
#######################################################
#                                                     #
#                        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   47 (  188),  selected   47 , name T0306AL381_3
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306AL381_3.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    H      21      M       1           -
LGA    D      22      K       2           -
LGA    K      23      L       3           -
LGA    L      24      A       4           -
LGA    L      25      V       5           -
LGA    M      26      V       6           #
LGA    V      27      T       7          1.290
LGA    E      28      G       8          2.217
LGA    M      29      Q       9          1.106
LGA    I      30      I      10          0.736
LGA    D      31      V      11          2.544
LGA    Q      33      C      12          3.869
LGA    G      34      T      13          2.930
LGA    N      35      V      14          2.214
LGA    P      36      R      15          4.009
LGA    D      37      H      16          1.536
LGA    G      38      H      17          3.601
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    Q      39      H      21          2.741
LGA    C      40      D      22          3.414
LGA    A      41      K      23          2.237
LGA    V      42      L      24          2.162
LGA    A      43      L      25          2.094
LGA    I      44      M      26          2.023
LGA    D      45      V      27          2.815
LGA    -       -      E      28           -
LGA    -       -      M      29           -
LGA    -       -      I      30           -
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      D      37           -
LGA    N      46      G      38          5.321
LGA    I      47      Q      39          1.808
LGA    G      48      C      40          1.757
LGA    A      49      A      41          3.038
LGA    G      50      V      42          2.513
LGA    T      51      A      43          1.765
LGA    G      52      I      44          0.860
LGA    E      53      D      45          0.972
LGA    W      54      N      46          2.155
LGA    V      55      I      47          4.004
LGA    L      56      G      48          1.482
LGA    L      57      A      49          1.855
LGA    V      58      G      50          0.476
LGA    S      59      T      51          1.072
LGA    G      60      G      52          2.105
LGA    S      61      -       -           -
LGA    S      62      -       -           -
LGA    A      63      -       -           -
LGA    R      64      E      53          4.903
LGA    Q      65      W      54           -
LGA    A      66      V      55           -
LGA    -       -      L      56           -
LGA    -       -      L      57           -
LGA    -       -      V      58           -
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    H      67      I      81           #
LGA    K      68      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)   47   95    5.0     34    2.61     8.82     24.457     1.256

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.591778 * X  +  -0.566516 * Y  +  -0.573462 * Z  + 190.773621
  Y_new =  -0.137418 * X  +  -0.630090 * Y  +   0.764266 * Z  + -25.150055
  Z_new =  -0.794302 * X  +   0.531079 * Y  +   0.295024 * Z  + 136.963043 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.063727   -2.077866  [ DEG:    60.9470   -119.0530 ]
  Theta =   0.917858    2.223735  [ DEG:    52.5894    127.4106 ]
  Phi   =  -2.913424    0.228168  [ DEG:  -166.9269     13.0731 ]
 
# 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: T0306AL381_3                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306AL381_3.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   47   95   5.0   34   2.61    8.82  24.457
REMARK  ---------------------------------------------------------- 
