
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0299AL381_3-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299AL381_3-D1.T0299_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      38      M       1           -
LGA    Y      39      T       2           -
LGA    I      40      R       3           -
LGA    N      41      -       -           -
LGA    S      42      Y       4          4.165
LGA    G      43      A       5          3.197
LGA    -       -      L       6           -
LGA    -       -      L       7           -
LGA    -       -      V       8           -
LGA    -       -      R       9           -
LGA    -       -      G      10           -
LGA    -       -      I      11           -
LGA    -       -      N      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    -       -      V      19           -
LGA    -       -      V      20           -
LGA    -       -      M      21           -
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    -       -      L      24           -
LGA    -       -      R      25           -
LGA    -       -      Q      26           -
LGA    -       -      E      27           -
LGA    -       -      L      28           -
LGA    -       -      T      29           -
LGA    -       -      N      30           -
LGA    -       -      L      31           -
LGA    -       -      G      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    -       -      E      37           -
LGA    -       -      S      38           -
LGA    -       -      Y      39           -
LGA    -       -      I      40           -
LGA    -       -      N      41           -
LGA    -       -      S      42           -
LGA    -       -      G      43           -
LGA    -       -      N      44           -
LGA    -       -      I      45           -
LGA    N      44      F      46          5.071
LGA    I      45      F      47          1.113
LGA    F      46      -       -           -
LGA    F      47      T      48          3.707
LGA    T      48      S      49          3.087
LGA    S      49      -       -           -
LGA    I      50      -       -           -
LGA    D      51      -       -           -
LGA    S      52      -       -           -
LGA    K      53      I      50          2.286
LGA    A      54      -       -           -
LGA    Q      55      D      51          3.055
LGA    L      56      S      52          1.493
LGA    V      57      K      53          1.251
LGA    E      58      A      54          1.183
LGA    K      59      Q      55          0.786
LGA    L      60      L      56          1.021
LGA    E      61      V      57          1.364
LGA    T      62      E      58          1.055
LGA    F      63      K      59          0.981
LGA    F      64      L      60          0.918
LGA    A      65      E      61          0.727
LGA    V      66      T      62          1.063
LGA    H      67      F      63          1.450
LGA    Y      68      F      64          1.232
LGA    P      69      A      65          1.182
LGA    -       -      V      66           -
LGA    -       -      H      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      F      70           -
LGA    F      70      I      71          3.700
LGA    I      71      Q      72          2.775
LGA    Q      72      S      73          1.618
LGA    S      73      F      74          1.695
LGA    F      74      S      75          1.408
LGA    S      75      L      76          2.812
LGA    L      76      L      77          5.140
LGA    L      77      S      78          4.648
LGA    -       -      A     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      F     171           -
LGA    -       -      D     172           -
LGA    -       -      K     173           -
LGA    S      78      I     174          3.542
LGA    -       -      G     175           -
LGA    -       -      Q     176           -
LGA    -       -      M     177           -
LGA    -       -      L     178           -
LGA    -       -      K     179           -
LGA    -       -      K     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   91    5.0     31    2.59     6.45     26.909     1.152

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.667172 * X  +  -0.563823 * Y  +  -0.486812 * Z  +  52.181679
  Y_new =   0.742785 * X  +   0.454288 * Y  +   0.491827 * Z  + -20.794640
  Z_new =  -0.056150 * X  +  -0.689729 * Y  +   0.721887 * Z  + -34.228642 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.762621    2.378972  [ DEG:   -43.6950    136.3050 ]
  Theta =   0.056180    3.085413  [ DEG:     3.2189    176.7811 ]
