
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0306AL586_1
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306AL586_1.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      L       3           -
LGA    -       -      A       4           -
LGA    -       -      V       5           -
LGA    -       -      V       6           -
LGA    -       -      T       7           -
LGA    -       -      G       8           -
LGA    -       -      Q       9           -
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    -       -      L      24           -
LGA    -       -      L      25           -
LGA    -       -      M      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      M      29           -
LGA    M       1      I      30          4.505
LGA    K       2      D      31          3.840
LGA    L       3      -       -           -
LGA    A       4      -       -           -
LGA    V       5      -       -           -
LGA    V       6      -       -           -
LGA    T       7      -       -           -
LGA    G       8      -       -           -
LGA    Q       9      -       -           -
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      P      32          2.115
LGA    A      20      Q      33          2.437
LGA    H      21      G      34          4.260
LGA    D      22      N      35           -
LGA    -       -      P      36           -
LGA    -       -      D      37           -
LGA    -       -      G      38           -
LGA    -       -      Q      39           -
LGA    -       -      C      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      A      43           -
LGA    -       -      I      44           -
LGA    -       -      D      45           -
LGA    -       -      N      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    -       -      A      49           -
LGA    -       -      G      50           -
LGA    -       -      T      51           -
LGA    K      23      G      52          5.588
LGA    L      24      E      53          1.723
LGA    L      25      W      54          1.595
LGA    M      26      V      55          2.579
LGA    V      27      L      56          2.336
LGA    E      28      L      57          2.158
LGA    M      29      V      58          1.010
LGA    I      30      S      59          2.428
LGA    D      31      G      60          2.790
LGA    P      32      S      61          3.669
LGA    Q      33      S      62           -
LGA    G      34      A      63          4.490
LGA    N      35      R      64          2.760
LGA    P      36      Q      65          3.001
LGA    D      37      A      66          1.731
LGA    G      38      H      67          5.473
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    Q      39      C      77          3.555
LGA    C      40      V      78          1.616
LGA    A      41      I      79          1.975
LGA    V      42      G      80          2.947
LGA    A      43      I      81          1.910
LGA    -       -      V      82           -
LGA    I      44      D      83          2.932
LGA    D      45      E      84          3.294
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    N      46      H      94          0.890
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   95    5.0     28    3.09     0.00     18.001     0.879

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.839981 * X  +  -0.255589 * Y  +   0.478650 * Z  +  73.695900
  Y_new =  -0.174002 * X  +  -0.708655 * Y  +  -0.683762 * Z  +  67.828377
  Z_new =   0.513960 * X  +  -0.657633 * Y  +   0.550784 * Z  +  58.092560 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.873589    2.268003  [ DEG:   -50.0530    129.9470 ]
  Theta =  -0.539795   -2.601798  [ DEG:   -30.9280   -149.0720 ]
  Phi   =  -2.937332    0.204260  [ DEG:  -168.2968     11.7033 ]
 
