
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0372AL333_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372AL333_3-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    F      31      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      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    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    S      32      Y      41           #
LGA    -       -      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    -       -      K      55           -
LGA    G      71      F      56          4.209
LGA    D      72      W      57          2.933
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    L      73      L      62          3.879
LGA    K      74      A      63          4.413
LGA    A      75      -       -           -
LGA    V      76      Y      64          1.098
LGA    L      77      M      65          1.255
LGA    R      78      -       -           -
LGA    K      79      -       -           -
LGA    L      80      M      66          3.876
LGA    I      81      P      67          3.472
LGA    E      82      -       -           -
LGA    D      83      -       -           -
LGA    A      84      V      68          2.104
LGA    D      85      G      69          3.693
LGA    K      86      -       -           -
LGA    E      87      -       -           -
LGA    G      95      -       -           -
LGA    V      96      -       -           -
LGA    C      97      -       -           -
LGA    S      98      N      70          1.286
LGA    N      99      G      71          2.258
LGA    M     100      D      72          2.377
LGA    R     101      L      73          3.150
LGA    A     102      K      74          1.838
LGA    D     103      A      75          0.924
LGA    L     104      V      76          1.622
LGA    E     105      L      77          2.214
LGA    A     106      R      78          2.010
LGA    I     107      K      79          1.902
LGA    L     108      L      80          1.192
LGA    P     109      I      81          2.715
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)   34  126    5.0     22    2.69     9.09     12.524     0.788

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.894925 * X  +  -0.333382 * Y  +  -0.296589 * Z  +  -1.795230
  Y_new =  -0.387380 * X  +  -0.910351 * Y  +  -0.145594 * Z  +  41.953068
  Z_new =  -0.221462 * X  +   0.245188 * Y  +  -0.943842 * Z  +  24.030462 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.887434   -0.254159  [ DEG:   165.4378    -14.5622 ]
  Theta =   0.223313    2.918279  [ DEG:    12.7949    167.2051 ]
  Phi   =  -0.408512    2.733081  [ DEG:   -23.4060    156.5940 ]
 
# 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: T0372AL333_3-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL333_3-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34  126   5.0   22   2.69    9.09  12.524
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL333_3-D1
REMARK Aligment from pdb entry: 1lva_A
ATOM      1  N   PHE    31      32.640  39.514   2.021  1.00  0.00              
ATOM      2  CA  PHE    31      33.238  40.320   0.959  1.00  0.00              
ATOM      3  C   PHE    31      34.529  39.719   0.427  1.00  0.00              
ATOM      4  O   PHE    31      35.162  38.900   1.081  1.00  0.00              
ATOM      5  N   SER    32      34.912  40.146  -0.768  1.00  0.00              
ATOM      6  CA  SER    32      36.150  39.708  -1.385  1.00  0.00              
ATOM      7  C   SER    32      37.185  40.707  -0.869  1.00  0.00              
ATOM      8  O   SER    32      36.819  41.798  -0.426  1.00  0.00              
ATOM      9  N   GLY    71      38.463  40.349  -0.922  1.00  0.00              
ATOM     10  CA  GLY    71      39.504  41.252  -0.449  1.00  0.00              
ATOM     11  C   GLY    71      39.467  42.603  -1.160  1.00  0.00              
ATOM     12  O   GLY    71      39.836  43.616  -0.575  1.00  0.00              
ATOM     13  N   ASP    72      39.018  42.619  -2.413  1.00  0.00              
ATOM     14  CA  ASP    72      38.907  43.862  -3.163  1.00  0.00              
ATOM     15  C   ASP    72      37.750  44.699  -2.612  1.00  0.00              
ATOM     16  O   ASP    72      37.848  45.924  -2.510  1.00  0.00              
ATOM     17  N   LEU    73      36.656  44.031  -2.259  1.00  0.00              
ATOM     18  CA  LEU    73      35.500  44.717  -1.699  1.00  0.00              
ATOM     19  C   LEU    73      35.885  45.300  -0.341  1.00  0.00              
ATOM     20  O   LEU    73      35.522  46.438  -0.014  1.00  0.00              
ATOM     21  N   LYS    74      36.631  44.518   0.439  1.00  0.00              
