
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0372AL044_1-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372AL044_1-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    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    K      74      T       8          1.361
LGA    R      78      L       9          3.304
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    K      79      R      12           #
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    L      80      I      15          3.479
LGA    I      81      T      16          1.230
LGA    E      82      A      17          3.302
LGA    -       -      F      18           -
LGA    D      83      T      19          2.805
LGA    A      84      M      20          1.605
LGA    D      85      K      21          3.426
LGA    K      86      S      22          3.323
LGA    E      87      D      23          2.307
LGA    K      88      R      24          0.681
LGA    H      89      R      25          1.339
LGA    N      90      N      26          2.278
LGA    F      91      C      27          2.553
LGA    C      92      D      28          2.491
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    M      93      N      33          2.648
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    L      94      S      36          4.115
LGA    G      95      W      37          2.361
LGA    V      96      R      38          5.460
LGA    C      97      F      39          4.553
LGA    M     100      -       -           -
LGA    R     101      -       -           -
LGA    L     104      L      40          3.185
LGA    A     106      Y      41          1.969
LGA    I     107      D      42           #
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    L     108      K      55           #
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
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    P     109      L      94           #
LGA    E     110      G      95          4.273
LGA    R     111      V      96          5.657
LGA    F     112      C      97          4.561
LGA    -       -      S      98           -
LGA    I     113      N      99          2.607
LGA    D     117      M     100          2.494
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)   33  126    5.0     27    3.19     7.41     13.182     0.822

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.263498 * X  +  -0.861998 * Y  +   0.433046 * Z  +  32.249477
  Y_new =  -0.904656 * X  +   0.376664 * Y  +   0.199305 * Z  +  63.124676
  Z_new =  -0.334913 * X  +  -0.339241 * Y  +  -0.879061 * Z  +  29.740362 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.773289    0.368303  [ DEG:  -158.8978     21.1022 ]
  Theta =   0.341513    2.800080  [ DEG:    19.5673    160.4327 ]
  Phi   =  -1.854224    1.287369  [ DEG:  -106.2392     73.7608 ]
 
# 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_1-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_1-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33  126   5.0   27   3.19    7.41  13.182
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_1-D1
REMARK Aligment from pdb entry: 2go8_A
ATOM      1  N   LYS    74      50.596  51.880   6.721  1.00  0.00              
ATOM      2  CA  LYS    74      51.299  51.050   7.688  1.00  0.00              
ATOM      3  C   LYS    74      51.170  51.781   9.002  1.00  0.00              
ATOM      4  O   LYS    74      50.319  51.453   9.830  1.00  0.00              
ATOM      5  N   ARG    78      52.074  52.720   9.248  1.00  0.00              
ATOM      6  CA  ARG    78      51.875  53.536  10.416  1.00  0.00              
ATOM      7  C   ARG    78      50.726  54.226   9.779  1.00  0.00              
ATOM      8  O   ARG    78      49.730  54.513  10.432  1.00  0.00              
ATOM      9  N   LYS    79      44.808  56.507   9.099  1.00  0.00              
ATOM     10  CA  LYS    79      43.599  56.442   8.328  1.00  0.00              
ATOM     11  C   LYS    79      42.491  55.853   9.186  1.00  0.00              
ATOM     12  O   LYS    79      41.329  56.076   8.898  1.00  0.00              
ATOM     13  N   LEU    80      42.828  55.131  10.254  1.00  0.00              
ATOM     14  CA  LEU    80      41.781  54.601  11.109  1.00  0.00              
ATOM     15  C   LEU    80      41.330  55.543  12.213  1.00  0.00              
ATOM     16  O   LEU    80      40.147  55.566  12.517  1.00  0.00              
ATOM     17  N   ILE    81      42.240  56.303  12.822  1.00  0.00              
ATOM     18  CA  ILE    81      41.838  57.196  13.903  1.00  0.00              
