
#######################################################
#                                                     #
#                        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   14 (  119),  selected   14 , name T0378TS389_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS389_5-D1.T0378_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    N       5      A       4          1.267
LGA    Q       6      N       5          0.816
LGA    I       7      Q       6          0.377
LGA    K       8      I       7          0.646
LGA    F       9      K       8          0.544
LGA    L      10      F       9          0.655
LGA    R      11      L      10          0.733
LGA    S      12      R      11          1.104
LGA    L      13      S      12          1.173
LGA    R      14      L      13          1.531
LGA    E      15      R      14          1.671
LGA    I      75      E      15          1.227
LGA    S      76      R      16          2.564
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    T      77      R      19          4.477
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    -       -      R      43           -
LGA    -       -      M      44           -
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   14   89    5.0     14    1.69     0.00     14.922     0.783

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.012979 * X  +   0.502375 * Y  +  -0.864552 * Z  +  27.008158
  Y_new =  -0.949764 * X  +  -0.264195 * Y  +  -0.167778 * Z  +  31.526903
  Z_new =  -0.312698 * X  +   0.823298 * Y  +   0.473709 * Z  +  48.842731 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.048677   -2.092916  [ DEG:    60.0848   -119.9152 ]
  Theta =   0.318032    2.823560  [ DEG:    18.2219    161.7781 ]
  Phi   =  -1.557131    1.584461  [ DEG:   -89.2171     90.7829 ]
 
# 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: T0378TS389_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS389_5-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   14   89   5.0   14   1.69    0.00  14.922
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS389_5-D1
PFRMAT TS
TARGET T0378
MODEL  5
PARENT N/A
ATOM      2  N   ASN     5       4.669  37.023  53.170  1.00  0.00
ATOM      3  CA  ASN     5       5.933  37.393  52.545  1.00  0.00
ATOM      4  CB  ASN     5       6.197  38.892  52.715  1.00  0.00
ATOM      5  CG  ASN     5       5.301  39.743  51.838  1.00  0.00
ATOM      6  ND2 ASN     5       5.168  41.017  52.189  1.00  0.00
ATOM      7  OD1 ASN     5       4.738  39.261  50.856  1.00  0.00
ATOM      8  O   ASN     5       7.960  36.108  52.473  1.00  0.00
ATOM      9  C   ASN     5       7.095  36.632  53.174  1.00  0.00
ATOM     10  N   GLN     6       7.104  36.571  54.502  1.00  0.00
ATOM     11  CA  GLN     6       8.162  35.880  55.224  1.00  0.00
ATOM     12  CB  GLN     6       7.933  35.981  56.733  1.00  0.00
ATOM     13  CG  GLN     6       8.157  37.372  57.303  1.00  0.00
ATOM     14  CD  GLN     6       7.847  37.453  58.785  1.00  0.00
ATOM     15  OE1 GLN     6       7.421  36.472  59.393  1.00  0.00
ATOM     16  NE2 GLN     6       8.060  38.626  59.369  1.00  0.00
ATOM     17  O   GLN     6       9.246  33.759  54.912  1.00  0.00
ATOM     18  C   GLN     6       8.197  34.402  54.842  1.00  0.00
ATOM     19  N   ILE     7       7.047  33.870  54.436  1.00  0.00