  Phi   =   0.838975   -2.302618  [ DEG:    48.0697   -131.9303 ]
 
# 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: T0299AL381_3-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL381_3-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   91   5.0   31   2.59    6.45  26.909
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL381_3-D1
REMARK Aligment from pdb entry: 1zbrA
ATOM      1  N   SER    38       1.362  40.397   4.386  1.00  0.00              
ATOM      2  CA  SER    38       1.002  41.589   3.629  1.00  0.00              
ATOM      3  C   SER    38      -0.090  41.282   2.609  1.00  0.00              
ATOM      4  O   SER    38      -0.088  40.226   1.988  1.00  0.00              
ATOM      5  N   TYR    39      -1.024  42.212   2.446  1.00  0.00              
ATOM      6  CA  TYR    39      -2.126  42.051   1.507  1.00  0.00              
ATOM      7  C   TYR    39      -2.212  43.297   0.629  1.00  0.00              
ATOM      8  O   TYR    39      -2.067  44.420   1.123  1.00  0.00              
ATOM      9  N   ILE    40      -2.449  43.089  -0.664  1.00  0.00              
ATOM     10  CA  ILE    40      -2.574  44.173  -1.643  1.00  0.00              
ATOM     11  C   ILE    40      -3.989  44.170  -2.236  1.00  0.00              
ATOM     12  O   ILE    40      -4.410  43.171  -2.816  1.00  0.00              
ATOM     13  N   ASN    41      -4.734  45.260  -2.089  1.00  0.00              
ATOM     14  CA  ASN    41      -6.080  45.304  -2.661  1.00  0.00              
ATOM     15  C   ASN    41      -6.318  46.644  -3.328  1.00  0.00              
ATOM     16  O   ASN    41      -5.371  47.315  -3.734  1.00  0.00              
ATOM     17  N   SER    42      -7.582  47.034  -3.433  1.00  0.00              
ATOM     18  CA  SER    42      -7.929  48.291  -4.077  1.00  0.00              
ATOM     19  C   SER    42      -9.147  48.930  -3.444  1.00  0.00              
ATOM     20  O   SER    42     -10.191  48.296  -3.309  1.00  0.00              
ATOM     21  N   GLY    43      -9.014  50.194  -3.060  1.00  0.00              
ATOM     22  CA  GLY    43     -10.119  50.916  -2.444  1.00  0.00              
ATOM     23  C   GLY    43     -11.409  50.866  -3.239  1.00  0.00              
ATOM     24  O   GLY    43     -12.486  50.817  -2.658  1.00  0.00              
ATOM     25  N   ASN    44     -11.300  50.870  -4.562  1.00  0.00              
ATOM     26  CA  ASN    44     -12.470  50.869  -5.428  1.00  0.00              
ATOM     27  C   ASN    44     -13.290  49.600  -5.322  1.00  0.00              
ATOM     28  O   ASN    44     -14.447  49.551  -5.742  1.00  0.00              
ATOM     29  N   ILE    45     -12.679  48.567  -4.771  1.00  0.00              
ATOM     30  CA  ILE    45     -13.346  47.286  -4.639  1.00  0.00              
ATOM     31  C   ILE    45     -13.664  47.036  -3.174  1.00  0.00              
ATOM     32  O   ILE    45     -14.761  46.611  -2.832  1.00  0.00              
ATOM     33  N   PHE    46     -12.709  47.336  -2.307  1.00  0.00              
ATOM     34  CA  PHE    46     -12.912  47.112  -0.889  1.00  0.00              
ATOM     35  C   PHE    46     -14.017  47.997  -0.310  1.00  0.00              
ATOM     36  O   PHE    46     -14.709  47.596   0.628  1.00  0.00              
ATOM     37  N   PHE    47     -14.205  49.185  -0.879  1.00  0.00              
ATOM     38  CA  PHE    47     -15.226  50.098  -0.384  1.00  0.00              
ATOM     39  C   PHE    47     -16.407  50.277  -1.322  1.00  0.00              
ATOM     40  O   PHE    47     -17.015  51.344  -1.361  1.00  0.00              
ATOM     41  N   THR    48     -16.728  49.222  -2.064  1.00  0.00              
ATOM     42  CA  THR    48     -17.863  49.217  -2.990  1.00  0.00              
ATOM     43  C   THR    48     -19.125  49.288  -2.126  1.00  0.00              
ATOM     44  O   THR    48     -19.228  48.602  -1.117  1.00  0.00              
ATOM     45  N   SER    49     -20.102  50.115  -2.511  1.00  0.00              
ATOM     46  CA  SER    49     -21.341  50.249  -1.735  1.00  0.00              
ATOM     47  C   SER    49     -22.206  48.995  -1.539  1.00  0.00              
ATOM     48  O   SER    49     -23.072  48.982  -0.671  1.00  0.00              
ATOM     49  N   ILE    50     -21.969  47.949  -2.325  1.00  0.00              
ATOM     50  CA  ILE    50     -22.749  46.728  -2.184  1.00  0.00              
ATOM     51  C   ILE    50     -21.899  45.574  -1.690  1.00  0.00              