ATOM     19  C   ILE    81      40.829  58.166  13.336  1.00  0.00              
ATOM     20  O   ILE    81      39.872  58.547  13.997  1.00  0.00              
ATOM     21  N   GLU    82      41.092  58.566  12.102  1.00  0.00              
ATOM     22  CA  GLU    82      40.297  59.493  11.329  1.00  0.00              
ATOM     23  C   GLU    82      38.859  58.959  11.088  1.00  0.00              
ATOM     24  O   GLU    82      37.909  59.690  11.256  1.00  0.00              
ATOM     25  N   ASP    83      37.249  56.701  12.840  1.00  0.00              
ATOM     26  CA  ASP    83      36.756  56.641  14.205  1.00  0.00              
ATOM     27  C   ASP    83      36.254  57.973  14.668  1.00  0.00              
ATOM     28  O   ASP    83      35.294  58.085  15.447  1.00  0.00              
ATOM     29  N   ALA    84      36.922  58.996  14.172  1.00  0.00              
ATOM     30  CA  ALA    84      36.599  60.340  14.586  1.00  0.00              
ATOM     31  C   ALA    84      35.421  61.006  13.902  1.00  0.00              
ATOM     32  O   ALA    84      34.876  61.996  14.384  1.00  0.00              
ATOM     33  N   ASP    85      35.019  60.463  12.771  1.00  0.00              
ATOM     34  CA  ASP    85      33.949  61.080  12.022  1.00  0.00              
ATOM     35  C   ASP    85      32.539  60.991  12.547  1.00  0.00              
ATOM     36  O   ASP    85      32.198  60.158  13.385  1.00  0.00              
ATOM     37  N   LYS    86      31.709  61.925  12.099  1.00  0.00              
ATOM     38  CA  LYS    86      30.305  61.966  12.492  1.00  0.00              
ATOM     39  C   LYS    86      29.703  60.760  11.757  1.00  0.00              
ATOM     40  O   LYS    86      30.042  60.498  10.598  1.00  0.00              
ATOM     41  N   GLU    87      28.867  59.989  12.441  1.00  0.00              
ATOM     42  CA  GLU    87      28.246  58.851  11.796  1.00  0.00              
ATOM     43  C   GLU    87      29.087  57.598  11.696  1.00  0.00              
ATOM     44  O   GLU    87      28.663  56.617  11.086  1.00  0.00              
ATOM     45  N   LYS    88      30.297  57.633  12.235  1.00  0.00              
ATOM     46  CA  LYS    88      31.131  56.441  12.195  1.00  0.00              
ATOM     47  C   LYS    88      30.582  55.473  13.234  1.00  0.00              
ATOM     48  O   LYS    88      30.415  55.839  14.392  1.00  0.00              
ATOM     49  N   HIS    89      30.312  54.237  12.822  1.00  0.00              
ATOM     50  CA  HIS    89      29.746  53.240  13.723  1.00  0.00              
ATOM     51  C   HIS    89      30.735  52.230  14.284  1.00  0.00              
ATOM     52  O   HIS    89      30.465  51.606  15.304  1.00  0.00              
ATOM     53  N   ASN    90      31.883  52.072  13.641  1.00  0.00              
ATOM     54  CA  ASN    90      32.862  51.120  14.141  1.00  0.00              
ATOM     55  C   ASN    90      33.695  50.552  13.010  1.00  0.00              
ATOM     56  O   ASN    90      33.457  50.872  11.844  1.00  0.00              
ATOM     57  N   PHE    91      34.681  49.721  13.345  1.00  0.00              
ATOM     58  CA  PHE    91      35.528  49.125  12.327  1.00  0.00              
ATOM     59  C   PHE    91      36.109  47.789  12.738  1.00  0.00              
ATOM     60  O   PHE    91      36.517  47.600  13.883  1.00  0.00              
ATOM     61  N   CYS    92      36.154  46.865  11.785  1.00  0.00              
ATOM     62  CA  CYS    92      36.738  45.561  12.036  1.00  0.00              
ATOM     63  C   CYS    92      37.885  45.420  11.038  1.00  0.00              
ATOM     64  O   CYS    92      37.697  45.514   9.822  1.00  0.00              
ATOM     65  N   MET    93      39.094  45.265  11.561  1.00  0.00              
ATOM     66  CA  MET    93      40.252  45.168  10.698  1.00  0.00              
ATOM     67  C   MET    93      41.067  43.939  11.005  1.00  0.00              
ATOM     68  O   MET    93      41.335  43.602  12.159  1.00  0.00              
ATOM     69  N   LEU    94      41.464  43.272   9.936  1.00  0.00              
ATOM     70  CA  LEU    94      42.169  42.021  10.054  1.00  0.00              
ATOM     71  C   LEU    94      43.160  41.939   8.890  1.00  0.00              
ATOM     72  O   LEU    94      42.823  42.286   7.753  1.00  0.00              
ATOM     73  N   GLY    95      44.385  41.510   9.175  1.00  0.00              
ATOM     74  CA  GLY    95      45.418  41.449   8.142  1.00  0.00              
ATOM     75  C   GLY    95      46.273  40.221   8.375  1.00  0.00              
