
#######################################################
#                                                     #
#                        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 T0372AL044_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372AL044_4-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    V      68      I       2           #
LGA    G      69      P       3           -
LGA    N      70      F       4           -
LGA    G      71      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    D      72      I      15          3.384
LGA    K      74      T      16          1.901
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    R      78      T      19          2.144
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    K      79      C      27          5.746
LGA    L      80      D      28          4.448
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    I      81      S      32          1.609
LGA    E      82      N      33          2.500
LGA    -       -      L      34           -
LGA    D      83      C      35          3.587
LGA    A      84      S      36          3.854
LGA    D      85      W      37          3.798
LGA    K      86      R      38           -
LGA    -       -      F      39           -
LGA    E      87      L      40          2.904
LGA    K      88      Y      41          1.340
LGA    H      89      D      42          0.958
LGA    N      90      T      43          0.935
LGA    F      91      Q      44          3.042
LGA    C      92      F      45          0.537
LGA    M      93      A      46          3.235
LGA    L      94      V      47          0.611
LGA    G      95      I      48          3.959
LGA    V      96      D      49          1.849
LGA    C      97      -       -           -
LGA    S      98      -       -           -
LGA    M     100      -       -           -
LGA    D     103      D      50          4.630
LGA    L     104      F      51          3.378
LGA    E     105      L      52          4.163
LGA    A     106      V      53          1.234
LGA    I     107      F      54          3.846
LGA    P     109      K      55          0.706
LGA    E     110      F      56          2.751
LGA    R     111      W      57          1.015
LGA    F     112      A      58          4.604
LGA    -       -      G      59           -
LGA    I     113      E      60          2.337
LGA    D     117      Q      61          1.720
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39  126    5.0     31    3.01     3.23     15.769     0.998

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.414638 * X  +  -0.140886 * Y  +  -0.899014 * Z  +  32.625713
  Y_new =  -0.647441 * X  +   0.648555 * Y  +  -0.400246 * Z  +  60.421104
  Z_new =   0.639449 * X  +   0.748016 * Y  +   0.177700 * Z  + -56.438751 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.337558   -1.804034  [ DEG:    76.6364   -103.3636 ]
  Theta =  -0.693781   -2.447811  [ DEG:   -39.7507   -140.2493 ]
  Phi   =  -1.001181    2.140412  [ DEG:   -57.3634    122.6366 ]
 
# 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: T0372AL044_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_4-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39  126   5.0   31   3.01    3.23  15.769
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_4-D1
REMARK Aligment from pdb entry: 1lq9_A
ATOM      1  N   VAL    68      36.624  50.974  -3.702  1.00  0.00              
ATOM      2  CA  VAL    68      36.969  52.385  -3.569  1.00  0.00              
ATOM      3  C   VAL    68      35.784  53.052  -2.881  1.00  0.00              
ATOM      4  O   VAL    68      34.702  53.071  -3.466  1.00  0.00              
ATOM      5  N   GLY    69      39.540  69.994   7.919  1.00  0.00              
ATOM      6  CA  GLY    69      39.626  69.609   9.328  1.00  0.00              
ATOM      7  C   GLY    69      38.936  68.258   9.534  1.00  0.00              
ATOM      8  O   GLY    69      39.434  67.374  10.249  1.00  0.00              
