
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0306AL243_3
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306AL243_3.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    V       6      K       2          1.868
LGA    T       7      L       3          1.527
LGA    G       8      A       4          0.574
LGA    Q       9      V       5          0.300
LGA    I      10      V       6          0.325
LGA    V      11      T       7          0.342
LGA    C      12      G       8          0.593
LGA    T      13      Q       9          2.104
LGA    V      14      I      10          3.618
LGA    R      15      V      11          4.071
LGA    H      16      C      12          2.811
LGA    H      17      T      13          1.501
LGA    G      18      V      14          4.140
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    H      21      L      19           #
LGA    D      22      A      20          5.696
LGA    K      23      H      21          1.462
LGA    L      24      D      22          2.564
LGA    L      25      K      23          1.710
LGA    M      26      L      24          1.550
LGA    V      27      L      25          1.512
LGA    E      28      M      26          1.258
LGA    I      30      V      27          0.598
LGA    D      31      E      28          1.065
LGA    P      32      M      29          1.166
LGA    -       -      I      30           -
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    G      34      P      36          1.112
LGA    N      35      D      37          1.065
LGA    G      38      G      38          2.862
LGA    -       -      Q      39           -
LGA    Q      39      C      40          0.975
LGA    C      40      A      41          1.581
LGA    A      41      V      42          1.633
LGA    V      42      A      43          1.278
LGA    A      43      I      44          2.020
LGA    I      44      D      45          2.658
LGA    G      48      N      46          4.021
LGA    A      49      I      47          5.067
LGA    -       -      G      48           -
LGA    G      50      A      49           #
LGA    T      51      G      50          3.067
LGA    -       -      T      51           -
LGA    G      52      G      52          1.281
LGA    E      53      E      53          0.580
LGA    W      54      W      54          0.525
LGA    V      55      V      55          0.739
LGA    L      56      L      56          0.708
LGA    L      57      L      57          0.828
LGA    V      58      V      58          1.717
LGA    -       -      S      59           -
LGA    -       -      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)   44   95    5.0     42    2.23    19.05     35.063     1.802

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.357686 * X  +  -0.749771 * Y  +  -0.556690 * Z  +  41.698833
  Y_new =   0.328332 * X  +  -0.457097 * Y  +   0.826596 * Z  +  14.884399
  Z_new =  -0.874219 * X  +  -0.478442 * Y  +   0.082677 * Z  +  77.019279 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.399682    1.741910  [ DEG:   -80.1959     99.8041 ]
  Theta =   1.063824    2.077768  [ DEG:    60.9526    119.0474 ]
  Phi   =   0.742635   -2.398957  [ DEG:    42.5499   -137.4501 ]
 
# 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: T0306AL243_3                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306AL243_3.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44   95   5.0   42   2.23   19.05  35.063
REMARK  ---------------------------------------------------------- 
MOLECULE T0306AL243_3
REMARK Aligment from pdb entry: 2cwpA
ATOM      1  N   VAL     6      44.482  34.646  64.202  1.00  0.00              
ATOM      2  CA  VAL     6      45.660  34.183  64.898  1.00  0.00              
ATOM      3  C   VAL     6      45.776  32.682  64.733  1.00  0.00              
ATOM      4  O   VAL     6      44.798  31.995  64.446  1.00  0.00              
ATOM      5  N   THR     7      46.986  32.181  64.916  1.00  0.00              
ATOM      6  CA  THR     7      47.235  30.766  64.814  1.00  0.00              
ATOM      7  C   THR     7      46.762  30.147  66.114  1.00  0.00              
ATOM      8  O   THR     7      47.091  30.653  67.194  1.00  0.00              
ATOM      9  N   GLY     8      45.986  29.070  66.013  1.00  0.00              
ATOM     10  CA  GLY     8      45.486  28.410  67.210  1.00  0.00              
ATOM     11  C   GLY     8      45.677  26.912  67.153  1.00  0.00              