ATOM     76  O   GLY    95      46.866  40.097   9.433  1.00  0.00              
ATOM     77  N   VAL    96      46.293  39.279   7.432  1.00  0.00              
ATOM     78  CA  VAL    96      47.131  38.090   7.626  1.00  0.00              
ATOM     79  C   VAL    96      48.585  38.354   7.255  1.00  0.00              
ATOM     80  O   VAL    96      48.952  39.356   6.625  1.00  0.00              
ATOM     81  N   CYS    97      49.386  37.385   7.667  1.00  0.00              
ATOM     82  CA  CYS    97      50.812  37.286   7.431  1.00  0.00              
ATOM     83  C   CYS    97      51.241  37.610   6.016  1.00  0.00              
ATOM     84  O   CYS    97      52.030  38.531   5.816  1.00  0.00              
ATOM     85  N   MET   100      50.717  36.827   5.075  1.00  0.00              
ATOM     86  CA  MET   100      51.004  36.903   3.662  1.00  0.00              
ATOM     87  C   MET   100      50.558  38.158   2.922  1.00  0.00              
ATOM     88  O   MET   100      50.757  38.235   1.715  1.00  0.00              
ATOM     89  N   ARG   101      49.954  39.121   3.618  1.00  0.00              
ATOM     90  CA  ARG   101      49.525  40.344   2.963  1.00  0.00              
ATOM     91  C   ARG   101      48.040  40.457   2.687  1.00  0.00              
ATOM     92  O   ARG   101      47.564  41.526   2.322  1.00  0.00              
ATOM     93  N   LEU   104      47.302  39.364   2.824  1.00  0.00              
ATOM     94  CA  LEU   104      45.873  39.405   2.573  1.00  0.00              
ATOM     95  C   LEU   104      45.126  40.073   3.700  1.00  0.00              
ATOM     96  O   LEU   104      45.367  39.771   4.871  1.00  0.00              
ATOM     97  N   ALA   106      44.176  40.936   3.350  1.00  0.00              
ATOM     98  CA  ALA   106      43.469  41.649   4.388  1.00  0.00              
ATOM     99  C   ALA   106      42.095  42.202   4.099  1.00  0.00              
ATOM    100  O   ALA   106      41.798  42.617   2.980  1.00  0.00              
ATOM    101  N   ILE   107      41.239  42.186   5.117  1.00  0.00              
ATOM    102  CA  ILE   107      39.905  42.742   4.982  1.00  0.00              
ATOM    103  C   ILE   107      39.604  43.723   6.124  1.00  0.00              
ATOM    104  O   ILE   107      39.761  43.420   7.316  1.00  0.00              
ATOM    105  N   LEU   108      39.163  44.914   5.758  1.00  0.00              
ATOM    106  CA  LEU   108      38.808  45.903   6.753  1.00  0.00              
ATOM    107  C   LEU   108      37.414  46.429   6.431  1.00  0.00              
ATOM    108  O   LEU   108      37.156  46.905   5.330  1.00  0.00              
ATOM    109  N   PRO   109      34.285  48.981   7.590  1.00  0.00              
ATOM    110  CA  PRO   109      33.914  50.083   8.450  1.00  0.00              
ATOM    111  C   PRO   109      32.424  50.286   8.309  1.00  0.00              
ATOM    112  O   PRO   109      31.874  50.194   7.221  1.00  0.00              
ATOM    113  N   GLU   110      31.775  50.547   9.432  1.00  0.00              
ATOM    114  CA  GLU   110      30.337  50.719   9.448  1.00  0.00              
ATOM    115  C   GLU   110      29.946  52.180   9.645  1.00  0.00              
ATOM    116  O   GLU   110      30.527  52.893  10.464  1.00  0.00              
ATOM    117  N   ARG   111      28.963  52.618   8.869  1.00  0.00              
ATOM    118  CA  ARG   111      28.521  54.001   8.881  1.00  0.00              
ATOM    119  C   ARG   111      27.035  54.132   8.912  1.00  0.00              
ATOM    120  O   ARG   111      26.325  53.294   8.375  1.00  0.00              
ATOM    121  N   PHE   112      26.564  55.213   9.518  1.00  0.00              
ATOM    122  CA  PHE   112      25.137  55.446   9.632  1.00  0.00              
ATOM    123  C   PHE   112      24.445  55.947   8.388  1.00  0.00              
ATOM    124  O   PHE   112      23.234  55.846   8.294  1.00  0.00              
ATOM    125  N   ILE   113      25.174  56.501   7.435  1.00  0.00              
ATOM    126  CA  ILE   113      24.495  57.002   6.260  1.00  0.00              
ATOM    127  C   ILE   113      25.423  57.114   5.091  1.00  0.00              
ATOM    128  O   ILE   113      26.637  57.204   5.244  1.00  0.00              
ATOM    129  N   ASP   117      24.842  57.082   3.907  1.00  0.00              
ATOM    130  CA  ASP   117      25.627  57.237   2.707  1.00  0.00              
ATOM    131  C   ASP   117      26.243  58.614   2.811  1.00  0.00              
ATOM    132  O   ASP   117      27.384  58.807   2.416  1.00  0.00              
END