MOLECULE T0306AL381_3
REMARK Aligment from pdb entry: 1j2qH
ATOM      1  N   HIS    21      46.109  33.417  82.613  1.00  0.00              
ATOM      2  CA  HIS    21      47.481  33.772  82.935  1.00  0.00              
ATOM      3  C   HIS    21      48.342  32.653  83.454  1.00  0.00              
ATOM      4  O   HIS    21      49.506  32.845  83.746  1.00  0.00              
ATOM      5  N   ASP    22      47.755  31.471  83.534  1.00  0.00              
ATOM      6  CA  ASP    22      48.432  30.252  83.968  1.00  0.00              
ATOM      7  C   ASP    22      47.500  29.184  83.406  1.00  0.00              
ATOM      8  O   ASP    22      47.024  28.317  84.120  1.00  0.00              
ATOM      9  N   LYS    23      47.243  29.238  82.092  1.00  0.00              
ATOM     10  CA  LYS    23      46.362  28.319  81.372  1.00  0.00              
ATOM     11  C   LYS    23      46.591  26.826  81.476  1.00  0.00              
ATOM     12  O   LYS    23      47.703  26.349  81.710  1.00  0.00              
ATOM     13  N   LEU    24      45.505  26.091  81.306  1.00  0.00              
ATOM     14  CA  LEU    24      45.572  24.648  81.315  1.00  0.00              
ATOM     15  C   LEU    24      46.081  24.291  79.916  1.00  0.00              
ATOM     16  O   LEU    24      45.414  24.575  78.920  1.00  0.00              
ATOM     17  N   LEU    25      47.257  23.687  79.835  1.00  0.00              
ATOM     18  CA  LEU    25      47.835  23.325  78.544  1.00  0.00              
ATOM     19  C   LEU    25      47.066  22.178  77.895  1.00  0.00              
ATOM     20  O   LEU    25      47.453  21.011  77.960  1.00  0.00              
ATOM     21  N   MET    26      45.983  22.540  77.226  1.00  0.00              
ATOM     22  CA  MET    26      45.136  21.553  76.622  1.00  0.00              
ATOM     23  C   MET    26      44.458  22.077  75.346  1.00  0.00              
ATOM     24  O   MET    26      44.170  23.271  75.243  1.00  0.00              
ATOM     25  N   VAL    27      44.238  21.183  74.376  1.00  0.00              
ATOM     26  CA  VAL    27      43.545  21.515  73.123  1.00  0.00              
ATOM     27  C   VAL    27      42.314  20.614  73.110  1.00  0.00              
ATOM     28  O   VAL    27      42.430  19.391  73.035  1.00  0.00              
ATOM     29  N   GLU    28      41.130  21.197  73.181  1.00  0.00              
ATOM     30  CA  GLU    28      39.955  20.357  73.220  1.00  0.00              
ATOM     31  C   GLU    28      39.131  20.394  71.967  1.00  0.00              
ATOM     32  O   GLU    28      39.114  21.384  71.224  1.00  0.00              
ATOM     33  N   MET    29      38.432  19.280  71.764  1.00  0.00              
ATOM     34  CA  MET    29      37.538  19.072  70.646  1.00  0.00              
ATOM     35  C   MET    29      36.256  18.605  71.308  1.00  0.00              
ATOM     36  O   MET    29      36.246  17.543  71.939  1.00  0.00              
ATOM     37  N   ILE    30      35.198  19.411  71.220  1.00  0.00              
ATOM     38  CA  ILE    30      33.910  19.048  71.815  1.00  0.00              
ATOM     39  C   ILE    30      32.831  19.112  70.742  1.00  0.00              
ATOM     40  O   ILE    30      32.556  20.180  70.189  1.00  0.00              
ATOM     41  N   ASP    31      32.213  17.974  70.447  1.00  0.00              
ATOM     42  CA  ASP    31      31.196  17.966  69.414  1.00  0.00              
ATOM     43  C   ASP    31      30.223  16.813  69.496  1.00  0.00              
ATOM     44  O   ASP    31      30.374  15.906  70.329  1.00  0.00              
ATOM     45  N   GLN    33      29.227  16.851  68.615  1.00  0.00              
ATOM     46  CA  GLN    33      28.202  15.827  68.592  1.00  0.00              
