
#######################################################
#                                                     #
#                        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   39 (  156),  selected   39 , name T0349AL381_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL381_5-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    -       -      L      12           -
LGA    L      13      L      13          0.161
LGA    S      14      S      14          0.905
LGA    A      15      A      15          1.352
LGA    V      16      V      16          1.028
LGA    G      17      G      17          1.472
LGA    A      18      A      18          1.280
LGA    L      19      L      19          1.167
LGA    L      20      L      20          0.864
LGA    D      21      D      21          0.675
LGA    G      22      G      22          0.239
LGA    A      23      A      23          0.412
LGA    D      24      D      24          1.178
LGA    I      25      I      25          0.332
LGA    G      26      G      26          1.771
LGA    H      27      H      27          1.826
LGA    L      28      L      28          1.367
LGA    V      29      V      29          1.338
LGA    R      46      P      45          3.787
LGA    -       -      R      46           -
LGA    R      47      R      47          0.581
LGA    V      48      V      48          1.176
LGA    L      49      L      49          1.626
LGA    V      50      V      50          0.938
LGA    H      51      H      51          0.687
LGA    E      52      E      52          1.150
LGA    D      53      D      53          1.639
LGA    D      54      D      54          1.114
LGA    L      55      L      55          0.663
LGA    A      56      A      56          0.870
LGA    G      57      G      57          0.528
LGA    A      58      A      58          0.562
LGA    R      59      R      59          1.082
LGA    R      60      R      60          1.017
LGA    L      61      L      61          0.541
LGA    L      62      L      62          0.139
LGA    T      63      T      63          0.593
LGA    D      64      D      64          2.000
LGA    A      65      A      65          2.964
LGA    -       -      G      66           -
LGA    G      66      L      67          1.714
LGA    L      67      A      68          1.928
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39   57    5.0     39    1.35    92.31     64.820     2.685

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.943599 * X  +   0.057910 * Y  +  -0.325987 * Z  +  31.530996
  Y_new =   0.305692 * X  +  -0.225807 * Y  +  -0.924967 * Z  +  38.411533
  Z_new =  -0.127175 * X  +  -0.972449 * Y  +   0.195369 * Z  +   6.167877 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.372532    1.769061  [ DEG:   -78.6403    101.3597 ]
  Theta =   0.127520    3.014073  [ DEG:     7.3064    172.6936 ]
  Phi   =   2.828298   -0.313295  [ DEG:   162.0495    -17.9505 ]
 
# 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: T0349AL381_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL381_5-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39   57   5.0   39   1.35   92.31  64.820
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL381_5-D1
REMARK Aligment from pdb entry: 1zhvA
ATOM      1  N   LEU    13      -3.632  -2.886   5.980  1.00  0.00              
ATOM      2  CA  LEU    13      -3.911  -1.624   5.307  1.00  0.00              
ATOM      3  C   LEU    13      -4.271  -0.561   6.342  1.00  0.00              
ATOM      4  O   LEU    13      -3.783   0.566   6.283  1.00  0.00              
ATOM      5  N   SER    14      -5.120  -0.923   7.298  1.00  0.00              
ATOM      6  CA  SER    14      -5.523   0.011   8.339  1.00  0.00              
ATOM      7  C   SER    14      -4.319   0.609   9.068  1.00  0.00              
ATOM      8  O   SER    14      -4.252   1.821   9.278  1.00  0.00              
ATOM      9  N   ALA    15      -3.368  -0.245   9.437  1.00  0.00              