ATOM     22  CA  LYS    74      37.064  44.959   1.758  1.00  0.00              
ATOM     23  C   LYS    74      37.921  46.213   1.667  1.00  0.00              
ATOM     24  O   LYS    74      37.750  47.143   2.453  1.00  0.00              
ATOM     25  N   ALA    75      38.839  46.246   0.705  1.00  0.00              
ATOM     26  CA  ALA    75      39.704  47.406   0.566  1.00  0.00              
ATOM     27  C   ALA    75      38.906  48.646   0.195  1.00  0.00              
ATOM     28  O   ALA    75      39.111  49.718   0.764  1.00  0.00              
ATOM     29  N   VAL    76      37.999  48.497  -0.761  1.00  0.00              
ATOM     30  CA  VAL    76      37.170  49.611  -1.196  1.00  0.00              
ATOM     31  C   VAL    76      36.338  50.174  -0.030  1.00  0.00              
ATOM     32  O   VAL    76      36.139  51.390   0.079  1.00  0.00              
ATOM     33  N   LEU    77      35.855  49.292   0.844  1.00  0.00              
ATOM     34  CA  LEU    77      35.068  49.740   1.989  1.00  0.00              
ATOM     35  C   LEU    77      35.970  50.526   2.926  1.00  0.00              
ATOM     36  O   LEU    77      35.564  51.551   3.492  1.00  0.00              
ATOM     37  N   ARG    78      37.203  50.038   3.071  1.00  0.00              
ATOM     38  CA  ARG    78      38.219  50.667   3.911  1.00  0.00              
ATOM     39  C   ARG    78      38.620  52.035   3.345  1.00  0.00              
ATOM     40  O   ARG    78      38.566  53.047   4.054  1.00  0.00              
ATOM     41  N   LYS    79      39.009  52.077   2.074  1.00  0.00              
ATOM     42  CA  LYS    79      39.390  53.345   1.462  1.00  0.00              
ATOM     43  C   LYS    79      38.236  54.334   1.465  1.00  0.00              
ATOM     44  O   LYS    79      38.423  55.543   1.666  1.00  0.00              
ATOM     45  N   LEU    80      37.039  53.807   1.236  1.00  0.00              
ATOM     46  CA  LEU    80      35.849  54.628   1.198  1.00  0.00              
ATOM     47  C   LEU    80      35.629  55.282   2.556  1.00  0.00              
ATOM     48  O   LEU    80      35.425  56.497   2.648  1.00  0.00              
ATOM     49  N   ILE    81      35.676  54.482   3.614  1.00  0.00              
ATOM     50  CA  ILE    81      35.485  55.024   4.952  1.00  0.00              
ATOM     51  C   ILE    81      36.571  56.041   5.309  1.00  0.00              
ATOM     52  O   ILE    81      36.301  57.059   5.959  1.00  0.00              
ATOM     53  N   GLU    82      37.802  55.766   4.896  1.00  0.00              
ATOM     54  CA  GLU    82      38.888  56.677   5.213  1.00  0.00              
ATOM     55  C   GLU    82      38.735  58.029   4.525  1.00  0.00              
ATOM     56  O   GLU    82      39.048  59.062   5.115  1.00  0.00              
ATOM     57  N   ASP    83      38.253  58.038   3.284  1.00  0.00              
ATOM     58  CA  ASP    83      38.073  59.307   2.587  1.00  0.00              
ATOM     59  C   ASP    83      37.107  60.191   3.370  1.00  0.00              
ATOM     60  O   ASP    83      37.335  61.394   3.526  1.00  0.00              
ATOM     61  N   ALA    84      36.022  59.598   3.863  1.00  0.00              
ATOM     62  CA  ALA    84      35.063  60.376   4.633  1.00  0.00              
ATOM     63  C   ALA    84      35.660  60.754   5.991  1.00  0.00              
ATOM     64  O   ALA    84      35.463  61.870   6.467  1.00  0.00              
ATOM     65  N   ASP    85      36.400  59.837   6.609  1.00  0.00              
ATOM     66  CA  ASP    85      37.017  60.132   7.896  1.00  0.00              
ATOM     67  C   ASP    85      37.958  61.327   7.780  1.00  0.00              
ATOM     68  O   ASP    85      37.877  62.261   8.566  1.00  0.00              
ATOM     69  N   LYS    86      38.850  61.294   6.795  1.00  0.00              
ATOM     70  CA  LYS    86      39.800  62.381   6.589  1.00  0.00              
ATOM     71  C   LYS    86      39.086  63.694   6.263  1.00  0.00              
ATOM     72  O   LYS    86      39.493  64.761   6.709  1.00  0.00              
ATOM     73  N   GLU    87      38.017  63.608   5.485  1.00  0.00              
ATOM     74  CA  GLU    87      37.265  64.793   5.113  1.00  0.00              
ATOM     75  C   GLU    87      36.637  65.528   6.299  1.00  0.00              
ATOM     76  O   GLU    87      36.368  66.730   6.217  1.00  0.00              
ATOM     77  N   GLY    95      36.400  64.797   7.384  1.00  0.00              
ATOM     78  CA  GLY    95      35.787  65.333   8.602  1.00  0.00              