ATOM      9  N   ASN    70      37.779  68.096   8.911  1.00  0.00              
ATOM     10  CA  ASN    70      37.063  66.804   9.004  1.00  0.00              
ATOM     11  C   ASN    70      37.800  65.722   8.243  1.00  0.00              
ATOM     12  O   ASN    70      37.825  64.571   8.712  1.00  0.00              
ATOM     13  N   GLY    71      38.657  62.286  10.188  1.00  0.00              
ATOM     14  CA  GLY    71      38.151  61.011   9.698  1.00  0.00              
ATOM     15  C   GLY    71      39.288  60.034   9.467  1.00  0.00              
ATOM     16  O   GLY    71      39.165  58.845   9.814  1.00  0.00              
ATOM     17  N   ASP    72      40.400  60.480   8.887  1.00  0.00              
ATOM     18  CA  ASP    72      41.528  59.559   8.740  1.00  0.00              
ATOM     19  C   ASP    72      42.057  59.172  10.128  1.00  0.00              
ATOM     20  O   ASP    72      42.400  57.992  10.325  1.00  0.00              
ATOM     21  N   LYS    74      42.143  60.102  11.071  1.00  0.00              
ATOM     22  CA  LYS    74      42.610  59.804  12.446  1.00  0.00              
ATOM     23  C   LYS    74      41.693  58.759  13.087  1.00  0.00              
ATOM     24  O   LYS    74      42.143  57.840  13.762  1.00  0.00              
ATOM     25  N   ARG    78      40.372  58.878  12.846  1.00  0.00              
ATOM     26  CA  ARG    78      39.432  57.897  13.377  1.00  0.00              
ATOM     27  C   ARG    78      39.628  56.557  12.709  1.00  0.00              
ATOM     28  O   ARG    78      39.726  55.504  13.377  1.00  0.00              
ATOM     29  N   LYS    79      39.998  51.685  15.943  1.00  0.00              
ATOM     30  CA  LYS    79      38.648  51.131  15.809  1.00  0.00              
ATOM     31  C   LYS    79      38.648  49.892  14.933  1.00  0.00              
ATOM     32  O   LYS    79      37.826  49.015  15.116  1.00  0.00              
ATOM     33  N   LEU    80      39.545  49.824  13.935  1.00  0.00              
ATOM     34  CA  LEU    80      39.554  48.674  13.058  1.00  0.00              
ATOM     35  C   LEU    80      40.814  47.836  13.173  1.00  0.00              
ATOM     36  O   LEU    80      41.157  47.106  12.239  1.00  0.00              
ATOM     37  N   ILE    81      41.434  47.821  14.355  1.00  0.00              
ATOM     38  CA  ILE    81      42.535  46.934  14.587  1.00  0.00              
ATOM     39  C   ILE    81      42.134  45.500  14.225  1.00  0.00              
ATOM     40  O   ILE    81      42.956  44.752  13.648  1.00  0.00              
ATOM     41  N   GLU    82      40.887  45.072  14.513  1.00  0.00              
ATOM     42  CA  GLU    82      40.470  43.706  14.229  1.00  0.00              
ATOM     43  C   GLU    82      40.591  43.311  12.770  1.00  0.00              
ATOM     44  O   GLU    82      40.725  42.121  12.442  1.00  0.00              
ATOM     45  N   ASP    83      42.891  43.814  10.624  1.00  0.00              
ATOM     46  CA  ASP    83      44.210  43.552  10.084  1.00  0.00              
ATOM     47  C   ASP    83      44.546  42.092   9.873  1.00  0.00              
ATOM     48  O   ASP    83      45.214  41.807   8.866  1.00  0.00              
ATOM     49  N   ALA    84      44.034  41.233  10.731  1.00  0.00              
ATOM     50  CA  ALA    84      44.401  39.807  10.630  1.00  0.00              
ATOM     51  C   ALA    84      43.322  38.991   9.976  1.00  0.00              
ATOM     52  O   ALA    84      43.406  37.777   9.923  1.00  0.00              
ATOM     53  N   ASP    85      42.250  39.581   9.467  1.00  0.00              
ATOM     54  CA  ASP    85      41.169  38.804   8.830  1.00  0.00              
ATOM     55  C   ASP    85      41.693  38.171   7.573  1.00  0.00              
ATOM     56  O   ASP    85      42.355  38.831   6.743  1.00  0.00              
ATOM     57  N   LYS    86      41.324  36.916   7.304  1.00  0.00              