ATOM     20  CA  ILE     7       6.948  32.472  54.031  1.00  0.00
ATOM     21  CB  ILE     7       5.485  32.055  53.792  1.00  0.00
ATOM     22  CG1 ILE     7       4.708  32.060  55.109  1.00  0.00
ATOM     23  CG2 ILE     7       5.420  30.657  53.198  1.00  0.00
ATOM     24  CD1 ILE     7       3.211  31.920  54.935  1.00  0.00
ATOM     25  O   ILE     7       8.361  31.238  52.530  1.00  0.00
ATOM     26  C   ILE     7       7.731  32.275  52.739  1.00  0.00
ATOM     27  N   LYS     8       7.679  33.285  51.874  1.00  0.00
ATOM     28  CA  LYS     8       8.368  33.245  50.593  1.00  0.00
ATOM     29  CB  LYS     8       8.056  34.499  49.776  1.00  0.00
ATOM     30  CG  LYS     8       6.629  34.563  49.258  1.00  0.00
ATOM     31  CD  LYS     8       6.386  35.832  48.455  1.00  0.00
ATOM     32  CE  LYS     8       4.952  35.905  47.956  1.00  0.00
ATOM     33  NZ  LYS     8       4.694  37.158  47.197  1.00  0.00
ATOM     34  O   LYS     8      10.551  32.384  50.094  1.00  0.00
ATOM     35  C   LYS     8       9.881  33.169  50.766  1.00  0.00
ATOM     36  N   PHE     9      10.417  33.986  51.667  1.00  0.00
ATOM     37  CA  PHE     9      11.855  34.001  51.910  1.00  0.00
ATOM     38  CB  PHE     9      12.216  35.094  52.917  1.00  0.00
ATOM     39  CG  PHE     9      12.246  36.477  52.330  1.00  0.00
ATOM     40  CD1 PHE     9      11.189  37.347  52.519  1.00  0.00
ATOM     41  CD2 PHE     9      13.334  36.904  51.588  1.00  0.00
ATOM     42  CE1 PHE     9      11.217  38.619  51.976  1.00  0.00
ATOM     43  CE2 PHE     9      13.363  38.175  51.047  1.00  0.00
ATOM     44  CZ  PHE     9      12.310  39.032  51.238  1.00  0.00
ATOM     45  O   PHE     9      13.345  32.126  52.074  1.00  0.00
ATOM     46  C   PHE     9      12.305  32.653  52.467  1.00  0.00
ATOM     47  N   LEU    10      11.513  32.094  53.379  1.00  0.00
ATOM     48  CA  LEU    10      11.829  30.799  53.971  1.00  0.00
ATOM     49  CB  LEU    10      10.842  30.467  55.094  1.00  0.00
ATOM     50  CG  LEU    10      10.941  31.323  56.358  1.00  0.00
ATOM     51  CD1 LEU    10       9.798  31.011  57.311  1.00  0.00
ATOM     52  CD2 LEU    10      12.250  31.058  57.085  1.00  0.00
ATOM     53  O   LEU    10      12.526  28.759  52.912  1.00  0.00
ATOM     54  C   LEU    10      11.745  29.714  52.908  1.00  0.00
ATOM     55  N   ARG    11      10.789  29.868  51.998  1.00  0.00
ATOM     56  CA  ARG    11      10.598  28.920  50.910  1.00  0.00
ATOM     57  CB  ARG    11       9.376  29.305  50.073  1.00  0.00
ATOM     58  CG  ARG    11       9.061  28.328  48.951  1.00  0.00
ATOM     59  CD  ARG    11       7.897  28.818  48.105  1.00  0.00
ATOM     60  NE  ARG    11       8.226  30.041  47.377  1.00  0.00
ATOM     61  CZ  ARG    11       8.958  30.077  46.269  1.00  0.00
ATOM     62  NH1 ARG    11       9.206  31.235  45.674  1.00  0.00
ATOM     63  NH2 ARG    11       9.440  28.953  45.756  1.00  0.00
ATOM     64  O   ARG    11      12.406  27.928  49.665  1.00  0.00
ATOM     65  C   ARG    11      11.856  28.960  50.052  1.00  0.00
ATOM     66  N   SER    12      12.310  30.175  49.768  1.00  0.00
ATOM     67  CA  SER    12      13.496  30.379  48.954  1.00  0.00
ATOM     68  CB  SER    12      13.681  31.865  48.639  1.00  0.00
ATOM     69  OG  SER    12      12.634  32.347  47.815  1.00  0.00
ATOM     70  O   SER    12      15.647  29.321  49.084  1.00  0.00