# 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: T0306AL586_1                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306AL586_1.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   95   5.0   28   3.09    0.00  18.001
REMARK  ---------------------------------------------------------- 
MOLECULE T0306AL586_1
REMARK Aligment from pdb entry: 1v05_A
ATOM      1  N   MET     1      51.187  33.198  69.631  1.00  0.00              
ATOM      2  CA  MET     1      52.029  34.156  70.352  1.00  0.00              
ATOM      3  C   MET     1      51.497  35.595  70.276  1.00  0.00              
ATOM      4  O   MET     1      51.359  36.284  71.289  1.00  0.00              
ATOM      5  N   LYS     2      51.221  36.062  69.074  1.00  0.00              
ATOM      6  CA  LYS     2      50.704  37.405  68.838  1.00  0.00              
ATOM      7  C   LYS     2      49.556  37.323  67.873  1.00  0.00              
ATOM      8  O   LYS     2      49.614  36.568  66.902  1.00  0.00              
ATOM      9  N   LEU     3      48.515  38.090  68.123  1.00  0.00              
ATOM     10  CA  LEU     3      47.421  38.306  67.180  1.00  0.00              
ATOM     11  C   LEU     3      47.207  39.799  67.117  1.00  0.00              
ATOM     12  O   LEU     3      47.127  40.492  68.142  1.00  0.00              
ATOM     13  N   ALA     4      47.160  40.335  65.915  1.00  0.00              
ATOM     14  CA  ALA     4      47.085  41.762  65.693  1.00  0.00              
ATOM     15  C   ALA     4      46.082  42.023  64.614  1.00  0.00              
ATOM     16  O   ALA     4      46.151  41.446  63.515  1.00  0.00              
ATOM     17  N   VAL     5      45.133  42.897  64.906  1.00  0.00              
ATOM     18  CA  VAL     5      44.061  43.248  64.000  1.00  0.00              
ATOM     19  C   VAL     5      44.067  44.734  63.806  1.00  0.00              
ATOM     20  O   VAL     5      43.929  45.496  64.782  1.00  0.00              
ATOM     21  N   VAL     6      44.254  45.160  62.566  1.00  0.00              
ATOM     22  CA  VAL     6      44.392  46.563  62.196  1.00  0.00              
ATOM     23  C   VAL     6      43.242  46.964  61.277  1.00  0.00              
ATOM     24  O   VAL     6      43.067  46.376  60.206  1.00  0.00              
ATOM     25  N   THR     7      42.477  47.975  61.653  1.00  0.00              
ATOM     26  CA  THR     7      41.474  48.551  60.788  1.00  0.00              
ATOM     27  C   THR     7      42.130  49.421  59.743  1.00  0.00              
ATOM     28  O   THR     7      42.867  50.335  60.074  1.00  0.00              
ATOM     29  N   GLY     8      41.862  49.099  58.483  1.00  0.00              
ATOM     30  CA  GLY     8      42.397  49.778  57.305  1.00  0.00              
ATOM     31  C   GLY     8      41.458  50.808  56.700  1.00  0.00              
ATOM     32  O   GLY     8      41.792  51.439  55.702  1.00  0.00              
ATOM     33  N   GLN     9      40.294  50.973  57.281  1.00  0.00              
ATOM     34  CA  GLN     9      39.252  51.814  56.718  1.00  0.00              
ATOM     35  C   GLN     9      38.090  50.985  56.233  1.00  0.00              
ATOM     36  O   GLN     9      38.245  49.860  55.764  1.00  0.00              
ATOM     37  N   ILE    10      36.883  51.538  56.358  1.00  0.00              
ATOM     38  CA  ILE    10      35.664  50.923  55.813  1.00  0.00              
ATOM     39  C   ILE    10      35.367  49.516  56.328  1.00  0.00              
ATOM     40  O   ILE    10      34.767  48.695  55.617  1.00  0.00              
ATOM     41  N   VAL    11      35.805  49.228  57.542  1.00  0.00              
ATOM     42  CA  VAL    11      35.640  47.911  58.146  1.00  0.00              
ATOM     43  C   VAL    11      36.327  46.809  57.358  1.00  0.00              