ATOM     47  C   GLN    33      26.955  16.367  67.906  1.00  0.00              
ATOM     48  O   GLN    33      27.046  17.274  67.063  1.00  0.00              
ATOM     49  N   GLY    34      25.789  15.827  68.258  1.00  0.00              
ATOM     50  CA  GLY    34      24.532  16.262  67.645  1.00  0.00              
ATOM     51  C   GLY    34      23.594  16.796  68.717  1.00  0.00              
ATOM     52  O   GLY    34      23.514  16.232  69.807  1.00  0.00              
ATOM     53  N   ASN    35      22.888  17.876  68.413  1.00  0.00              
ATOM     54  CA  ASN    35      21.967  18.456  69.379  1.00  0.00              
ATOM     55  C   ASN    35      20.842  19.199  68.669  1.00  0.00              
ATOM     56  O   ASN    35      20.826  19.294  67.439  1.00  0.00              
ATOM     57  N   PRO    36      19.903  19.730  69.441  1.00  0.00              
ATOM     58  CA  PRO    36      18.774  20.435  68.852  1.00  0.00              
ATOM     59  C   PRO    36      19.170  21.452  67.782  1.00  0.00              
ATOM     60  O   PRO    36      18.378  21.762  66.893  1.00  0.00              
ATOM     61  N   ASP    37      20.393  21.965  67.856  1.00  0.00              
ATOM     62  CA  ASP    37      20.853  22.963  66.888  1.00  0.00              
ATOM     63  C   ASP    37      21.412  22.368  65.606  1.00  0.00              
ATOM     64  O   ASP    37      21.525  23.064  64.590  1.00  0.00              
ATOM     65  N   GLY    38      21.755  21.082  65.663  1.00  0.00              
ATOM     66  CA  GLY    38      22.301  20.394  64.504  1.00  0.00              
ATOM     67  C   GLY    38      23.521  19.558  64.848  1.00  0.00              
ATOM     68  O   GLY    38      23.582  18.910  65.908  1.00  0.00              
ATOM     69  N   GLN    39      24.491  19.564  63.938  1.00  0.00              
ATOM     70  CA  GLN    39      25.730  18.827  64.136  1.00  0.00              
ATOM     71  C   GLN    39      26.859  19.851  64.140  1.00  0.00              
ATOM     72  O   GLN    39      26.834  20.806  63.361  1.00  0.00              
ATOM     73  N   CYS    40      27.834  19.674  65.026  1.00  0.00              
ATOM     74  CA  CYS    40      28.963  20.603  65.083  1.00  0.00              
ATOM     75  C   CYS    40      30.107  20.087  65.946  1.00  0.00              
ATOM     76  O   CYS    40      29.952  19.134  66.722  1.00  0.00              
ATOM     77  N   ALA    41      31.265  20.714  65.773  1.00  0.00              
ATOM     78  CA  ALA    41      32.457  20.374  66.530  1.00  0.00              
ATOM     79  C   ALA    41      33.161  21.661  66.905  1.00  0.00              
ATOM     80  O   ALA    41      33.234  22.593  66.110  1.00  0.00              
ATOM     81  N   VAL    42      33.677  21.729  68.118  1.00  0.00              
ATOM     82  CA  VAL    42      34.394  22.927  68.533  1.00  0.00              
ATOM     83  C   VAL    42      35.818  22.579  68.924  1.00  0.00              
ATOM     84  O   VAL    42      36.062  21.604  69.647  1.00  0.00              
ATOM     85  N   ALA    43      36.765  23.357  68.417  1.00  0.00              
ATOM     86  CA  ALA    43      38.157  23.168  68.775  1.00  0.00              
ATOM     87  C   ALA    43      38.445  24.295  69.783  1.00  0.00              
ATOM     88  O   ALA    43      38.236  25.478  69.489  1.00  0.00              
ATOM     89  N   ILE    44      38.900  23.940  70.977  1.00  0.00              
ATOM     90  CA  ILE    44      39.140  24.961  71.980  1.00  0.00              
ATOM     91  C   ILE    44      40.560  24.907  72.478  1.00  0.00              
ATOM     92  O   ILE    44      41.075  23.817  72.748  1.00  0.00              
ATOM     93  N   ASP    45      41.184  26.083  72.595  1.00  0.00              