ATOM     12  O   GLY     8      45.553  26.322  66.079  1.00  0.00              
ATOM     13  N   GLN     9      45.984  26.292  68.296  1.00  0.00              
ATOM     14  CA  GLN     9      46.180  24.840  68.362  1.00  0.00              
ATOM     15  C   GLN     9      44.915  24.166  68.861  1.00  0.00              
ATOM     16  O   GLN     9      44.413  24.494  69.930  1.00  0.00              
ATOM     17  N   ILE    10      44.392  23.227  68.086  1.00  0.00              
ATOM     18  CA  ILE    10      43.176  22.521  68.480  1.00  0.00              
ATOM     19  C   ILE    10      43.499  21.474  69.549  1.00  0.00              
ATOM     20  O   ILE    10      44.046  20.417  69.247  1.00  0.00              
ATOM     21  N   VAL    11      43.177  21.789  70.798  1.00  0.00              
ATOM     22  CA  VAL    11      43.436  20.885  71.913  1.00  0.00              
ATOM     23  C   VAL    11      42.464  19.711  71.870  1.00  0.00              
ATOM     24  O   VAL    11      42.854  18.562  72.053  1.00  0.00              
ATOM     25  N   CYS    12      41.199  20.014  71.616  1.00  0.00              
ATOM     26  CA  CYS    12      40.175  18.989  71.537  1.00  0.00              
ATOM     27  C   CYS    12      39.108  19.382  70.525  1.00  0.00              
ATOM     28  O   CYS    12      38.837  20.570  70.308  1.00  0.00              
ATOM     29  N   THR    13      38.500  18.371  69.921  1.00  0.00              
ATOM     30  CA  THR    13      37.461  18.570  68.924  1.00  0.00              
ATOM     31  C   THR    13      36.460  17.422  69.000  1.00  0.00              
ATOM     32  O   THR    13      36.841  16.251  68.916  1.00  0.00              
ATOM     33  N   VAL    14      35.186  17.751  69.172  1.00  0.00              
ATOM     34  CA  VAL    14      34.155  16.719  69.240  1.00  0.00              
ATOM     35  C   VAL    14      32.846  17.208  68.656  1.00  0.00              
ATOM     36  O   VAL    14      32.471  18.367  68.824  1.00  0.00              
ATOM     37  N   ARG    15      32.146  16.311  67.969  1.00  0.00              
ATOM     38  CA  ARG    15      30.881  16.667  67.355  1.00  0.00              
ATOM     39  C   ARG    15      29.941  17.180  68.434  1.00  0.00              
ATOM     40  O   ARG    15      30.006  16.733  69.576  1.00  0.00              
ATOM     41  N   HIS    16      29.092  18.137  68.076  1.00  0.00              
ATOM     42  CA  HIS    16      28.117  18.680  69.018  1.00  0.00              
ATOM     43  C   HIS    16      26.900  17.759  68.936  1.00  0.00              
ATOM     44  O   HIS    16      26.453  17.404  67.846  1.00  0.00              
ATOM     45  N   HIS    17      26.384  17.369  70.100  1.00  0.00              
ATOM     46  CA  HIS    17      25.239  16.458  70.201  1.00  0.00              
ATOM     47  C   HIS    17      24.019  16.915  69.406  1.00  0.00              
ATOM     48  O   HIS    17      23.654  18.090  69.430  1.00  0.00              
ATOM     49  N   GLY    18      23.388  15.973  68.713  1.00  0.00              
ATOM     50  CA  GLY    18      22.197  16.254  67.916  1.00  0.00              
ATOM     51  C   GLY    18      22.441  17.146  66.709  1.00  0.00              
ATOM     52  O   GLY    18      21.567  17.915  66.311  1.00  0.00              
ATOM     53  N   HIS    21      23.637  17.045  66.137  1.00  0.00              
ATOM     54  CA  HIS    21      23.988  17.819  64.955  1.00  0.00              
ATOM     55  C   HIS    21      24.751  16.883  64.043  1.00  0.00              
ATOM     56  O   HIS    21      25.359  15.917  64.502  1.00  0.00              
ATOM     57  N   ASP    22      24.723  17.174  62.751  1.00  0.00              
ATOM     58  CA  ASP    22      25.419  16.341  61.783  1.00  0.00              
ATOM     59  C   ASP    22      26.668  17.020  61.250  1.00  0.00              
ATOM     60  O   ASP    22      27.605  16.357  60.812  1.00  0.00              
ATOM     61  N   LYS    23      26.688  18.346  61.310  1.00  0.00              
ATOM     62  CA  LYS    23      27.818  19.115  60.793  1.00  0.00              
ATOM     63  C   LYS    23      28.645  19.875  61.826  1.00  0.00              
ATOM     64  O   LYS    23      29.775  20.262  61.540  1.00  0.00              
ATOM     65  N   LEU    24      28.097  20.091  63.018  1.00  0.00              
ATOM     66  CA  LEU    24      28.809  20.876  64.013  1.00  0.00              