ATOM     44  O   VAL    11      35.911  45.661  57.354  1.00  0.00              
ATOM     45  N   CYS    12      37.414  47.181  56.712  1.00  0.00              
ATOM     46  CA  CYS    12      38.355  46.235  56.136  1.00  0.00              
ATOM     47  C   CYS    12      39.509  46.145  57.122  1.00  0.00              
ATOM     48  O   CYS    12      40.091  47.158  57.492  1.00  0.00              
ATOM     49  N   THR    13      39.833  44.928  57.539  1.00  0.00              
ATOM     50  CA  THR    13      40.891  44.690  58.505  1.00  0.00              
ATOM     51  C   THR    13      42.019  43.839  57.977  1.00  0.00              
ATOM     52  O   THR    13      41.784  42.903  57.203  1.00  0.00              
ATOM     53  N   VAL    14      43.223  44.142  58.404  1.00  0.00              
ATOM     54  CA  VAL    14      44.346  43.256  58.223  1.00  0.00              
ATOM     55  C   VAL    14      44.632  42.556  59.523  1.00  0.00              
ATOM     56  O   VAL    14      44.733  43.196  60.571  1.00  0.00              
ATOM     57  N   ARG    15      44.764  41.240  59.463  1.00  0.00              
ATOM     58  CA  ARG    15      45.091  40.421  60.604  1.00  0.00              
ATOM     59  C   ARG    15      46.463  39.809  60.401  1.00  0.00              
ATOM     60  O   ARG    15      46.736  39.261  59.343  1.00  0.00              
ATOM     61  N   HIS    16      47.301  39.883  61.422  1.00  0.00              
ATOM     62  CA  HIS    16      48.595  39.242  61.421  1.00  0.00              
ATOM     63  C   HIS    16      48.742  38.452  62.702  1.00  0.00              
ATOM     64  O   HIS    16      48.359  38.892  63.775  1.00  0.00              
ATOM     65  N   HIS    17      49.282  37.261  62.607  1.00  0.00              
ATOM     66  CA  HIS    17      49.494  36.437  63.782  1.00  0.00              
ATOM     67  C   HIS    17      50.778  35.645  63.693  1.00  0.00              
ATOM     68  O   HIS    17      51.352  35.449  62.613  1.00  0.00              
ATOM     69  N   GLY    18      51.252  35.201  64.852  1.00  0.00              
ATOM     70  CA  GLY    18      52.481  34.424  64.923  1.00  0.00              
ATOM     71  C   GLY    18      52.260  33.183  65.751  1.00  0.00              
ATOM     72  O   GLY    18      51.400  33.142  66.633  1.00  0.00              
ATOM     73  N   LEU    19      53.036  32.158  65.443  1.00  0.00              
ATOM     74  CA  LEU    19      52.935  30.854  66.073  1.00  0.00              
ATOM     75  C   LEU    19      54.342  30.414  66.474  1.00  0.00              
ATOM     76  O   LEU    19      55.331  30.824  65.863  1.00  0.00              
ATOM     77  N   ALA    20      54.419  29.545  67.474  1.00  0.00              
ATOM     78  CA  ALA    20      55.706  29.125  68.033  1.00  0.00              
ATOM     79  C   ALA    20      56.032  27.662  67.826  1.00  0.00              
ATOM     80  O   ALA    20      57.173  27.267  68.026  1.00  0.00              
ATOM     81  N   HIS    21      55.060  26.860  67.441  1.00  0.00              
ATOM     82  CA  HIS    21      55.234  25.427  67.347  1.00  0.00              
ATOM     83  C   HIS    21      54.487  24.883  66.159  1.00  0.00              
ATOM     84  O   HIS    21      53.356  25.296  65.866  1.00  0.00              
ATOM     85  N   ASP    22      55.093  23.912  65.501  1.00  0.00              
ATOM     86  CA  ASP    22      54.458  23.244  64.408  1.00  0.00              
ATOM     87  C   ASP    22      53.207  22.504  64.866  1.00  0.00              
ATOM     88  O   ASP    22      53.086  22.112  66.022  1.00  0.00              
ATOM     89  N   LYS    23      52.278  22.347  63.934  1.00  0.00              
ATOM     90  CA  LYS    23      51.075  21.603  64.179  1.00  0.00              