ATOM     10  CA  ALA    15      -2.187   0.197  10.175  1.00  0.00              
ATOM     11  C   ALA    15      -1.388   1.248   9.419  1.00  0.00              
ATOM     12  O   ALA    15      -0.732   2.099  10.026  1.00  0.00              
ATOM     13  N   VAL    16      -1.456   1.200   8.094  1.00  0.00              
ATOM     14  CA  VAL    16      -0.722   2.146   7.272  1.00  0.00              
ATOM     15  C   VAL    16      -1.507   3.423   6.977  1.00  0.00              
ATOM     16  O   VAL    16      -0.985   4.522   7.129  1.00  0.00              
ATOM     17  N   GLY    17      -2.769   3.292   6.584  1.00  0.00              
ATOM     18  CA  GLY    17      -3.538   4.489   6.265  1.00  0.00              
ATOM     19  C   GLY    17      -4.050   5.286   7.460  1.00  0.00              
ATOM     20  O   GLY    17      -4.307   6.483   7.335  1.00  0.00              
ATOM     21  N   ALA    18      -4.182   4.653   8.622  1.00  0.00              
ATOM     22  CA  ALA    18      -4.679   5.379   9.793  1.00  0.00              
ATOM     23  C   ALA    18      -3.835   6.615  10.123  1.00  0.00              
ATOM     24  O   ALA    18      -4.370   7.715  10.277  1.00  0.00              
ATOM     25  N   LEU    19      -2.505   6.456  10.241  1.00  0.00              
ATOM     26  CA  LEU    19      -1.688   7.637  10.555  1.00  0.00              
ATOM     27  C   LEU    19      -1.688   8.706   9.468  1.00  0.00              
ATOM     28  O   LEU    19      -1.435   9.880   9.739  1.00  0.00              
ATOM     29  N   LEU    20      -1.979   8.310   8.236  1.00  0.00              
ATOM     30  CA  LEU    20      -2.008   9.268   7.139  1.00  0.00              
ATOM     31  C   LEU    20      -3.344  10.010   7.079  1.00  0.00              
ATOM     32  O   LEU    20      -3.389  11.243   7.082  1.00  0.00              
ATOM     33  N   ASP    21      -4.435   9.251   7.045  1.00  0.00              
ATOM     34  CA  ASP    21      -5.770   9.830   6.965  1.00  0.00              
ATOM     35  C   ASP    21      -6.138  10.708   8.154  1.00  0.00              
ATOM     36  O   ASP    21      -6.811  11.728   7.986  1.00  0.00              
ATOM     37  N   GLY    22      -5.697  10.320   9.346  1.00  0.00              
ATOM     38  CA  GLY    22      -5.993  11.091  10.550  1.00  0.00              
ATOM     39  C   GLY    22      -5.161  12.366  10.590  1.00  0.00              
ATOM     40  O   GLY    22      -5.428  13.263  11.389  1.00  0.00              
ATOM     41  N   ALA    23      -4.164  12.460   9.718  1.00  0.00              
ATOM     42  CA  ALA    23      -3.313  13.643   9.692  1.00  0.00              
ATOM     43  C   ALA    23      -3.333  14.444   8.388  1.00  0.00              
ATOM     44  O   ALA    23      -2.330  15.036   7.989  1.00  0.00              
ATOM     45  N   ASP    24      -4.489  14.457   7.730  1.00  0.00              
ATOM     46  CA  ASP    24      -4.653  15.227   6.508  1.00  0.00              
ATOM     47  C   ASP    24      -3.984  14.761   5.229  1.00  0.00              
ATOM     48  O   ASP    24      -3.855  15.543   4.284  1.00  0.00              
ATOM     49  N   ILE    25      -3.557  13.505   5.176  1.00  0.00              
ATOM     50  CA  ILE    25      -2.915  13.003   3.968  1.00  0.00              
ATOM     51  C   ILE    25      -3.882  12.125   3.178  1.00  0.00              
ATOM     52  O   ILE    25      -4.357  11.109   3.677  1.00  0.00              
ATOM     53  N   GLY    26      -4.182  12.535   1.952  1.00  0.00              
ATOM     54  CA  GLY    26      -5.080  11.756   1.122  1.00  0.00              
ATOM     55  C   GLY    26      -4.400  10.471   0.706  1.00  0.00              
ATOM     56  O   GLY    26      -3.194  10.455   0.438  1.00  0.00              
ATOM     57  N   HIS    27      -5.169   9.388   0.660  1.00  0.00              
ATOM     58  CA  HIS    27      -4.631   8.088   0.277  1.00  0.00              