ATOM     67  C   LEU    24      29.879  20.176  64.820  1.00  0.00              
ATOM     68  O   LEU    24      29.707  19.047  65.256  1.00  0.00              
ATOM     69  N   LEU    25      30.994  20.873  65.011  1.00  0.00              
ATOM     70  CA  LEU    25      32.102  20.366  65.812  1.00  0.00              
ATOM     71  C   LEU    25      32.546  21.468  66.773  1.00  0.00              
ATOM     72  O   LEU    25      32.749  22.624  66.369  1.00  0.00              
ATOM     73  N   MET    26      32.685  21.111  68.045  1.00  0.00              
ATOM     74  CA  MET    26      33.133  22.064  69.051  1.00  0.00              
ATOM     75  C   MET    26      34.633  21.898  69.204  1.00  0.00              
ATOM     76  O   MET    26      35.129  20.777  69.332  1.00  0.00              
ATOM     77  N   VAL    27      35.354  23.013  69.168  1.00  0.00              
ATOM     78  CA  VAL    27      36.798  22.976  69.306  1.00  0.00              
ATOM     79  C   VAL    27      37.240  23.763  70.527  1.00  0.00              
ATOM     80  O   VAL    27      36.652  24.790  70.862  1.00  0.00              
ATOM     81  N   GLU    28      38.275  23.276  71.194  1.00  0.00              
ATOM     82  CA  GLU    28      38.835  23.987  72.331  1.00  0.00              
ATOM     83  C   GLU    28      40.198  24.342  71.758  1.00  0.00              
ATOM     84  O   GLU    28      41.047  23.465  71.534  1.00  0.00              
ATOM     85  N   ILE    30      40.396  25.629  71.509  1.00  0.00              
ATOM     86  CA  ILE    30      41.621  26.103  70.879  1.00  0.00              
ATOM     87  C   ILE    30      42.515  26.929  71.779  1.00  0.00              
ATOM     88  O   ILE    30      42.062  27.875  72.430  1.00  0.00              
ATOM     89  N   ASP    31      43.791  26.561  71.794  1.00  0.00              
ATOM     90  CA  ASP    31      44.808  27.231  72.590  1.00  0.00              
ATOM     91  C   ASP    31      45.534  28.266  71.729  1.00  0.00              
ATOM     92  O   ASP    31      46.216  27.891  70.780  1.00  0.00              
ATOM     93  N   PRO    32      45.375  29.550  72.046  1.00  0.00              
ATOM     94  CA  PRO    32      46.057  30.635  71.317  1.00  0.00              
ATOM     95  C   PRO    32      47.262  31.173  72.093  1.00  0.00              
ATOM     96  O   PRO    32      47.714  32.299  71.854  1.00  0.00              
ATOM     97  N   GLY    34      47.764  30.376  73.031  1.00  0.00              
ATOM     98  CA  GLY    34      48.910  30.790  73.822  1.00  0.00              
ATOM     99  C   GLY    34      48.538  31.452  75.134  1.00  0.00              
ATOM    100  O   GLY    34      48.632  30.838  76.194  1.00  0.00              
ATOM    101  N   ASN    35      48.106  32.708  75.055  1.00  0.00              
ATOM    102  CA  ASN    35      47.721  33.498  76.230  1.00  0.00              
ATOM    103  C   ASN    35      46.299  33.188  76.681  1.00  0.00              
ATOM    104  O   ASN    35      45.896  33.527  77.798  1.00  0.00              
ATOM    105  N   GLY    38      45.531  32.563  75.801  1.00  0.00              
ATOM    106  CA  GLY    38      44.156  32.242  76.127  1.00  0.00              
ATOM    107  C   GLY    38      43.697  31.006  75.389  1.00  0.00              
ATOM    108  O   GLY    38      44.338  30.545  74.443  1.00  0.00              
ATOM    109  N   GLN    39      42.566  30.490  75.840  1.00  0.00              
ATOM    110  CA  GLN    39      41.948  29.323  75.256  1.00  0.00              
ATOM    111  C   GLN    39      40.571  29.798  74.827  1.00  0.00              
ATOM    112  O   GLN    39      39.989  30.680  75.460  1.00  0.00              
ATOM    113  N   CYS    40      40.050  29.241  73.743  1.00  0.00              
ATOM    114  CA  CYS    40      38.733  29.650  73.277  1.00  0.00              
ATOM    115  C   CYS    40      37.940  28.475  72.734  1.00  0.00              
ATOM    116  O   CYS    40      38.505  27.481  72.275  1.00  0.00              
ATOM    117  N   ALA    41      36.624  28.594  72.803  1.00  0.00              
ATOM    118  CA  ALA    41      35.736  27.562  72.308  1.00  0.00              
ATOM    119  C   ALA    41      35.248  28.040  70.968  1.00  0.00              
ATOM    120  O   ALA    41      34.669  29.124  70.856  1.00  0.00              
ATOM    121  N   VAL    42      35.492  27.231  69.944  1.00  0.00              
