
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0372AL044_5-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372AL044_5-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      72      D       6          2.794
LGA    K      74      I       7          2.370
LGA    R      78      T       8          4.243
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    K      79      R      12           #
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    L      80      I      15          3.219
LGA    I      81      T      16          1.470
LGA    E      82      A      17          2.803
LGA    -       -      F      18           -
LGA    D      83      T      19          2.970
LGA    A      84      M      20          1.884
LGA    -       -      K      21           -
LGA    D      85      S      22          0.383
LGA    K      86      D      23          1.436
LGA    E      87      R      24          3.381
LGA    K      88      R      25          3.544
LGA    H      89      N      26          2.525
LGA    N      90      C      27          2.932
LGA    -       -      D      28           -
LGA    F      91      L      29          0.523
LGA    C      92      S      30          3.681
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    M      93      L      34          0.867
LGA    L      94      C      35          3.611
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    G      95      R      38          1.271
LGA    V      96      F      39          1.656
LGA    C      97      L      40          4.951
LGA    S      98      Y      41           -
LGA    M     100      -       -           -
LGA    D     103      D      42           #
LGA    L     104      T      43          4.778
LGA    E     105      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    A     106      F      54          5.415
LGA    I     107      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    P     109      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    E     110      G      95          3.609
LGA    R     111      V      96          4.890
LGA    F     112      C      97          3.653
LGA    -       -      S      98           -
LGA    I     113      N      99          2.010
LGA    D     117      M     100          1.896
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)   35  126    5.0     28    3.12     3.57     13.981     0.871

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.425560 * X  +  -0.872152 * Y  +  -0.241347 * Z  +  43.694782
  Y_new =   0.900089 * X  +   0.380402 * Y  +   0.212447 * Z  +  34.247158
  Z_new =  -0.093477 * X  +  -0.307643 * Y  +   0.946899 * Z  + -27.619625 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.314137    2.827455  [ DEG:   -17.9987    162.0013 ]
  Theta =   0.093614    3.047979  [ DEG:     5.3637    174.6363 ]
  Phi   =   1.129146   -2.012447  [ DEG:    64.6953   -115.3047 ]
 
# 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_5-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_5-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35  126   5.0   28   3.12    3.57  13.981
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_5-D1
REMARK Aligment from pdb entry: 1x7v_A
ATOM      1  N   ASP    72      52.359  51.734   1.683  1.00  0.00              
ATOM      2  CA  ASP    72      50.893  51.719   1.705  1.00  0.00              
ATOM      3  C   ASP    72      50.277  51.516   3.132  1.00  0.00              
ATOM      4  O   ASP    72      49.286  52.180   3.508  1.00  0.00              
ATOM      5  N   LYS    74      50.836  50.612   3.921  1.00  0.00              
ATOM      6  CA  LYS    74      50.433  50.400   5.306  1.00  0.00              
ATOM      7  C   LYS    74      50.540  51.692   6.112  1.00  0.00              
ATOM      8  O   LYS    74      49.636  51.982   6.881  1.00  0.00              
ATOM      9  N   ARG    78      51.647  52.433   5.943  1.00  0.00              
ATOM     10  CA  ARG    78      51.865  53.723   6.615  1.00  0.00              
ATOM     11  C   ARG    78      50.704  54.645   6.288  1.00  0.00              
ATOM     12  O   ARG    78      50.124  55.247   7.166  1.00  0.00              
ATOM     13  N   LYS    79      44.552  56.625   8.255  1.00  0.00              
ATOM     14  CA  LYS    79      43.081  56.780   8.110  1.00  0.00              
ATOM     15  C   LYS    79      42.269  56.403   9.351  1.00  0.00              
ATOM     16  O   LYS    79      41.113  56.849   9.524  1.00  0.00              
ATOM     17  N   LEU    80      42.819  55.513  10.179  1.00  0.00              
ATOM     18  CA  LEU    80      41.993  54.792  11.112  1.00  0.00              
ATOM     19  C   LEU    80      41.433  55.643  12.277  1.00  0.00              
ATOM     20  O   LEU    80      40.211  55.653  12.502  1.00  0.00              