ATOM     58  CA  LYS    86      41.812  36.280   6.088  1.00  0.00              
ATOM     59  C   LYS    86      41.343  37.009   4.851  1.00  0.00              
ATOM     60  O   LYS    86      40.164  37.367   4.695  1.00  0.00              
ATOM     61  N   GLU    87      42.249  37.275   3.926  1.00  0.00              
ATOM     62  CA  GLU    87      41.948  37.897   2.649  1.00  0.00              
ATOM     63  C   GLU    87      42.112  39.402   2.669  1.00  0.00              
ATOM     64  O   GLU    87      42.136  39.999   1.584  1.00  0.00              
ATOM     65  N   LYS    88      42.224  40.048   3.832  1.00  0.00              
ATOM     66  CA  LYS    88      42.417  41.484   3.891  1.00  0.00              
ATOM     67  C   LYS    88      43.843  41.831   3.480  1.00  0.00              
ATOM     68  O   LYS    88      44.795  41.311   4.097  1.00  0.00              
ATOM     69  N   HIS    89      44.024  42.691   2.509  1.00  0.00              
ATOM     70  CA  HIS    89      45.369  43.092   2.102  1.00  0.00              
ATOM     71  C   HIS    89      45.703  44.502   2.521  1.00  0.00              
ATOM     72  O   HIS    89      46.820  44.747   2.974  1.00  0.00              
ATOM     73  N   ASN    90      44.829  45.465   2.358  1.00  0.00              
ATOM     74  CA  ASN    90      45.114  46.810   2.783  1.00  0.00              
ATOM     75  C   ASN    90      43.877  47.686   2.686  1.00  0.00              
ATOM     76  O   ASN    90      42.930  47.441   1.934  1.00  0.00              
ATOM     77  N   PHE    91      43.948  48.813   3.395  1.00  0.00              
ATOM     78  CA  PHE    91      42.998  49.912   3.232  1.00  0.00              
ATOM     79  C   PHE    91      43.799  51.196   3.330  1.00  0.00              
ATOM     80  O   PHE    91      44.443  51.443   4.356  1.00  0.00              
ATOM     81  N   CYS    92      43.831  52.000   2.290  1.00  0.00              
ATOM     82  CA  CYS    92      44.608  53.250   2.273  1.00  0.00              
ATOM     83  C   CYS    92      43.630  54.408   2.221  1.00  0.00              
ATOM     84  O   CYS    92      42.830  54.495   1.253  1.00  0.00              
ATOM     85  N   MET    93      43.689  55.276   3.198  1.00  0.00              
ATOM     86  CA  MET    93      42.818  56.460   3.278  1.00  0.00              
ATOM     87  C   MET    93      43.555  57.675   2.777  1.00  0.00              
ATOM     88  O   MET    93      44.668  57.953   3.208  1.00  0.00              
ATOM     89  N   LEU    94      42.889  58.402   1.894  1.00  0.00              
ATOM     90  CA  LEU    94      43.451  59.555   1.224  1.00  0.00              
ATOM     91  C   LEU    94      42.562  60.757   1.481  1.00  0.00              
ATOM     92  O   LEU    94      41.347  60.648   1.509  1.00  0.00              
ATOM     93  N   GLY    95      43.184  61.936   1.569  1.00  0.00              
ATOM     94  CA  GLY    95      42.416  63.189   1.628  1.00  0.00              
ATOM     95  C   GLY    95      42.386  63.748   0.205  1.00  0.00              
ATOM     96  O   GLY    95      43.441  64.024  -0.392  1.00  0.00              
ATOM     97  N   VAL    96      41.209  63.997  -0.349  1.00  0.00              
ATOM     98  CA  VAL    96      41.156  64.683  -1.655  1.00  0.00              
ATOM     99  C   VAL    96      41.799  66.047  -1.507  1.00  0.00              
ATOM    100  O   VAL    96      41.697  66.729  -0.474  1.00  0.00              
ATOM    101  N   CYS    97      42.506  66.495  -2.552  1.00  0.00              
ATOM    102  CA  CYS    97      43.235  67.753  -2.466  1.00  0.00              
ATOM    103  C   CYS    97      42.294  68.932  -2.342  1.00  0.00              
ATOM    104  O   CYS    97      42.675  69.980  -1.772  1.00  0.00              
ATOM    105  N   SER    98      41.035  68.812  -2.771  1.00  0.00              
ATOM    106  CA  SER    98      40.082  69.903  -2.686  1.00  0.00              
ATOM    107  C   SER    98      39.384  69.958  -1.336  1.00  0.00              
