
#######################################################
#                                                     #
#                        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   37 (  148),  selected   37 , name T0306AL242_4
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306AL242_4.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V       6      M       1          2.448
LGA    T       7      K       2          4.113
LGA    G       8      L       3          3.265
LGA    Q       9      A       4           #
LGA    I      10      V       5          3.540
LGA    V      11      V       6          5.035
LGA    C      12      T       7           #
LGA    T      13      G       8          5.099
LGA    V      14      Q       9          1.673
LGA    -       -      I      10           -
LGA    -       -      V      11           -
LGA    -       -      C      12           -
LGA    -       -      T      13           -
LGA    -       -      V      14           -
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    -       -      K      23           -
LGA    R      15      L      24          3.142
LGA    H      16      L      25          4.920
LGA    H      17      M      26          2.133
LGA    G      18      V      27          1.594
LGA    L      19      -       -           -
LGA    A      20      -       -           -
LGA    H      21      E      28          1.321
LGA    D      22      -       -           -
LGA    K      23      -       -           -
LGA    L      24      M      29          4.589
LGA    L      25      I      30          2.214
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    M      26      D      37          3.804
LGA    V      27      G      38          3.730
LGA    E      28      Q      39          2.538
LGA    M      29      C      40          2.316
LGA    I      30      A      41          3.359
LGA    D      31      V      42          4.207
LGA    P      32      A      43          0.618
LGA    Q      33      I      44          4.628
LGA    G      34      D      45          1.817
LGA    -       -      N      46           -
LGA    -       -      I      47           -
LGA    N      35      G      48          3.799
LGA    P      36      A      49          1.498
LGA    -       -      G      50           -
LGA    -       -      T      51           -
LGA    -       -      G      52           -
LGA    -       -      E      53           -
LGA    D      37      W      54           #
LGA    G      38      V      55          4.462
LGA    -       -      L      56           -
LGA    Q      39      L      57          2.719
LGA    C      40      V      58           #
LGA    A      41      S      59          3.966
LGA    V      42      G      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      A      63           -
LGA    -       -      R      64           -
LGA    -       -      Q      65           -
LGA    -       -      A      66           -
LGA    -       -      H      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    -       -      S      72           -
LGA    -       -      P      73           -
LGA    -       -      V      74           -
LGA    -       -      D      75           -
LGA    -       -      L      76           -
LGA    -       -      C      77           -
LGA    -       -      V      78           -
LGA    -       -      I      79           -
LGA    -       -      G      80           -
LGA    -       -      I      81           -
LGA    -       -      V      82           -
LGA    -       -      D      83           -
LGA    -       -      E      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      S      87           -
LGA    -       -      G      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      I      92           -
LGA    -       -      F      93           -
LGA    -       -      H      94           -
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37   95    5.0     28    3.40     3.57     16.906     0.801

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.135707 * X  +   0.033017 * Y  +   0.990199 * Z  +  40.796028
  Y_new =  -0.745210 * X  +   0.662006 * Y  +   0.080057 * Z  +  27.575890