ATOM     59  C   HIS    27      -5.380   7.450  -0.888  1.00  0.00              
ATOM     60  O   HIS    27      -6.571   7.687  -1.089  1.00  0.00              
ATOM     61  N   LEU    28      -4.658   6.637  -1.649  1.00  0.00              
ATOM     62  CA  LEU    28      -5.210   5.940  -2.807  1.00  0.00              
ATOM     63  C   LEU    28      -4.653   4.529  -2.665  1.00  0.00              
ATOM     64  O   LEU    28      -3.451   4.314  -2.784  1.00  0.00              
ATOM     65  N   VAL    29      -5.530   3.569  -2.400  1.00  0.00              
ATOM     66  CA  VAL    29      -5.097   2.196  -2.187  1.00  0.00              
ATOM     67  C   VAL    29      -5.518   1.234  -3.271  1.00  0.00              
ATOM     68  O   VAL    29      -6.656   1.252  -3.717  1.00  0.00              
ATOM     93  N   ARG    46      -0.810  -5.134  -1.384  1.00  0.00              
ATOM     94  CA  ARG    46      -1.349  -3.802  -1.624  1.00  0.00              
ATOM     95  C   ARG    46      -0.288  -2.808  -2.048  1.00  0.00              
ATOM     96  O   ARG    46       0.898  -2.973  -1.764  1.00  0.00              
ATOM     97  N   ARG    47      -0.753  -1.766  -2.726  1.00  0.00              
ATOM     98  CA  ARG    47       0.085  -0.648  -3.125  1.00  0.00              
ATOM     99  C   ARG    47      -0.651   0.582  -2.615  1.00  0.00              
ATOM    100  O   ARG    47      -1.877   0.582  -2.505  1.00  0.00              
ATOM    101  N   VAL    48       0.101   1.620  -2.279  1.00  0.00              
ATOM    102  CA  VAL    48      -0.471   2.857  -1.762  1.00  0.00              
ATOM    103  C   VAL    48       0.110   4.038  -2.511  1.00  0.00              
ATOM    104  O   VAL    48       1.315   4.093  -2.732  1.00  0.00              
ATOM    105  N   LEU    49      -0.741   4.969  -2.919  1.00  0.00              
ATOM    106  CA  LEU    49      -0.241   6.169  -3.559  1.00  0.00              
ATOM    107  C   LEU    49      -0.686   7.369  -2.732  1.00  0.00              
ATOM    108  O   LEU    49      -1.770   7.376  -2.149  1.00  0.00              
ATOM    109  N   VAL    50       0.190   8.359  -2.651  1.00  0.00              
ATOM    110  CA  VAL    50      -0.099   9.597  -1.950  1.00  0.00              
ATOM    111  C   VAL    50       0.417  10.671  -2.890  1.00  0.00              
ATOM    112  O   VAL    50       1.231  10.385  -3.769  1.00  0.00              
ATOM    113  N   HIS    51      -0.062  11.898  -2.728  1.00  0.00              
ATOM    114  CA  HIS    51       0.411  12.972  -3.584  1.00  0.00              
ATOM    115  C   HIS    51       1.894  13.148  -3.307  1.00  0.00              
ATOM    116  O   HIS    51       2.343  13.041  -2.159  1.00  0.00              
ATOM    117  N   GLU    52       2.658  13.407  -4.359  1.00  0.00              
ATOM    118  CA  GLU    52       4.091  13.573  -4.214  1.00  0.00              
ATOM    119  C   GLU    52       4.488  14.684  -3.262  1.00  0.00              
ATOM    120  O   GLU    52       5.518  14.593  -2.607  1.00  0.00              
ATOM    121  N   ASP    53       3.676  15.727  -3.177  1.00  0.00              
ATOM    122  CA  ASP    53       3.988  16.824  -2.275  1.00  0.00              
ATOM    123  C   ASP    53       3.806  16.407  -0.815  1.00  0.00              
ATOM    124  O   ASP    53       4.237  17.120   0.094  1.00  0.00              
ATOM    125  N   ASP    54       3.178  15.251  -0.595  1.00  0.00              
ATOM    126  CA  ASP    54       2.960  14.726   0.757  1.00  0.00              
ATOM    127  C   ASP    54       3.973  13.640   1.119  1.00  0.00              
ATOM    128  O   ASP    54       3.885  13.032   2.186  1.00  0.00              
ATOM    129  N   LEU    55       4.942  13.413   0.240  1.00  0.00              
ATOM    130  CA  LEU    55       5.939  12.369   0.451  1.00  0.00              
ATOM    131  C   LEU    55       6.738  12.482   1.749  1.00  0.00              