ATOM     79  C   GLY    95      34.500  66.121   8.344  1.00  0.00              
ATOM     80  O   GLY    95      33.477  65.528   7.988  1.00  0.00              
ATOM     81  N   VAL    96      34.545  67.444   8.504  1.00  0.00              
ATOM     82  CA  VAL    96      33.351  68.275   8.328  1.00  0.00              
ATOM     83  C   VAL    96      33.212  68.918   6.948  1.00  0.00              
ATOM     84  O   VAL    96      32.437  69.863   6.756  1.00  0.00              
ATOM     85  N   CYS    97      33.983  68.412   5.995  1.00  0.00              
ATOM     86  CA  CYS    97      33.919  68.886   4.619  1.00  0.00              
ATOM     87  C   CYS    97      33.905  67.615   3.756  1.00  0.00              
ATOM     88  O   CYS    97      34.789  67.394   2.929  1.00  0.00              
ATOM     89  N   SER    98      32.892  66.753   3.959  1.00  0.00              
ATOM     90  CA  SER    98      32.779  65.507   3.201  1.00  0.00              
ATOM     91  C   SER    98      32.711  65.717   1.710  1.00  0.00              
ATOM     92  O   SER    98      32.164  66.703   1.225  1.00  0.00              
ATOM     93  N   ASN    99      33.284  64.787   0.954  1.00  0.00              
ATOM     94  CA  ASN    99      33.240  64.926  -0.497  1.00  0.00              
ATOM     95  C   ASN    99      31.796  64.614  -0.877  1.00  0.00              
ATOM     96  O   ASN    99      31.095  63.913  -0.130  1.00  0.00              
ATOM     97  N   MET   100      31.332  65.123  -2.011  1.00  0.00              
ATOM     98  CA  MET   100      29.956  64.835  -2.430  1.00  0.00              
ATOM     99  C   MET   100      29.896  63.451  -3.082  1.00  0.00              
ATOM    100  O   MET   100      30.927  62.830  -3.330  1.00  0.00              
ATOM    101  N   ARG   101      28.684  62.971  -3.347  1.00  0.00              
ATOM    102  CA  ARG   101      28.479  61.672  -3.982  1.00  0.00              
ATOM    103  C   ARG   101      29.206  61.639  -5.332  1.00  0.00              
ATOM    104  O   ARG   101      29.960  60.710  -5.626  1.00  0.00              
ATOM    105  N   ALA   102      28.976  62.658  -6.156  1.00  0.00              
ATOM    106  CA  ALA   102      29.622  62.734  -7.466  1.00  0.00              
ATOM    107  C   ALA   102      31.138  62.746  -7.347  1.00  0.00              
ATOM    108  O   ALA   102      31.825  62.053  -8.097  1.00  0.00              
ATOM    109  N   ASP   103      31.663  63.533  -6.408  1.00  0.00              
ATOM    110  CA  ASP   103      33.106  63.614  -6.200  1.00  0.00              
ATOM    111  C   ASP   103      33.692  62.234  -5.917  1.00  0.00              
ATOM    112  O   ASP   103      34.647  61.806  -6.565  1.00  0.00              
ATOM    113  N   LEU   104      33.121  61.543  -4.937  1.00  0.00              
ATOM    114  CA  LEU   104      33.597  60.211  -4.583  1.00  0.00              
ATOM    115  C   LEU   104      33.478  59.287  -5.790  1.00  0.00              
ATOM    116  O   LEU   104      34.368  58.483  -6.062  1.00  0.00              
ATOM    117  N   GLU   105      32.367  59.406  -6.507  1.00  0.00              
ATOM    118  CA  GLU   105      32.133  58.582  -7.682  1.00  0.00              
ATOM    119  C   GLU   105      33.301  58.703  -8.656  1.00  0.00              
ATOM    120  O   GLU   105      33.829  57.701  -9.139  1.00  0.00              
ATOM    121  N   ALA   106      33.699  59.939  -8.941  1.00  0.00              
ATOM    122  CA  ALA   106      34.796  60.169  -9.863  1.00  0.00              
ATOM    123  C   ALA   106      36.135  59.673  -9.342  1.00  0.00              
ATOM    124  O   ALA   106      36.847  58.930 -10.023  1.00  0.00              
ATOM    125  N   ILE   107      36.470  60.085  -8.125  1.00  0.00              
ATOM    126  CA  ILE   107      37.724  59.708  -7.492  1.00  0.00              
ATOM    127  C   ILE   107      37.984  58.207  -7.571  1.00  0.00              
ATOM    128  O   ILE   107      39.020  57.778  -8.072  1.00  0.00              
ATOM    129  N   LEU   108      37.042  57.413  -7.078  1.00  0.00              
ATOM    130  CA  LEU   108      37.180  55.958  -7.091  1.00  0.00              
ATOM    131  C   LEU   108      36.695  55.382  -8.414  1.00  0.00              
ATOM    132  O   LEU   108      36.693  54.168  -8.616  1.00  0.00              
ATOM    133  N   PRO   109      36.271  56.266  -9.307  1.00  0.00              
ATOM    134  CA  PRO   109      35.756  55.866 -10.608  1.00  0.00              
ATOM    135  C   PRO   109      34.786  54.693 -10.508  1.00  0.00              
ATOM    136  O   PRO   109      35.086  53.576 -10.937  1.00  0.00              
END