  Z_new =  -0.652875 * X  +  -0.748770 * Y  +   0.114444 * Z  +  68.755707 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.419128    1.722465  [ DEG:   -81.3101     98.6899 ]
  Theta =   0.711374    2.430219  [ DEG:    40.7587    139.2413 ]
  Phi   =  -1.390665    1.750928  [ DEG:   -79.6792    100.3208 ]
 
# 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: T0306AL242_4                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306AL242_4.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37   95   5.0   28   3.40    3.57  16.906
REMARK  ---------------------------------------------------------- 
MOLECULE T0306AL242_4
REMARK Aligment from pdb entry: 1hp2_A
ATOM      1  N   VAL     6      41.527  35.483  64.915  1.00  0.00              
ATOM      2  CA  VAL     6      42.508  34.771  64.045  1.00  0.00              
ATOM      3  C   VAL     6      42.398  33.257  64.255  1.00  0.00              
ATOM      4  O   VAL     6      41.720  32.795  65.152  1.00  0.00              
ATOM      5  N   THR     7      43.059  32.483  63.438  1.00  0.00              
ATOM      6  CA  THR     7      42.992  31.001  63.596  1.00  0.00              
ATOM      7  C   THR     7      44.396  30.424  63.780  1.00  0.00              
ATOM      8  O   THR     7      45.385  31.104  63.601  1.00  0.00              
ATOM      9  N   GLY     8      44.488  29.170  64.130  1.00  0.00              
ATOM     10  CA  GLY     8      45.831  28.548  64.319  1.00  0.00              
ATOM     11  C   GLY     8      45.908  27.229  63.544  1.00  0.00              
ATOM     12  O   GLY     8      44.939  26.501  63.441  1.00  0.00              
ATOM     13  N   GLN     9      47.053  26.918  62.996  1.00  0.00              
ATOM     14  CA  GLN     9      47.192  25.650  62.225  1.00  0.00              
ATOM     15  C   GLN     9      47.078  24.442  63.160  1.00  0.00              
ATOM     16  O   GLN     9      46.909  23.321  62.722  1.00  0.00              
ATOM     17  N   ILE    10      47.164  24.660  64.443  1.00  0.00              
ATOM     18  CA  ILE    10      47.056  23.521  65.399  1.00  0.00              
ATOM     19  C   ILE    10      45.902  22.604  64.988  1.00  0.00              
ATOM     20  O   ILE    10      44.746  22.920  65.181  1.00  0.00              
ATOM     21  N   VAL    11      46.207  21.468  64.420  1.00  0.00              
ATOM     22  CA  VAL    11      45.124  20.536  63.993  1.00  0.00              
ATOM     23  C   VAL    11      44.207  20.214  65.174  1.00  0.00              
ATOM     24  O   VAL    11      44.414  19.257  65.892  1.00  0.00              
ATOM     25  N   CYS    12      43.191  21.005  65.381  1.00  0.00              
ATOM     26  CA  CYS    12      42.261  20.739  66.515  1.00  0.00              
ATOM     27  C   CYS    12      41.341  19.564  66.173  1.00  0.00              
ATOM     28  O   CYS    12      41.076  19.287  65.019  1.00  0.00              
ATOM     29  N   THR    13      40.857  18.863  67.161  1.00  0.00              
ATOM     30  CA  THR    13      39.965  17.703  66.882  1.00  0.00              
ATOM     31  C   THR    13      38.675  17.799  67.702  1.00  0.00              
ATOM     32  O   THR    13      37.746  17.041  67.499  1.00  0.00              
ATOM     33  N   VAL    14      38.607  18.713  68.629  1.00  0.00              
ATOM     34  CA  VAL    14      37.372  18.834  69.456  1.00  0.00              
ATOM     35  C   VAL    14      37.050  20.306  69.710  1.00  0.00              
ATOM     36  O   VAL    14      37.895  21.080  70.115  1.00  0.00              
ATOM     37  N   ARG    15      35.825  20.696  69.484  1.00  0.00              
ATOM     38  CA  ARG    15      35.430  22.113  69.717  1.00  0.00              
ATOM     39  C   ARG    15      35.888  22.591  71.105  1.00  0.00              
ATOM     40  O   ARG    15      36.479  23.646  71.222  1.00  0.00              
ATOM     41  N   HIS    16      35.597  21.810  72.121  1.00  0.00              
ATOM     42  CA  HIS    16      35.986  22.186  73.502  1.00  0.00              
ATOM     43  C   HIS    16      37.509  22.248  73.640  1.00  0.00              
ATOM     44  O   HIS    16      38.036  22.887  74.529  1.00  0.00              