ATOM    122  CA  VAL    42      35.097  27.594  68.599  1.00  0.00              
ATOM    123  C   VAL    42      34.334  26.489  67.895  1.00  0.00              
ATOM    124  O   VAL    42      34.779  25.342  67.841  1.00  0.00              
ATOM    125  N   ALA    43      33.181  26.853  67.345  1.00  0.00              
ATOM    126  CA  ALA    43      32.348  25.912  66.621  1.00  0.00              
ATOM    127  C   ALA    43      32.554  26.049  65.104  1.00  0.00              
ATOM    128  O   ALA    43      32.652  27.158  64.577  1.00  0.00              
ATOM    129  N   ILE    44      32.640  24.912  64.419  1.00  0.00              
ATOM    130  CA  ILE    44      32.788  24.870  62.963  1.00  0.00              
ATOM    131  C   ILE    44      31.786  23.819  62.473  1.00  0.00              
ATOM    132  O   ILE    44      31.566  22.817  63.148  1.00  0.00              
ATOM    133  N   GLY    48      31.170  24.036  61.315  1.00  0.00              
ATOM    134  CA  GLY    48      30.185  23.081  60.829  1.00  0.00              
ATOM    135  C   GLY    48      30.615  22.304  59.598  1.00  0.00              
ATOM    136  O   GLY    48      29.933  22.320  58.581  1.00  0.00              
ATOM    137  N   ALA    49      31.724  21.586  59.702  1.00  0.00              
ATOM    138  CA  ALA    49      32.249  20.836  58.569  1.00  0.00              
ATOM    139  C   ALA    49      32.228  19.326  58.770  1.00  0.00              
ATOM    140  O   ALA    49      32.687  18.590  57.894  1.00  0.00              
ATOM    141  N   GLY    50      36.254  15.113  63.187  1.00  0.00              
ATOM    142  CA  GLY    50      36.900  15.750  64.341  1.00  0.00              
ATOM    143  C   GLY    50      38.366  15.372  64.552  1.00  0.00              
ATOM    144  O   GLY    50      39.188  16.233  64.883  1.00  0.00              
ATOM    145  N   THR    51      42.065  17.740  65.664  1.00  0.00              
ATOM    146  CA  THR    51      42.765  17.599  66.931  1.00  0.00              
ATOM    147  C   THR    51      44.258  17.468  66.770  1.00  0.00              
ATOM    148  O   THR    51      44.731  16.673  65.974  1.00  0.00              
ATOM    149  N   GLY    52      44.990  18.251  67.553  1.00  0.00              
ATOM    150  CA  GLY    52      46.432  18.211  67.508  1.00  0.00              
ATOM    151  C   GLY    52      47.058  19.149  66.495  1.00  0.00              
ATOM    152  O   GLY    52      48.271  19.348  66.517  1.00  0.00              
ATOM    153  N   GLU    53      46.255  19.732  65.608  1.00  0.00              
ATOM    154  CA  GLU    53      46.817  20.631  64.593  1.00  0.00              
ATOM    155  C   GLU    53      46.589  22.118  64.865  1.00  0.00              
ATOM    156  O   GLU    53      45.744  22.495  65.676  1.00  0.00              
ATOM    157  N   TRP    54      47.354  22.952  64.159  1.00  0.00              
ATOM    158  CA  TRP    54      47.236  24.401  64.249  1.00  0.00              
ATOM    159  C   TRP    54      46.509  24.894  62.999  1.00  0.00              
ATOM    160  O   TRP    54      46.732  24.365  61.902  1.00  0.00              
ATOM    161  N   VAL    55      45.660  25.907  63.169  1.00  0.00              
ATOM    162  CA  VAL    55      44.908  26.495  62.064  1.00  0.00              
ATOM    163  C   VAL    55      44.742  27.998  62.283  1.00  0.00              
ATOM    164  O   VAL    55      45.062  28.525  63.354  1.00  0.00              
ATOM    165  N   LEU    56      44.221  28.664  61.257  1.00  0.00              
ATOM    166  CA  LEU    56      43.963  30.088  61.312  1.00  0.00              
ATOM    167  C   LEU    56      42.554  30.270  61.857  1.00  0.00              
ATOM    168  O   LEU    56      41.632  29.577  61.435  1.00  0.00              
ATOM    169  N   LEU    57      42.386  31.199  62.782  1.00  0.00              
ATOM    170  CA  LEU    57      41.073  31.466  63.368  1.00  0.00              
ATOM    171  C   LEU    57      40.854  32.976  63.458  1.00  0.00              
ATOM    172  O   LEU    57      41.785  33.714  63.813  1.00  0.00              
ATOM    173  N   VAL    58      39.645  33.437  63.128  1.00  0.00              
ATOM    174  CA  VAL    58      39.303  34.856  63.271  1.00  0.00              
ATOM    175  C   VAL    58      38.834  34.909  64.729  1.00  0.00              
ATOM    176  O   VAL    58      37.873  34.221  65.072  1.00  0.00              
END