ATOM    132  O   LEU    55       6.887  11.496   2.481  1.00  0.00              
ATOM    133  N   ALA    56       7.247  13.673   2.042  1.00  0.00              
ATOM    134  CA  ALA    56       8.038  13.881   3.251  1.00  0.00              
ATOM    135  C   ALA    56       7.214  13.699   4.524  1.00  0.00              
ATOM    136  O   ALA    56       7.663  13.064   5.476  1.00  0.00              
ATOM    137  N   GLY    57       6.005  14.251   4.539  1.00  0.00              
ATOM    138  CA  GLY    57       5.140  14.108   5.707  1.00  0.00              
ATOM    139  C   GLY    57       4.707  12.653   5.864  1.00  0.00              
ATOM    140  O   GLY    57       4.639  12.134   6.974  1.00  0.00              
ATOM    141  N   ALA    58       4.440  11.991   4.742  1.00  0.00              
ATOM    142  CA  ALA    58       4.020  10.598   4.777  1.00  0.00              
ATOM    143  C   ALA    58       5.104   9.732   5.407  1.00  0.00              
ATOM    144  O   ALA    58       4.824   8.888   6.263  1.00  0.00              
ATOM    145  N   ARG    59       6.347   9.947   4.993  1.00  0.00              
ATOM    146  CA  ARG    59       7.451   9.173   5.545  1.00  0.00              
ATOM    147  C   ARG    59       7.617   9.403   7.046  1.00  0.00              
ATOM    148  O   ARG    59       7.845   8.450   7.797  1.00  0.00              
ATOM    149  N   ARG    60       7.486  10.654   7.497  1.00  0.00              
ATOM    150  CA  ARG    60       7.623  10.950   8.923  1.00  0.00              
ATOM    151  C   ARG    60       6.516  10.270   9.722  1.00  0.00              
ATOM    152  O   ARG    60       6.775   9.665  10.760  1.00  0.00              
ATOM    153  N   LEU    61       5.286  10.369   9.228  1.00  0.00              
ATOM    154  CA  LEU    61       4.145   9.778   9.911  1.00  0.00              
ATOM    155  C   LEU    61       4.203   8.260   9.964  1.00  0.00              
ATOM    156  O   LEU    61       3.885   7.667  10.991  1.00  0.00              
ATOM    157  N   LEU    62       4.614   7.628   8.872  1.00  0.00              
ATOM    158  CA  LEU    62       4.685   6.173   8.857  1.00  0.00              
ATOM    159  C   LEU    62       5.800   5.651   9.760  1.00  0.00              
ATOM    160  O   LEU    62       5.633   4.635  10.434  1.00  0.00              
ATOM    161  N   THR    63       6.935   6.340   9.785  1.00  0.00              
ATOM    162  CA  THR    63       8.032   5.905  10.645  1.00  0.00              
ATOM    163  C   THR    63       7.619   6.019  12.110  1.00  0.00              
ATOM    164  O   THR    63       7.851   5.108  12.905  1.00  0.00              
ATOM    165  N   ASP    64       6.994   7.134  12.472  1.00  0.00              
ATOM    166  CA  ASP    64       6.561   7.322  13.853  1.00  0.00              
ATOM    167  C   ASP    64       5.563   6.235  14.253  1.00  0.00              
ATOM    168  O   ASP    64       5.505   5.828  15.416  1.00  0.00              
ATOM    169  N   ALA    65       4.797   5.753  13.275  1.00  0.00              
ATOM    170  CA  ALA    65       3.802   4.707  13.510  1.00  0.00              
ATOM    171  C   ALA    65       4.435   3.314  13.609  1.00  0.00              
ATOM    172  O   ALA    65       3.743   2.318  13.832  1.00  0.00              
ATOM    173  N   GLY    66       5.752   3.250  13.433  1.00  0.00              
ATOM    174  CA  GLY    66       6.459   1.988  13.545  1.00  0.00              
ATOM    175  C   GLY    66       6.743   1.230  12.264  1.00  0.00              
ATOM    176  O   GLY    66       7.305   0.134  12.303  1.00  0.00              
ATOM    177  N   LEU    67       6.353   1.790  11.126  1.00  0.00              
ATOM    178  CA  LEU    67       6.592   1.119   9.858  1.00  0.00              
ATOM    179  C   LEU    67       8.002   1.360   9.347  1.00  0.00              
ATOM    180  O   LEU    67       8.650   2.338   9.720  1.00  0.00              
END
