2.537  1.00  0.00              
ATOM     63  C   GLY    47      -7.406   5.193   2.330  1.00  0.00              
ATOM     64  O   GLY    47      -6.465   4.633   2.907  1.00  0.00              
ATOM     65  N   ALA    48      -7.224   6.181   1.466  1.00  0.00              
ATOM     66  CA  ALA    48      -5.912   6.753   1.173  1.00  0.00              
ATOM     67  C   ALA    48      -5.678   7.938   2.087  1.00  0.00              
ATOM     68  O   ALA    48      -6.351   8.971   1.967  1.00  0.00              
ATOM     69  N   THR    49      -4.735   7.788   3.032  1.00  0.00              
ATOM     70  CA  THR    49      -4.375   8.890   3.900  1.00  0.00              
ATOM     71  C   THR    49      -3.364   9.761   3.138  1.00  0.00              
ATOM     72  O   THR    49      -2.195   9.390   2.985  1.00  0.00              
ATOM     73  N   VAL    50      -3.815  10.925   2.667  1.00  0.00              
ATOM     74  CA  VAL    50      -2.903  11.847   2.034  1.00  0.00              
ATOM     75  C   VAL    50      -2.067  12.468   3.147  1.00  0.00              
ATOM     76  O   VAL    50      -2.493  12.765   4.242  1.00  0.00              
ATOM     77  N   SER    52       0.322  11.446   5.171  1.00  0.00              
ATOM     78  CA  SER    52       0.721  10.738   6.373  1.00  0.00              
ATOM     79  C   SER    52       2.227  11.038   6.538  1.00  0.00              
ATOM     80  O   SER    52       2.870  11.583   5.651  1.00  0.00              
ATOM     81  N   GLU    54       4.471   9.157   6.048  1.00  0.00              
ATOM     82  CA  GLU    54       5.112   8.334   5.027  1.00  0.00              
ATOM     83  C   GLU    54       4.702   8.765   3.651  1.00  0.00              
ATOM     84  O   GLU    54       4.933   8.052   2.660  1.00  0.00              
ATOM     85  N   ARG    56       1.586   9.829   0.951  1.00  0.00              
ATOM     86  CA  ARG    56       0.257   9.228   0.793  1.00  0.00              
ATOM     87  C   ARG    56       0.382   7.723   1.043  1.00  0.00              
ATOM     88  O   ARG    56       1.259   7.067   0.460  1.00  0.00              
ATOM     89  N   PHE    57      -0.494   7.184   1.880  1.00  0.00              
ATOM     90  CA  PHE    57      -0.403   5.760   2.225  1.00  0.00              
ATOM     91  C   PHE    57      -1.762   5.210   2.550  1.00  0.00              
ATOM     92  O   PHE    57      -2.594   5.887   3.214  1.00  0.00              
ATOM     93  N   CYS    58      -2.027   3.965   2.164  1.00  0.00              
ATOM     94  CA  CYS    58      -3.282   3.328   2.506  1.00  0.00              
ATOM     95  C   CYS    58      -3.328   2.955   4.024  1.00  0.00              
ATOM     96  O   CYS    58      -2.381   2.425   4.605  1.00  0.00              
ATOM     97  N   HIS    59      -4.492   3.241   4.608  1.00  0.00              
ATOM     98  CA  HIS    59      -4.795   2.924   6.013  1.00  0.00              
ATOM     99  C   HIS    59      -6.008   1.991   5.991  1.00  0.00              
ATOM    100  O   HIS    59      -6.992   2.281   5.300  1.00  0.00              
ATOM    101  N   SER    60      -5.934   0.888   6.727  1.00  0.00              
ATOM    102  CA  SER    60      -6.983  -0.109   6.738  1.00  0.00              
ATOM    103  C   SER    60      -7.566  -0.294   8.130  1.00  0.00              
ATOM    104  O   SER    60      -6.887  -0.174   9.161  1.00  0.00              
ATOM    105  N   GLN    61      -8.849  -0.662   8.176  1.00  0.00              
ATOM    106  CA  GLN    61      -9.556  -0.999   9.404  1.00  0.00              
ATOM    107  C   GLN    61      -9.789  -2.514   9.495  1.00  0.00              
ATOM    108  O   GLN    61     -10.149  -3.135   8.501  1.00  0.00              
ATOM    109  N   LYS    62      -9.635  -3.017  10.687  1.00  0.00              
ATOM    110  CA  LYS    62      -9.995  -4.405  11.008  1.00  0.00              
ATOM    111  C   LYS    62      -9.297  -5.448  10.153  1.00  0.00              
ATOM    112  O   LYS    62      -9.887  -6.422   9.699  1.00  0.00              
ATOM    113  N   ALA    63      -7.982  -5.282  10.021  1.00  0.00              
ATOM    114  CA  ALA    63      -7.166  -6.320   9.442  1.00  0.00              
ATOM    115  C   ALA    63      -7.012  -7.487  10.400  1.00  0.00              
ATOM    116  O   ALA    63      -7.003  -7.335  11.604  1.00  0.00              
ATOM    117  N   PRO    64      -6.814  -8.698   9.866  1.00  0.00              
ATOM    118  CA  PRO    64      -6.456  -9.808  10.741  1.00  0.00              
ATOM    119  C   PRO    64      -5.132  -9.489  11.471  1.00  0.00              
ATOM    120  O   PRO    64      -4.225  -8.820  10.974  1.00  0.00              
ATOM    121  N   VAL    67      -1.536  -9.816   9.768  1.00  0.00              
ATOM    122  CA  VAL    67      -1.043  -8.903   8.721  1.00  0.00              
ATOM    123  C   VAL    67      -0.053  -7.923   9.289  1.00  0.00              
ATOM    124  O   VAL    67      -0.312  -7.358  10.370  1.00  0.00              
ATOM    125  N   ILE    71       1.644  -4.427   9.776  1.00  0.00              
ATOM    126  CA  ILE    71       1.415  -2.999   9.609  1.00  0.00              
ATOM    127  C   ILE    71       2.735  -2.268   9.934  1.00  0.00              
ATOM    128  O   ILE    71       3.674  -2.841  10.485  1.00  0.00              
ATOM    129  N   LYS    72       2.768  -0.982   9.603  1.00  0.00              
ATOM    130  CA  LYS    72       4.000  -0.233   9.710  1.00  0.00              
ATOM    131  C   LYS    72       4.597  -0.213  11.088  1.00  0.00              
ATOM    132  O   LYS    72       3.943   0.036  12.107  1.00  0.00              
ATOM    133  N  ACYS    84      11.232   3.477   5.036  1.00  0.00              
ATOM    134  N  BCYS    84      11.171   3.418   5.128  1.00  0.00              
ATOM    135  CA ACYS    84      11.203   2.743   3.758  1.00  0.00              
ATOM    136  CA BCYS    84      11.076   3.013   3.746  1.00  0.00              
ATOM    137  C  ACYS    84      10.361   3.658   2.901  1.00  0.00              
ATOM    138  C  BCYS    84      10.332   4.091   2.956  1.00  0.00              
ATOM    139  O  ACYS    84       9.220   3.992   3.310  1.00  0.00              
ATOM    140  O  BCYS    84       9.264   4.613   3.293  1.00  0.00              
END