ATOM     52  O   ILE    50     -22.317  44.427  -1.737  1.00  0.00              
ATOM     53  N   ASP    51     -20.699  45.882  -1.218  1.00  0.00              
ATOM     54  CA  ASP    51     -19.819  44.858  -0.688  1.00  0.00              
ATOM     55  C   ASP    51     -20.125  44.758   0.797  1.00  0.00              
ATOM     56  O   ASP    51     -20.951  43.948   1.213  1.00  0.00              
ATOM     57  N   SER    52     -19.467  45.601   1.588  1.00  0.00              
ATOM     58  CA  SER    52     -19.667  45.632   3.034  1.00  0.00              
ATOM     59  C   SER    52     -19.952  47.063   3.536  1.00  0.00              
ATOM     60  O   SER    52     -19.291  47.559   4.455  1.00  0.00              
ATOM     61  N   LYS    53     -20.935  47.726   2.931  1.00  0.00              
ATOM     62  CA  LYS    53     -21.292  49.087   3.329  1.00  0.00              
ATOM     63  C   LYS    53     -21.833  49.108   4.762  1.00  0.00              
ATOM     64  O   LYS    53     -21.834  50.147   5.424  1.00  0.00              
ATOM     65  N   ALA    54     -22.301  47.958   5.237  1.00  0.00              
ATOM     66  CA  ALA    54     -22.805  47.879   6.599  1.00  0.00              
ATOM     67  C   ALA    54     -21.689  48.105   7.602  1.00  0.00              
ATOM     68  O   ALA    54     -21.935  48.299   8.798  1.00  0.00              
ATOM     69  N   GLN    55     -20.453  48.069   7.107  1.00  0.00              
ATOM     70  CA  GLN    55     -19.280  48.282   7.942  1.00  0.00              
ATOM     71  C   GLN    55     -18.557  49.521   7.495  1.00  0.00              
ATOM     72  O   GLN    55     -18.679  49.941   6.349  1.00  0.00              
ATOM     73  N   LEU    56     -17.785  50.090   8.409  1.00  0.00              
ATOM     74  CA  LEU    56     -17.018  51.293   8.131  1.00  0.00              
ATOM     75  C   LEU    56     -15.733  50.956   7.409  1.00  0.00              
ATOM     76  O   LEU    56     -15.250  49.826   7.453  1.00  0.00              
ATOM     77  N   VAL    57     -15.174  51.969   6.766  1.00  0.00              
ATOM     78  CA  VAL    57     -13.927  51.827   6.054  1.00  0.00              
ATOM     79  C   VAL    57     -12.929  51.082   6.946  1.00  0.00              
ATOM     80  O   VAL    57     -12.432  50.026   6.565  1.00  0.00              
ATOM     81  N   GLU    58     -12.641  51.624   8.132  1.00  0.00              
ATOM     82  CA  GLU    58     -11.676  50.997   9.049  1.00  0.00              
ATOM     83  C   GLU    58     -12.107  49.604   9.463  1.00  0.00              
ATOM     84  O   GLU    58     -11.278  48.713   9.634  1.00  0.00              
ATOM     85  N   LYS    59     -13.408  49.425   9.633  1.00  0.00              
ATOM     86  CA  LYS    59     -13.946  48.134  10.024  1.00  0.00              
ATOM     87  C   LYS    59     -13.577  47.080   8.989  1.00  0.00              
ATOM     88  O   LYS    59     -12.994  46.054   9.323  1.00  0.00              
ATOM     89  N   LEU    60     -13.915  47.334   7.730  1.00  0.00              
ATOM     90  CA  LEU    60     -13.612  46.390   6.654  1.00  0.00              
ATOM     91  C   LEU    60     -12.147  45.911   6.687  1.00  0.00              
ATOM     92  O   LEU    60     -11.864  44.710   6.600  1.00  0.00              
ATOM     93  N   GLU    61     -11.231  46.860   6.848  1.00  0.00              
ATOM     94  CA  GLU    61      -9.806  46.570   6.902  1.00  0.00              
ATOM     95  C   GLU    61      -9.436  45.722   8.122  1.00  0.00              
ATOM     96  O   GLU    61      -8.513  44.905   8.065  1.00  0.00              
ATOM     97  N   THR    62     -10.164  45.883   9.217  1.00  0.00              
ATOM     98  CA  THR    62      -9.859  45.085  10.390  1.00  0.00              
ATOM     99  C   THR    62     -10.355  43.661  10.211  1.00  0.00              
ATOM    100  O   THR    62      -9.837  42.749  10.831  1.00  0.00              
ATOM    101  N   PHE    63     -11.363  43.465   9.368  1.00  0.00              
ATOM    102  CA  PHE    63     -11.868  42.113   9.127  1.00  0.00              
ATOM    103  C   PHE    63     -10.839  41.337   8.304  1.00  0.00              
ATOM    104  O   PHE    63     -10.643  40.141   8.500  1.00  0.00              
ATOM    105  N   PHE    64     -10.196  42.025   7.369  1.00  0.00              
ATOM    106  CA  PHE    64      -9.194  41.398   6.527  1.00  0.00              
ATOM    107  C   PHE    64      -8.015  40.966   7.384  1.00  0.00              
ATOM    108  O   PHE    64      -7.524  39.848   7.270  1.00  0.00              