ATOM     94  CA  ASP    45      42.577  26.177  73.047  1.00  0.00              
ATOM     95  C   ASP    45      42.711  26.581  74.514  1.00  0.00              
ATOM     96  O   ASP    45      41.726  26.929  75.182  1.00  0.00              
ATOM     97  N   ASN    46      43.941  26.539  75.035  1.00  0.00              
ATOM     98  CA  ASN    46      44.217  26.894  76.424  1.00  0.00              
ATOM     99  C   ASN    46      43.560  28.169  76.912  1.00  0.00              
ATOM    100  O   ASN    46      43.139  28.252  78.054  1.00  0.00              
ATOM    101  N   ILE    47      43.456  29.158  76.044  1.00  0.00              
ATOM    102  CA  ILE    47      42.888  30.441  76.436  1.00  0.00              
ATOM    103  C   ILE    47      41.376  30.547  76.218  1.00  0.00              
ATOM    104  O   ILE    47      40.769  31.618  76.393  1.00  0.00              
ATOM    105  N   GLY    48      40.760  29.422  75.873  1.00  0.00              
ATOM    106  CA  GLY    48      39.328  29.446  75.650  1.00  0.00              
ATOM    107  C   GLY    48      38.913  30.040  74.312  1.00  0.00              
ATOM    108  O   GLY    48      37.857  30.648  74.205  1.00  0.00              
ATOM    109  N   ALA    49      39.759  29.886  73.301  1.00  0.00              
ATOM    110  CA  ALA    49      39.446  30.385  71.972  1.00  0.00              
ATOM    111  C   ALA    49      38.823  29.213  71.244  1.00  0.00              
ATOM    112  O   ALA    49      39.492  28.194  70.953  1.00  0.00              
ATOM    113  N   GLY    50      37.538  29.348  70.937  1.00  0.00              
ATOM    114  CA  GLY    50      36.817  28.256  70.304  1.00  0.00              
ATOM    115  C   GLY    50      36.445  28.473  68.860  1.00  0.00              
ATOM    116  O   GLY    50      35.748  29.424  68.538  1.00  0.00              
ATOM    117  N   THR    51      36.913  27.581  67.993  1.00  0.00              
ATOM    118  CA  THR    51      36.593  27.667  66.570  1.00  0.00              
ATOM    119  C   THR    51      35.523  26.635  66.275  1.00  0.00              
ATOM    120  O   THR    51      35.637  25.480  66.690  1.00  0.00              
ATOM    121  N   GLY    52      34.477  27.055  65.580  1.00  0.00              
ATOM    122  CA  GLY    52      33.407  26.134  65.245  1.00  0.00              
ATOM    123  C   GLY    52      33.731  25.397  63.950  1.00  0.00              
ATOM    124  O   GLY    52      33.645  25.951  62.860  1.00  0.00              
ATOM    125  N   GLU    53      34.110  24.138  64.085  1.00  0.00              
ATOM    126  CA  GLU    53      34.463  23.309  62.947  1.00  0.00              
ATOM    127  C   GLU    53      33.246  22.875  62.127  1.00  0.00              
ATOM    128  O   GLU    53      32.434  22.047  62.568  1.00  0.00              
ATOM    129  N   TRP    54      33.124  23.434  60.928  1.00  0.00              
ATOM    130  CA  TRP    54      32.001  23.093  60.067  1.00  0.00              
ATOM    131  C   TRP    54      32.265  21.893  59.152  1.00  0.00              
ATOM    132  O   TRP    54      31.429  21.559  58.319  1.00  0.00              
ATOM    133  N   VAL    55      33.415  21.242  59.306  1.00  0.00              
ATOM    134  CA  VAL    55      33.724  20.084  58.480  1.00  0.00              
ATOM    135  C   VAL    55      34.892  19.209  58.933  1.00  0.00              
ATOM    136  O   VAL    55      34.694  18.065  59.343  1.00  0.00              
ATOM    137  N   LEU    56      36.103  19.757  58.875  1.00  0.00              
ATOM    138  CA  LEU    56      37.315  19.027  59.226  1.00  0.00              
ATOM    139  C   LEU    56      38.126  19.685  60.348  1.00  0.00              
ATOM    140  O   LEU    56      38.114  20.901  60.502  1.00  0.00              
ATOM    141  N   LEU    57      38.821  18.870  61.136  1.00  0.00              