ATOM     21  N   ILE    81      42.299  56.327  13.026  1.00  0.00              
ATOM     22  CA  ILE    81      41.823  57.072  14.181  1.00  0.00              
ATOM     23  C   ILE    81      40.833  58.160  13.747  1.00  0.00              
ATOM     24  O   ILE    81      39.748  58.270  14.348  1.00  0.00              
ATOM     25  N   GLU    82      41.175  58.967  12.731  1.00  0.00              
ATOM     26  CA  GLU    82      40.212  60.019  12.399  1.00  0.00              
ATOM     27  C   GLU    82      38.907  59.451  11.849  1.00  0.00              
ATOM     28  O   GLU    82      37.815  60.045  12.073  1.00  0.00              
ATOM     29  N   ASP    83      37.452  56.533  12.653  1.00  0.00              
ATOM     30  CA  ASP    83      36.689  55.943  13.753  1.00  0.00              
ATOM     31  C   ASP    83      35.891  57.022  14.534  1.00  0.00              
ATOM     32  O   ASP    83      34.799  56.738  15.061  1.00  0.00              
ATOM     33  N   ALA    84      36.422  58.253  14.565  1.00  0.00              
ATOM     34  CA  ALA    84      35.834  59.367  15.299  1.00  0.00              
ATOM     35  C   ALA    84      34.634  59.958  14.564  1.00  0.00              
ATOM     36  O   ALA    84      33.825  60.671  15.169  1.00  0.00              
ATOM     37  N   ASP    85      34.539  59.707  13.251  1.00  0.00              
ATOM     38  CA  ASP    85      33.494  60.361  12.448  1.00  0.00              
ATOM     39  C   ASP    85      32.081  59.956  12.878  1.00  0.00              
ATOM     40  O   ASP    85      31.829  58.820  13.218  1.00  0.00              
ATOM     41  N   LYS    86      31.165  60.929  12.823  1.00  0.00              
ATOM     42  CA  LYS    86      29.742  60.672  13.010  1.00  0.00              
ATOM     43  C   LYS    86      29.327  59.492  12.131  1.00  0.00              
ATOM     44  O   LYS    86      29.723  59.420  10.949  1.00  0.00              
ATOM     45  N   GLU    87      28.536  58.585  12.696  1.00  0.00              
ATOM     46  CA  GLU    87      27.999  57.465  11.976  1.00  0.00              
ATOM     47  C   GLU    87      28.967  56.316  11.705  1.00  0.00              
ATOM     48  O   GLU    87      28.577  55.371  11.016  1.00  0.00              
ATOM     49  N   LYS    88      30.225  56.415  12.164  1.00  0.00              
ATOM     50  CA  LYS    88      31.186  55.331  11.953  1.00  0.00              
ATOM     51  C   LYS    88      31.037  54.297  13.042  1.00  0.00              
ATOM     52  O   LYS    88      31.369  54.545  14.217  1.00  0.00              
ATOM     53  N   HIS    89      30.512  53.144  12.660  1.00  0.00              
ATOM     54  CA  HIS    89      30.309  52.032  13.584  1.00  0.00              
ATOM     55  C   HIS    89      31.469  51.051  13.636  1.00  0.00              
ATOM     56  O   HIS    89      31.599  50.306  14.575  1.00  0.00              
ATOM     57  N   ASN    90      32.296  51.042  12.612  1.00  0.00              
ATOM     58  CA  ASN    90      33.502  50.187  12.616  1.00  0.00              
ATOM     59  C   ASN    90      34.430  50.766  11.566  1.00  0.00              
ATOM     60  O   ASN    90      34.000  51.163  10.510  1.00  0.00              
ATOM     61  N   PHE    91      35.728  50.755  11.845  1.00  0.00              
ATOM     62  CA  PHE    91      36.720  51.134  10.845  1.00  0.00              
ATOM     63  C   PHE    91      38.026  50.494  11.276  1.00  0.00              
ATOM     64  O   PHE    91      38.752  51.034  12.136  1.00  0.00              
ATOM     65  N   CYS    92      38.271  49.311  10.713  1.00  0.00              
ATOM     66  CA  CYS    92      39.365  48.464  11.127  1.00  0.00              
ATOM     67  C   CYS    92      40.243  48.080   9.927  1.00  0.00              
ATOM     68  O   CYS    92      39.740  47.685   8.907  1.00  0.00              
ATOM     69  N   MET    93      41.559  48.228  10.097  1.00  0.00              
ATOM     70  CA  MET    93      42.576  47.900   9.116  1.00  0.00              
ATOM     71  C   MET    93      43.220  46.542   9.397  1.00  0.00              
ATOM     72  O   MET    93      43.495  46.199  10.514  1.00  0.00              
ATOM     73  N   LEU    94      43.459  45.766   8.351  1.00  0.00              
ATOM     74  CA  LEU    94      44.003  44.402   8.491  1.00  0.00              
ATOM     75  C   LEU    94      45.023  44.168   7.362  1.00  0.00              
ATOM     76  O   LEU    94      44.917  44.771   6.289  1.00  0.00              
ATOM     77  N   GLY    95      45.952  43.252   7.581  1.00  0.00              
ATOM     78  CA  GLY    95      46.847  42.828   6.516  1.00  0.00              
ATOM     79  C   GLY    95      46.601  41.323   6.293  1.00  0.00              
ATOM     80  O   GLY    95      46.392  40.543   7.240  1.00  0.00              