ATOM    109  N   ALA    65      -7.570  41.867   8.251  1.00  0.00              
ATOM    110  CA  ALA    65      -6.449  41.588   9.123  1.00  0.00              
ATOM    111  C   ALA    65      -6.740  40.396  10.020  1.00  0.00              
ATOM    112  O   ALA    65      -5.850  39.596  10.311  1.00  0.00              
ATOM    113  N   VAL    66      -7.990  40.267  10.448  1.00  0.00              
ATOM    114  CA  VAL    66      -8.381  39.149  11.301  1.00  0.00              
ATOM    115  C   VAL    66      -8.654  37.869  10.495  1.00  0.00              
ATOM    116  O   VAL    66      -8.095  36.806  10.778  1.00  0.00              
ATOM    117  N   HIS    67      -9.517  37.986   9.491  1.00  0.00              
ATOM    118  CA  HIS    67      -9.888  36.864   8.636  1.00  0.00              
ATOM    119  C   HIS    67      -8.712  36.209   7.925  1.00  0.00              
ATOM    120  O   HIS    67      -8.671  34.991   7.775  1.00  0.00              
ATOM    121  N   TYR    68      -7.764  37.027   7.482  1.00  0.00              
ATOM    122  CA  TYR    68      -6.603  36.538   6.753  1.00  0.00              
ATOM    123  C   TYR    68      -5.313  36.565   7.569  1.00  0.00              
ATOM    124  O   TYR    68      -4.281  36.068   7.121  1.00  0.00              
ATOM    125  N   PRO    69      -5.364  37.153   8.759  1.00  0.00              
ATOM    126  CA  PRO    69      -4.176  37.201   9.594  1.00  0.00              
ATOM    127  C   PRO    69      -3.088  38.133   9.095  1.00  0.00              
ATOM    128  O   PRO    69      -1.986  38.147   9.643  1.00  0.00              
ATOM    129  N   PHE    70      -3.385  38.916   8.060  1.00  0.00              
ATOM    130  CA  PHE    70      -2.410  39.855   7.513  1.00  0.00              
ATOM    131  C   PHE    70      -2.204  41.056   8.440  1.00  0.00              
ATOM    132  O   PHE    70      -3.163  41.623   8.970  1.00  0.00              
ATOM    133  N   ILE    71      -0.938  41.424   8.629  1.00  0.00              
ATOM    134  CA  ILE    71      -0.551  42.541   9.488  1.00  0.00              
ATOM    135  C   ILE    71      -0.834  43.880   8.835  1.00  0.00              
ATOM    136  O   ILE    71      -1.297  44.815   9.486  1.00  0.00              
ATOM    137  N   GLN    72      -0.542  43.967   7.544  1.00  0.00              
ATOM    138  CA  GLN    72      -0.745  45.200   6.798  1.00  0.00              
ATOM    139  C   GLN    72      -1.528  45.019   5.503  1.00  0.00              
ATOM    140  O   GLN    72      -1.340  44.041   4.771  1.00  0.00              
ATOM    141  N   SER    73      -2.417  45.967   5.231  1.00  0.00              
ATOM    142  CA  SER    73      -3.216  45.917   4.013  1.00  0.00              
ATOM    143  C   SER    73      -2.947  47.169   3.200  1.00  0.00              
ATOM    144  O   SER    73      -3.345  48.263   3.590  1.00  0.00              
ATOM    145  N   PHE    74      -2.255  47.009   2.078  1.00  0.00              
ATOM    146  CA  PHE    74      -1.934  48.142   1.224  1.00  0.00              
ATOM    147  C   PHE    74      -3.004  48.266   0.142  1.00  0.00              
ATOM    148  O   PHE    74      -3.064  47.442  -0.771  1.00  0.00              
ATOM    149  N   SER    75      -3.853  49.287   0.247  1.00  0.00              
ATOM    150  CA  SER    75      -4.930  49.493  -0.730  1.00  0.00              
ATOM    151  C   SER    75      -4.670  50.626  -1.713  1.00  0.00              
ATOM    152  O   SER    75      -4.522  51.777  -1.316  1.00  0.00              
ATOM    153  N   LEU    76      -4.649  50.300  -3.001  1.00  0.00              
ATOM    154  CA  LEU    76      -4.426  51.308  -4.027  1.00  0.00              
ATOM    155  C   LEU    76      -5.699  52.111  -4.267  1.00  0.00              
ATOM    156  O   LEU    76      -6.804  51.571  -4.191  1.00  0.00              
ATOM    157  N   LEU    77      -5.546  53.403  -4.543  1.00  0.00              
ATOM    158  CA  LEU    77      -6.700  54.248  -4.821  1.00  0.00              
ATOM    159  C   LEU    77      -6.719  54.640  -6.290  1.00  0.00              
ATOM    160  O   LEU    77      -7.553  55.430  -6.727  1.00  0.00              
ATOM    161  N   SER    78      -5.802  54.047  -7.052  1.00  0.00              
ATOM    162  CA  SER    78      -5.703  54.286  -8.488  1.00  0.00              
ATOM    163  C   SER    78      -5.614  52.947  -9.230  1.00  0.00              
ATOM    164  O   SER    78      -5.175  51.944  -8.669  1.00  0.00              
END