ATOM     71  C   SER    12      14.735  29.882  49.690  1.00  0.00
ATOM     72  N   LEU    13      14.754  30.081  51.004  1.00  0.00
ATOM     73  CA  LEU    13      15.875  29.654  51.831  1.00  0.00
ATOM     74  CB  LEU    13      15.655  30.069  53.287  1.00  0.00
ATOM     75  CG  LEU    13      16.768  29.699  54.272  1.00  0.00
ATOM     76  CD1 LEU    13      18.075  30.372  53.883  1.00  0.00
ATOM     77  CD2 LEU    13      16.406  30.139  55.682  1.00  0.00
ATOM     78  O   LEU    13      17.072  27.576  51.657  1.00  0.00
ATOM     79  C   LEU    13      15.983  28.133  51.741  1.00  0.00
ATOM     80  N   ARG    14      14.835  27.468  51.757  1.00  0.00
ATOM     81  CA  ARG    14      14.801  26.016  51.679  1.00  0.00
ATOM     82  CB  ARG    14      13.361  25.508  51.757  1.00  0.00
ATOM     83  CG  ARG    14      12.721  25.662  53.127  1.00  0.00
ATOM     84  CD  ARG    14      11.278  25.183  53.122  1.00  0.00
ATOM     85  NE  ARG    14      10.635  25.370  54.420  1.00  0.00
ATOM     86  CZ  ARG    14       9.361  25.085  54.670  1.00  0.00
ATOM     87  NH1 ARG    14       8.861  25.288  55.882  1.00  0.00
ATOM     88  NH2 ARG    14       8.590  24.598  53.708  1.00  0.00
ATOM     89  O   ARG    14      16.215  24.601  50.347  1.00  0.00
ATOM     90  C   ARG    14      15.409  25.527  50.364  1.00  0.00
ATOM     91  N   GLU    15      15.015  26.155  49.261  1.00  0.00
ATOM     92  CA  GLU    15      15.542  25.789  47.948  1.00  0.00
ATOM     93  CB  GLU    15      14.921  26.666  46.859  1.00  0.00
ATOM     94  CG  GLU    15      13.454  26.378  46.590  1.00  0.00
ATOM     95  CD  GLU    15      12.842  27.344  45.596  1.00  0.00
ATOM     96  OE1 GLU    15      13.546  28.287  45.173  1.00  0.00
ATOM     97  OE2 GLU    15      11.660  27.162  45.238  1.00  0.00
ATOM     98  O   GLU    15      17.798  25.165  47.384  1.00  0.00
ATOM     99  C   GLU    15      17.056  25.978  47.937  1.00  0.00
ATOM    100  N   ILE    75      17.509  27.063  48.551  1.00  0.00
ATOM    101  CA  ILE    75      18.934  27.348  48.622  1.00  0.00
ATOM    102  CB  ILE    75      19.203  28.722  49.262  1.00  0.00
ATOM    103  CG1 ILE    75      18.694  29.843  48.353  1.00  0.00
ATOM    104  CG2 ILE    75      20.696  28.923  49.486  1.00  0.00
ATOM    105  CD1 ILE    75      18.675  31.203  49.016  1.00  0.00
ATOM    106  O   ILE    75      20.675  25.766  49.069  1.00  0.00
ATOM    107  C   ILE    75      19.633  26.284  49.461  1.00  0.00
ATOM    108  N   SER    76      19.059  25.952  50.614  1.00  0.00
ATOM    109  CA  SER    76      19.670  24.943  51.471  1.00  0.00
ATOM    110  CB  SER    76      18.865  24.779  52.762  1.00  0.00
ATOM    111  OG  SER    76      17.576  24.255  52.497  1.00  0.00
ATOM    112  O   SER    76      20.650  22.793  51.029  1.00  0.00
ATOM    113  C   SER    76      19.733  23.577  50.783  1.00  0.00
ATOM    114  N   THR    77      18.776  23.298  49.904  1.00  0.00
ATOM    115  CA  THR    77      18.766  22.019  49.201  1.00  0.00
ATOM    116  CB  THR    77      17.444  21.800  48.442  1.00  0.00
ATOM    117  CG2 THR    77      16.270  21.806  49.411  1.00  0.00
ATOM    118  OG1 THR    77      17.259  22.850  47.485  1.00  0.00
ATOM    119  O   THR    77      20.156  20.808  47.661  1.00  0.00
ATOM    120  C   THR    77      19.885  21.896  48.164  1.00  0.00
TER
END