ATOM     45  N   HIS    17      38.224  21.596  72.764  1.00  0.00              
ATOM     46  CA  HIS    17      39.712  21.632  72.846  1.00  0.00              
ATOM     47  C   HIS    17      40.222  22.982  72.340  1.00  0.00              
ATOM     48  O   HIS    17      41.237  23.487  72.786  1.00  0.00              
ATOM     49  N   GLY    18      39.518  23.573  71.413  1.00  0.00              
ATOM     50  CA  GLY    18      39.948  24.893  70.875  1.00  0.00              
ATOM     51  C   GLY    18      39.807  25.970  71.955  1.00  0.00              
ATOM     52  O   GLY    18      40.447  27.002  71.901  1.00  0.00              
ATOM     53  N   LEU    19      38.980  25.738  72.939  1.00  0.00              
ATOM     54  CA  LEU    19      38.814  26.752  74.018  1.00  0.00              
ATOM     55  C   LEU    19      40.134  26.918  74.781  1.00  0.00              
ATOM     56  O   LEU    19      40.687  28.000  74.815  1.00  0.00              
ATOM     57  N   ALA    20      40.619  25.841  75.354  1.00  0.00              
ATOM     58  CA  ALA    20      41.902  25.899  76.091  1.00  0.00              
ATOM     59  C   ALA    20      43.009  26.371  75.145  1.00  0.00              
ATOM     60  O   ALA    20      43.942  27.037  75.545  1.00  0.00              
ATOM     61  N   HIS    21      42.901  26.031  73.887  1.00  0.00              
ATOM     62  CA  HIS    21      43.936  26.460  72.904  1.00  0.00              
ATOM     63  C   HIS    21      43.835  27.968  72.656  1.00  0.00              
ATOM     64  O   HIS    21      44.790  28.699  72.835  1.00  0.00              
ATOM     65  N   ASP    22      42.686  28.442  72.254  1.00  0.00              
ATOM     66  CA  ASP    22      42.539  29.904  72.010  1.00  0.00              
ATOM     67  C   ASP    22      43.060  30.665  73.227  1.00  0.00              
ATOM     68  O   ASP    22      43.835  31.593  73.112  1.00  0.00              
ATOM     69  N   LYS    23      42.654  30.256  74.397  1.00  0.00              
ATOM     70  CA  LYS    23      43.138  30.935  75.629  1.00  0.00              
ATOM     71  C   LYS    23      44.664  30.850  75.685  1.00  0.00              
ATOM     72  O   LYS    23      45.334  31.752  76.142  1.00  0.00              
ATOM     73  N   LEU    24      45.216  29.766  75.208  1.00  0.00              
ATOM     74  CA  LEU    24      46.697  29.614  75.213  1.00  0.00              
ATOM     75  C   LEU    24      47.286  30.340  74.000  1.00  0.00              
ATOM     76  O   LEU    24      48.468  30.610  73.936  1.00  0.00              
ATOM     77  N   LEU    25      46.462  30.659  73.039  1.00  0.00              
ATOM     78  CA  LEU    25      46.963  31.370  71.828  1.00  0.00              
ATOM     79  C   LEU    25      46.932  32.884  72.053  1.00  0.00              
ATOM     80  O   LEU    25      47.944  33.553  71.972  1.00  0.00              
ATOM     81  N   MET    26      45.782  33.434  72.340  1.00  0.00              
ATOM     82  CA  MET    26      45.703  34.906  72.571  1.00  0.00              
ATOM     83  C   MET    26      45.543  35.201  74.067  1.00  0.00              
ATOM     84  O   MET    26      45.965  36.234  74.549  1.00  0.00              
ATOM     85  N   VAL    27      44.945  34.305  74.804  1.00  0.00              
ATOM     86  CA  VAL    27      44.774  34.546  76.265  1.00  0.00              
ATOM     87  C   VAL    27      43.329  34.251  76.680  1.00  0.00              
ATOM     88  O   VAL    27      43.027  34.116  77.849  1.00  0.00              
ATOM     89  N   GLU    28      42.432  34.152  75.736  1.00  0.00              
ATOM     90  CA  GLU    28      41.009  33.870  76.090  1.00  0.00              
ATOM     91  C   GLU    28      40.552  32.550  75.464  1.00  0.00              
ATOM     92  O   GLU    28      40.949  32.198  74.371  1.00  0.00              
ATOM     93  N   MET    29      39.719  31.816  76.151  1.00  0.00              
ATOM     94  CA  MET    29      39.234  30.517  75.600  1.00  0.00              
ATOM     95  C   MET    29      37.954  30.728  74.785  1.00  0.00              
ATOM     96  O   MET    29      36.899  30.233  75.132  1.00  0.00              