ATOM    142  CA  LEU    57      39.649  19.384  62.225  1.00  0.00              
ATOM    143  C   LEU    57      40.573  18.309  62.799  1.00  0.00              
ATOM    144  O   LEU    57      40.186  17.147  62.937  1.00  0.00              
ATOM    145  N   VAL    58      41.800  18.702  63.118  1.00  0.00              
ATOM    146  CA  VAL    58      42.774  17.784  63.687  1.00  0.00              
ATOM    147  C   VAL    58      43.396  18.517  64.869  1.00  0.00              
ATOM    148  O   VAL    58      43.409  19.749  64.918  1.00  0.00              
ATOM    149  N   SER    59      43.927  17.748  65.812  1.00  0.00              
ATOM    150  CA  SER    59      44.472  18.313  67.024  1.00  0.00              
ATOM    151  C   SER    59      45.661  17.501  67.492  1.00  0.00              
ATOM    152  O   SER    59      45.741  16.307  67.208  1.00  0.00              
ATOM    153  N   GLY    60      46.579  18.143  68.217  1.00  0.00              
ATOM    154  CA  GLY    60      47.752  17.436  68.708  1.00  0.00              
ATOM    155  C   GLY    60      49.004  17.512  67.848  1.00  0.00              
ATOM    156  O   GLY    60      48.989  18.021  66.729  1.00  0.00              
ATOM    157  N   SER    61      50.095  16.969  68.380  1.00  0.00              
ATOM    158  CA  SER    61      51.384  16.983  67.700  1.00  0.00              
ATOM    159  C   SER    61      51.371  16.413  66.289  1.00  0.00              
ATOM    160  O   SER    61      52.260  16.708  65.492  1.00  0.00              
ATOM    161  N   SER    62      50.357  15.608  65.982  1.00  0.00              
ATOM    162  CA  SER    62      50.268  15.014  64.660  1.00  0.00              
ATOM    163  C   SER    62      49.261  15.700  63.751  1.00  0.00              
ATOM    164  O   SER    62      49.228  15.448  62.547  1.00  0.00              
ATOM    165  N   ALA    63      48.450  16.588  64.311  1.00  0.00              
ATOM    166  CA  ALA    63      47.430  17.262  63.523  1.00  0.00              
ATOM    167  C   ALA    63      47.830  17.709  62.114  1.00  0.00              
ATOM    168  O   ALA    63      47.070  17.496  61.165  1.00  0.00              
ATOM    169  N   ARG    64      49.010  18.315  61.960  1.00  0.00              
ATOM    170  CA  ARG    64      49.443  18.815  60.641  1.00  0.00              
ATOM    171  C   ARG    64      49.566  17.754  59.559  1.00  0.00              
ATOM    172  O   ARG    64      49.331  18.032  58.385  1.00  0.00              
ATOM    173  N   GLN    65      49.950  16.546  59.945  1.00  0.00              
ATOM    174  CA  GLN    65      50.058  15.459  58.984  1.00  0.00              
ATOM    175  C   GLN    65      48.649  14.951  58.712  1.00  0.00              
ATOM    176  O   GLN    65      48.278  14.701  57.567  1.00  0.00              
ATOM    177  N   ALA    66      47.873  14.798  59.781  1.00  0.00              
ATOM    178  CA  ALA    66      46.496  14.347  59.670  1.00  0.00              
ATOM    179  C   ALA    66      45.732  15.298  58.763  1.00  0.00              
ATOM    180  O   ALA    66      44.967  14.859  57.912  1.00  0.00              
ATOM    181  N   HIS    67      45.939  16.599  58.938  1.00  0.00              
ATOM    182  CA  HIS    67      45.255  17.583  58.099  1.00  0.00              
ATOM    183  C   HIS    67      45.515  17.334  56.620  1.00  0.00              
ATOM    184  O   HIS    67      44.692  17.679  55.760  1.00  0.00              
ATOM    185  N   LYS    68      46.675  16.743  56.338  1.00  0.00              
ATOM    186  CA  LYS    68      47.057  16.442  54.972  1.00  0.00              
ATOM    187  C   LYS    68      46.029  15.580  54.280  1.00  0.00              
ATOM    188  O   LYS    68      45.424  16.001  53.298  1.00  0.00              
END