ATOM     91  C   LYS    23      49.947  22.047  63.296  1.00  0.00              
ATOM     92  O   LYS    23      50.093  22.850  62.372  1.00  0.00              
ATOM     93  N   LEU    24      48.780  21.497  63.571  1.00  0.00              
ATOM     94  CA  LEU    24      47.595  21.881  62.857  1.00  0.00              
ATOM     95  C   LEU    24      46.730  22.736  63.772  1.00  0.00              
ATOM     96  O   LEU    24      46.209  22.265  64.792  1.00  0.00              
ATOM     97  N   LEU    25      46.543  23.978  63.359  1.00  0.00              
ATOM     98  CA  LEU    25      45.841  24.971  64.142  1.00  0.00              
ATOM     99  C   LEU    25      44.456  25.219  63.565  1.00  0.00              
ATOM    100  O   LEU    25      44.182  24.914  62.413  1.00  0.00              
ATOM    101  N   MET    26      43.588  25.812  64.363  1.00  0.00              
ATOM    102  CA  MET    26      42.274  26.180  63.890  1.00  0.00              
ATOM    103  C   MET    26      42.119  27.658  64.083  1.00  0.00              
ATOM    104  O   MET    26      42.319  28.170  65.193  1.00  0.00              
ATOM    105  N   VAL    27      41.730  28.345  63.020  1.00  0.00              
ATOM    106  CA  VAL    27      41.553  29.782  63.027  1.00  0.00              
ATOM    107  C   VAL    27      40.062  30.070  62.927  1.00  0.00              
ATOM    108  O   VAL    27      39.396  29.574  62.020  1.00  0.00              
ATOM    109  N   GLU    28      39.545  30.858  63.868  1.00  0.00              
ATOM    110  CA  GLU    28      38.146  31.212  63.876  1.00  0.00              
ATOM    111  C   GLU    28      38.017  32.710  63.682  1.00  0.00              
ATOM    112  O   GLU    28      38.734  33.485  64.311  1.00  0.00              
ATOM    113  N   MET    29      37.163  33.110  62.765  1.00  0.00              
ATOM    114  CA  MET    29      36.871  34.506  62.515  1.00  0.00              
ATOM    115  C   MET    29      35.378  34.688  62.656  1.00  0.00              
ATOM    116  O   MET    29      34.592  33.992  61.985  1.00  0.00              
ATOM    117  N   ILE    30      34.990  35.577  63.567  1.00  0.00              
ATOM    118  CA  ILE    30      33.589  35.849  63.847  1.00  0.00              
ATOM    119  C   ILE    30      33.249  37.309  63.626  1.00  0.00              
ATOM    120  O   ILE    30      34.065  38.214  63.820  1.00  0.00              
ATOM    121  N   ASP    31      32.017  37.537  63.231  1.00  0.00              
ATOM    122  CA  ASP    31      31.466  38.881  63.140  1.00  0.00              
ATOM    123  C   ASP    31      30.320  38.866  64.132  1.00  0.00              
ATOM    124  O   ASP    31      29.329  38.157  63.953  1.00  0.00              
ATOM    125  N   PRO    32      30.496  39.597  65.226  1.00  0.00              
ATOM    126  CA  PRO    32      29.683  39.333  66.399  1.00  0.00              
ATOM    127  C   PRO    32      29.914  37.907  66.868  1.00  0.00              
ATOM    128  O   PRO    32      31.062  37.478  66.991  1.00  0.00              
ATOM    129  N   GLN    33      28.836  37.178  67.152  1.00  0.00              
ATOM    130  CA  GLN    33      28.952  35.800  67.621  1.00  0.00              
ATOM    131  C   GLN    33      28.795  34.814  66.475  1.00  0.00              
ATOM    132  O   GLN    33      28.675  33.614  66.705  1.00  0.00              
ATOM    133  N   GLY    34      28.818  35.318  65.244  1.00  0.00              
ATOM    134  CA  GLY    34      28.518  34.494  64.085  1.00  0.00              
ATOM    135  C   GLY    34      29.772  34.239  63.251  1.00  0.00              
ATOM    136  O   GLY    34      30.496  35.167  62.877  1.00  0.00              
ATOM    137  N   ASN    35      30.009  32.972  62.945  1.00  0.00              