ATOM     97  N   ILE    30      38.037  31.455  73.704  1.00  0.00              
ATOM     98  CA  ILE    30      36.822  31.692  72.869  1.00  0.00              
ATOM     99  C   ILE    30      37.117  31.370  71.400  1.00  0.00              
ATOM    100  O   ILE    30      37.763  32.128  70.705  1.00  0.00              
ATOM    101  N   ASP    31      36.646  30.248  70.925  1.00  0.00              
ATOM    102  CA  ASP    31      36.896  29.874  69.505  1.00  0.00              
ATOM    103  C   ASP    31      36.330  28.478  69.240  1.00  0.00              
ATOM    104  O   ASP    31      35.804  27.834  70.126  1.00  0.00              
ATOM    105  N   PRO    32      36.433  28.003  68.030  1.00  0.00              
ATOM    106  CA  PRO    32      35.901  26.645  67.714  1.00  0.00              
ATOM    107  C   PRO    32      36.904  25.881  66.848  1.00  0.00              
ATOM    108  O   PRO    32      37.990  26.354  66.576  1.00  0.00              
ATOM    109  N   GLN    33      36.551  24.703  66.409  1.00  0.00              
ATOM    110  CA  GLN    33      37.488  23.918  65.558  1.00  0.00              
ATOM    111  C   GLN    33      36.799  23.494  64.260  1.00  0.00              
ATOM    112  O   GLN    33      35.833  22.755  64.269  1.00  0.00              
ATOM    113  N   GLY    34      37.288  23.951  63.139  1.00  0.00              
ATOM    114  CA  GLY    34      36.657  23.570  61.842  1.00  0.00              
ATOM    115  C   GLY    34      37.706  23.554  60.727  1.00  0.00              
ATOM    116  O   GLY    34      38.763  24.140  60.846  1.00  0.00              
ATOM    117  N   ASN    35      37.418  22.887  59.642  1.00  0.00              
ATOM    118  CA  ASN    35      38.394  22.829  58.516  1.00  0.00              
ATOM    119  C   ASN    35      39.773  22.403  59.029  1.00  0.00              
ATOM    120  O   ASN    35      40.789  22.701  58.433  1.00  0.00              
ATOM    121  N   PRO    36      39.816  21.706  60.132  1.00  0.00              
ATOM    122  CA  PRO    36      41.128  21.259  60.683  1.00  0.00              
ATOM    123  C   PRO    36      41.911  22.468  61.197  1.00  0.00              
ATOM    124  O   PRO    36      43.106  22.574  61.000  1.00  0.00              
ATOM    125  N   ASP    37      41.250  23.380  61.858  1.00  0.00              
ATOM    126  CA  ASP    37      41.958  24.581  62.389  1.00  0.00              
ATOM    127  C   ASP    37      41.171  25.180  63.557  1.00  0.00              
ATOM    128  O   ASP    37      39.997  24.909  63.726  1.00  0.00              
ATOM    129  N   GLY    38      41.801  25.990  64.363  1.00  0.00              
ATOM    130  CA  GLY    38      41.075  26.600  65.519  1.00  0.00              
ATOM    131  C   GLY    38      40.643  28.026  65.177  1.00  0.00              
ATOM    132  O   GLY    38      41.409  28.809  64.651  1.00  0.00              
ATOM    133  N   GLN    39      39.421  28.371  65.472  1.00  0.00              
ATOM    134  CA  GLN    39      38.943  29.750  65.163  1.00  0.00              
ATOM    135  C   GLN    39      38.814  30.567  66.451  1.00  0.00              
ATOM    136  O   GLN    39      37.757  30.643  67.045  1.00  0.00              
ATOM    137  N   CYS    40      39.880  31.180  66.888  1.00  0.00              
ATOM    138  CA  CYS    40      39.810  31.995  68.135  1.00  0.00              
ATOM    139  C   CYS    40      39.474  33.450  67.791  1.00  0.00              
ATOM    140  O   CYS    40      40.021  34.022  66.868  1.00  0.00              
ATOM    141  N   ALA    41      38.579  34.050  68.523  1.00  0.00              
ATOM    142  CA  ALA    41      38.206  35.467  68.237  1.00  0.00              
ATOM    143  C   ALA    41      38.855  36.405  69.266  1.00  0.00              
ATOM    144  O   ALA    41      38.520  36.356  70.433  1.00  0.00              
ATOM    145  N   VAL    42      39.766  37.236  68.812  1.00  0.00              
ATOM    146  CA  VAL    42      40.451  38.183  69.723  1.00  0.00              
ATOM    147  C   VAL    42      39.436  39.128  70.373  1.00  0.00              
ATOM    148  O   VAL    42      39.452  40.302  70.041  1.00  0.00              
END