ATOM    108  O   SER    98      38.527  70.828  -1.150  1.00  0.00              
ATOM    109  N   MET   100      39.706  69.090  -0.389  1.00  0.00              
ATOM    110  CA  MET   100      39.178  69.156   0.952  1.00  0.00              
ATOM    111  C   MET   100      37.819  68.502   1.159  1.00  0.00              
ATOM    112  O   MET   100      37.359  68.479   2.306  1.00  0.00              
ATOM    113  N   ASP   103      37.193  67.991   0.104  1.00  0.00              
ATOM    114  CA  ASP   103      35.795  67.587   0.194  1.00  0.00              
ATOM    115  C   ASP   103      35.540  66.124   0.461  1.00  0.00              
ATOM    116  O   ASP   103      34.394  65.754   0.692  1.00  0.00              
ATOM    117  N   LEU   104      36.566  65.265   0.389  1.00  0.00              
ATOM    118  CA  LEU   104      36.279  63.830   0.531  1.00  0.00              
ATOM    119  C   LEU   104      37.483  63.125   1.112  1.00  0.00              
ATOM    120  O   LEU   104      38.628  63.549   0.966  1.00  0.00              
ATOM    121  N   GLU   105      38.958  59.221   0.654  1.00  0.00              
ATOM    122  CA  GLU   105      38.788  58.084  -0.239  1.00  0.00              
ATOM    123  C   GLU   105      39.607  56.924   0.295  1.00  0.00              
ATOM    124  O   GLU   105      40.816  57.076   0.538  1.00  0.00              
ATOM    125  N   ALA   106      38.969  55.763   0.450  1.00  0.00              
ATOM    126  CA  ALA   106      39.645  54.537   0.865  1.00  0.00              
ATOM    127  C   ALA   106      39.811  53.654  -0.393  1.00  0.00              
ATOM    128  O   ALA   106      38.803  53.309  -1.020  1.00  0.00              
ATOM    129  N   ILE   107      41.040  53.294  -0.709  1.00  0.00              
ATOM    130  CA  ILE   107      41.342  52.258  -1.696  1.00  0.00              
ATOM    131  C   ILE   107      41.626  50.987  -0.905  1.00  0.00              
ATOM    132  O   ILE   107      42.654  50.960  -0.186  1.00  0.00              
ATOM    133  N   PRO   109      40.798  49.987  -0.996  1.00  0.00              
ATOM    134  CA  PRO   109      40.938  48.758  -0.207  1.00  0.00              
ATOM    135  C   PRO   109      41.202  47.574  -1.108  1.00  0.00              
ATOM    136  O   PRO   109      40.493  47.322  -2.075  1.00  0.00              
ATOM    137  N   GLU   110      42.260  46.828  -0.776  1.00  0.00              
ATOM    138  CA  GLU   110      42.616  45.612  -1.489  1.00  0.00              
ATOM    139  C   GLU   110      42.242  44.367  -0.691  1.00  0.00              
ATOM    140  O   GLU   110      42.583  44.252   0.467  1.00  0.00              
ATOM    141  N   ARG   111      41.619  43.424  -1.413  1.00  0.00              
ATOM    142  CA  ARG   111      41.208  42.149  -0.850  1.00  0.00              
ATOM    143  C   ARG   111      41.687  41.048  -1.777  1.00  0.00              
ATOM    144  O   ARG   111      41.784  41.214  -3.012  1.00  0.00              
ATOM    145  N   PHE   112      41.888  39.831  -1.217  1.00  0.00              
ATOM    146  CA  PHE   112      42.313  38.708  -2.074  1.00  0.00              
ATOM    147  C   PHE   112      41.213  38.329  -3.044  1.00  0.00              
ATOM    148  O   PHE   112      41.496  37.885  -4.154  1.00  0.00              
ATOM    149  N   ILE   113      39.946  38.401  -2.624  1.00  0.00              
ATOM    150  CA  ILE   113      38.861  37.976  -3.503  1.00  0.00              
ATOM    151  C   ILE   113      37.582  38.593  -2.970  1.00  0.00              
ATOM    152  O   ILE   113      37.480  39.016  -1.807  1.00  0.00              
ATOM    153  N   ASP   117      36.559  38.585  -3.837  1.00  0.00              
ATOM    154  CA  ASP   117      35.235  39.032  -3.417  1.00  0.00              
ATOM    155  C   ASP   117      34.696  38.098  -2.326  1.00  0.00              
ATOM    156  O   ASP   117      34.048  38.565  -1.374  1.00  0.00              
END