ATOM    138  CA  ASN    35      31.136  32.578  62.102  1.00  0.00              
ATOM    139  C   ASN    35      30.979  33.168  60.719  1.00  0.00              
ATOM    140  O   ASN    35      29.901  33.133  60.138  1.00  0.00              
ATOM    141  N   PRO    36      32.062  33.721  60.182  1.00  0.00              
ATOM    142  CA  PRO    36      32.069  34.237  58.818  1.00  0.00              
ATOM    143  C   PRO    36      32.224  33.053  57.866  1.00  0.00              
ATOM    144  O   PRO    36      32.682  31.989  58.291  1.00  0.00              
ATOM    145  N   ASP    37      31.860  33.220  56.595  1.00  0.00              
ATOM    146  CA  ASP    37      32.059  32.140  55.620  1.00  0.00              
ATOM    147  C   ASP    37      33.498  31.641  55.593  1.00  0.00              
ATOM    148  O   ASP    37      34.450  32.419  55.513  1.00  0.00              
ATOM    149  N   GLY    38      33.645  30.330  55.722  1.00  0.00              
ATOM    150  CA  GLY    38      34.968  29.739  55.726  1.00  0.00              
ATOM    151  C   GLY    38      35.501  29.367  57.088  1.00  0.00              
ATOM    152  O   GLY    38      36.381  28.532  57.218  1.00  0.00              
ATOM    153  N   GLN    39      34.960  29.965  58.136  1.00  0.00              
ATOM    154  CA  GLN    39      35.413  29.666  59.479  1.00  0.00              
ATOM    155  C   GLN    39      34.652  28.472  60.009  1.00  0.00              
ATOM    156  O   GLN    39      33.427  28.423  59.848  1.00  0.00              
ATOM    157  N   CYS    40      35.311  27.528  60.685  1.00  0.00              
ATOM    158  CA  CYS    40      36.741  27.549  61.010  1.00  0.00              
ATOM    159  C   CYS    40      37.673  27.185  59.887  1.00  0.00              
ATOM    160  O   CYS    40      37.400  26.287  59.074  1.00  0.00              
ATOM    161  N   ALA    41      38.797  27.895  59.873  1.00  0.00              
ATOM    162  CA  ALA    41      39.863  27.662  58.915  1.00  0.00              
ATOM    163  C   ALA    41      40.894  26.735  59.520  1.00  0.00              
ATOM    164  O   ALA    41      41.274  26.852  60.683  1.00  0.00              
ATOM    165  N   VAL    42      41.388  25.817  58.703  1.00  0.00              
ATOM    166  CA  VAL    42      42.449  24.895  59.091  1.00  0.00              
ATOM    167  C   VAL    42      43.786  25.456  58.648  1.00  0.00              
ATOM    168  O   VAL    42      44.032  25.661  57.460  1.00  0.00              
ATOM    169  N   ALA    43      44.677  25.648  59.593  1.00  0.00              
ATOM    170  CA  ALA    43      45.962  26.265  59.299  1.00  0.00              
ATOM    171  C   ALA    43      47.060  25.276  59.598  1.00  0.00              
ATOM    172  O   ALA    43      47.230  24.859  60.738  1.00  0.00              
ATOM    173  N   ILE    44      47.841  24.901  58.590  1.00  0.00              
ATOM    174  CA  ILE    44      49.001  24.086  58.854  1.00  0.00              
ATOM    175  C   ILE    44      50.206  24.922  59.187  1.00  0.00              
ATOM    176  O   ILE    44      50.524  25.869  58.478  1.00  0.00              
ATOM    177  N   ASP    45      50.881  24.563  60.261  1.00  0.00              
ATOM    178  CA  ASP    45      52.167  25.128  60.611  1.00  0.00              
ATOM    179  C   ASP    45      53.169  24.001  60.403  1.00  0.00              
ATOM    180  O   ASP    45      53.299  23.120  61.250  1.00  0.00              
ATOM    181  N   ASN    46      53.863  24.007  59.266  1.00  0.00              
ATOM    182  CA  ASN    46      54.753  22.895  58.918  1.00  0.00              
ATOM    183  C   ASN    46      56.036  22.927  59.721  1.00  0.00              
ATOM    184  O   ASN    46      56.420  23.990  60.218  1.00  0.00              
END