ATOM     81  N   VAL    96      46.569  40.948   5.039  1.00  0.00              
ATOM     82  CA  VAL    96      46.515  39.537   4.635  1.00  0.00              
ATOM     83  C   VAL    96      47.572  38.643   5.298  1.00  0.00              
ATOM     84  O   VAL    96      48.714  39.051   5.468  1.00  0.00              
ATOM     85  N   CYS    97      47.185  37.437   5.640  1.00  0.00              
ATOM     86  CA  CYS    97      48.086  36.517   6.333  1.00  0.00              
ATOM     87  C   CYS    97      49.212  36.004   5.433  1.00  0.00              
ATOM     88  O   CYS    97      50.298  35.645   5.922  1.00  0.00              
ATOM     89  N   SER    98      48.978  35.930   4.127  1.00  0.00              
ATOM     90  CA  SER    98      49.960  35.335   3.201  1.00  0.00              
ATOM     91  C   SER    98      50.611  36.229   2.179  1.00  0.00              
ATOM     92  O   SER    98      51.627  35.813   1.585  1.00  0.00              
ATOM     93  N   MET   100      50.045  37.414   1.906  1.00  0.00              
ATOM     94  CA  MET   100      50.616  38.352   0.939  1.00  0.00              
ATOM     95  C   MET   100      50.651  39.712   1.615  1.00  0.00              
ATOM     96  O   MET   100      49.597  40.301   1.858  1.00  0.00              
ATOM     97  N   ASP   103      51.858  40.221   1.882  1.00  0.00              
ATOM     98  CA  ASP   103      52.035  41.485   2.601  1.00  0.00              
ATOM     99  C   ASP   103      51.457  42.703   1.844  1.00  0.00              
ATOM    100  O   ASP   103      51.161  43.718   2.445  1.00  0.00              
ATOM    101  N   LEU   104      48.540  42.939   0.477  1.00  0.00              
ATOM    102  CA  LEU   104      47.064  42.945   0.545  1.00  0.00              
ATOM    103  C   LEU   104      46.590  43.372   1.916  1.00  0.00              
ATOM    104  O   LEU   104      47.017  42.824   2.932  1.00  0.00              
ATOM    105  N   GLU   105      42.964  45.081   4.063  1.00  0.00              
ATOM    106  CA  GLU   105      41.490  45.057   4.080  1.00  0.00              
ATOM    107  C   GLU   105      41.027  46.058   5.072  1.00  0.00              
ATOM    108  O   GLU   105      41.444  45.987   6.239  1.00  0.00              
ATOM    109  N   ALA   106      40.166  46.999   4.645  1.00  0.00              
ATOM    110  CA  ALA   106      39.503  47.872   5.615  1.00  0.00              
ATOM    111  C   ALA   106      38.079  47.338   5.753  1.00  0.00              
ATOM    112  O   ALA   106      37.386  47.208   4.748  1.00  0.00              
ATOM    113  N   ILE   107      37.670  47.018   6.970  1.00  0.00              
ATOM    114  CA  ILE   107      36.295  46.602   7.271  1.00  0.00              
ATOM    115  C   ILE   107      35.666  47.789   7.961  1.00  0.00              
ATOM    116  O   ILE   107      36.114  48.246   9.020  1.00  0.00              
ATOM    117  N   PRO   109      34.590  48.285   7.364  1.00  0.00              
ATOM    118  CA  PRO   109      33.946  49.519   7.791  1.00  0.00              
ATOM    119  C   PRO   109      32.431  49.268   7.953  1.00  0.00              
ATOM    120  O   PRO   109      31.866  48.496   7.182  1.00  0.00              
ATOM    121  N   GLU   110      31.810  49.922   8.925  1.00  0.00              
ATOM    122  CA  GLU   110      30.347  49.968   9.034  1.00  0.00              
ATOM    123  C   GLU   110      29.944  51.436   9.181  1.00  0.00              
ATOM    124  O   GLU   110      30.525  52.213   9.971  1.00  0.00              
ATOM    125  N   ARG   111      28.903  51.817   8.466  1.00  0.00              
ATOM    126  CA  ARG   111      28.469  53.199   8.455  1.00  0.00              
ATOM    127  C   ARG   111      26.978  53.186   8.708  1.00  0.00              
ATOM    128  O   ARG   111      26.279  52.325   8.197  1.00  0.00              
ATOM    129  N   PHE   112      26.486  54.121   9.499  1.00  0.00              
ATOM    130  CA  PHE   112      25.056  54.152   9.833  1.00  0.00              
ATOM    131  C   PHE   112      24.187  54.219   8.567  1.00  0.00              
ATOM    132  O   PHE   112      23.149  53.583   8.498  1.00  0.00              
ATOM    133  N   ILE   113      24.587  55.003   7.585  1.00  0.00              
ATOM    134  CA  ILE   113      23.824  55.155   6.357  1.00  0.00              
ATOM    135  C   ILE   113      24.734  55.695   5.278  1.00  0.00              
ATOM    136  O   ILE   113      25.910  55.997   5.538  1.00  0.00              
ATOM    137  N   ASP   117      24.194  55.834   4.068  1.00  0.00              
ATOM    138  CA  ASP   117      24.946  56.369   2.939  1.00  0.00              
ATOM    139  C   ASP   117      25.465  57.783   3.171  1.00  0.00              
ATOM    140  O   ASP   117      26.561  58.109   2.712  1.00  0.00              
END
