
#######################################################
#                                                     #
#                        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   10 (   88),  selected   10 , name T0378TS186_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS186_4-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    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    L      66      K       8          1.561
LGA    P      67      F       9          0.917
LGA    E      68      L      10          0.862
LGA    S      69      R      11          1.291
LGA    F      70      S      12          1.187
LGA    D      71      L      13          1.795
LGA    F      72      R      14          1.861
LGA    K      73      E      15          1.184
LGA    R      74      R      16          2.372
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    I      75      R      19          4.356
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)   10   89    5.0     10    1.99    10.00     10.428     0.477

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.749705 * X  +  -0.601143 * Y  +  -0.276712 * Z  +  60.281082
  Y_new =  -0.204231 * X  +  -0.607899 * Y  +   0.767300 * Z  + -36.022007
  Z_new =  -0.629470 * X  +  -0.518735 * Y  +  -0.578517 * Z  + 135.275055 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.410623    0.730969  [ DEG:  -138.1185     41.8815 ]
  Theta =   0.680871    2.460722  [ DEG:    39.0110    140.9890 ]
  Phi   =  -0.265961    2.875632  [ DEG:   -15.2384    164.7616 ]
 
# 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: T0378TS186_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS186_4-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10   89   5.0   10   1.99   10.00  10.428
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS186_4-D1
PFRMAT TS
TARGET T0378
MODEL  4
PARENT 1zjr_A
ATOM      1  N   LEU    66       9.598  34.025  50.465  1.00  0.00
ATOM      2  CA  LEU    66      11.085  34.098  50.560  1.00  0.00
ATOM      3  C   LEU    66      11.639  32.929  51.368  1.00  0.00
ATOM      4  O   LEU    66      12.725  32.424  51.080  1.00  0.00
ATOM      5  CB  LEU    66      11.507  35.415  51.219  1.00  0.00
ATOM      6  CG  LEU    66      11.080  36.707  50.520  1.00  0.00
ATOM      7  CD1 LEU    66      11.538  37.905  51.339  1.00  0.00
ATOM      8  CD2 LEU    66      11.674  36.758  49.121  1.00  0.00
ATOM      9  N   PRO    67      10.888  32.509  52.381  1.00  0.00
ATOM     10  CA  PRO    67      11.304  31.403  53.236  1.00  0.00
ATOM     11  C   PRO    67      11.571  30.150  52.411  1.00  0.00
ATOM     12  O   PRO    67      12.578  29.468  52.606  1.00  0.00
ATOM     13  CB  PRO    67      10.122  31.207  54.188  1.00  0.00
ATOM     14  CG  PRO    67       9.506  32.561  54.302  1.00  0.00
ATOM     15  CD  PRO    67       9.565  33.164  52.926  1.00  0.00
ATOM     16  N   GLU    68      10.665  29.853  51.487  1.00  0.00
ATOM     17  CA  GLU    68      10.800  28.678  50.637  1.00  0.00
ATOM     18  C   GLU    68      12.080  28.758  49.809  1.00  0.00
ATOM     19  O   GLU    68      12.647  27.732  49.429  1.00  0.00
ATOM     20  CB  GLU    68       9.612  28.571  49.678  1.00  0.00
ATOM     21  CG  GLU    68       8.303  28.194  50.352  1.00  0.00
ATOM     22  CD  GLU    68       7.132  28.189  49.390  1.00  0.00
ATOM     23  OE1 GLU    68       7.331  28.549  48.211  1.00  0.00
ATOM     24  OE2 GLU    68       6.015  27.825  49.814  1.00  0.00
ATOM     25  N   SER    69      12.531  29.979  49.535  1.00  0.00
ATOM     26  CA  SER    69      13.751  30.192  48.762  1.00  0.00
ATOM     27  C   SER    69      14.943  29.714  49.580  1.00  0.00
ATOM     28  O   SER    69      15.904  29.165  49.040  1.00  0.00
ATOM     29  CB  SER    69      13.926  31.677  48.437  1.00  0.00
ATOM     30  OG  SER    69      12.904  32.132  47.567  1.00  0.00
ATOM     31  N   PHE    70      14.868  29.930  50.890  1.00  0.00
ATOM     32  CA  PHE    70      15.932  29.537  51.803  1.00  0.00
ATOM     33  C   PHE    70      16.122  28.025  51.833  1.00  0.00
ATOM     34  O   PHE    70      17.250  27.534  51.790  1.00  0.00
ATOM     35  CB  PHE    70      15.612  29.993  53.228  1.00  0.00
ATOM     36  CG  PHE    70      15.872  31.454  53.469  1.00  0.00
ATOM     37  CD1 PHE    70      14.830  32.366  53.475  1.00  0.00
ATOM     38  CD2 PHE    70      17.158  31.914  53.689  1.00  0.00
ATOM     39  CE1 PHE    70      15.070  33.709  53.697  1.00  0.00
ATOM     40  CE2 PHE    70      17.398  33.257  53.910  1.00  0.00
ATOM     41  CZ  PHE    70      16.361  34.154  53.915  1.00  0.00
ATOM     42  N   ASP    71      15.017  27.289  51.906  1.00  0.00
ATOM     43  CA  ASP    71      15.083  25.832  51.946  1.00  0.00
ATOM     44  C   ASP    71      15.675  25.301  50.643  1.00  0.00
ATOM     45  O   ASP    71      16.493  24.382  50.654  1.00  0.00
ATOM     46  CB  ASP    71      13.685  25.239  52.128  1.00  0.00
ATOM     47  CG  ASP    71      13.144  25.439  53.530  1.00  0.00
ATOM     48  OD1 ASP    71      13.931  25.821  54.421  1.00  0.00
ATOM     49  OD2 ASP    71      11.933  25.214  53.738  1.00  0.00
ATOM     50  N   PHE    72      15.264  25.887  49.522  1.00  0.00
ATOM     51  CA  PHE    72      15.773  25.477  48.216  1.00  0.00
ATOM     52  C   PHE    72      17.254  25.813  48.114  1.00  0.00
ATOM     53  O   PHE    72      18.032  25.069  47.513  1.00  0.00
ATOM     54  CB  PHE    72      15.023  26.203  47.097  1.00  0.00
ATOM     55  CG  PHE    72      15.478  25.822  45.718  1.00  0.00
ATOM     56  CD1 PHE    72      15.075  24.628  45.145  1.00  0.00
ATOM     57  CD2 PHE    72      16.308  26.658  44.991  1.00  0.00
ATOM     58  CE1 PHE    72      15.493  24.278  43.875  1.00  0.00
ATOM     59  CE2 PHE    72      16.727  26.307  43.721  1.00  0.00
ATOM     60  CZ  PHE    72      16.322  25.123  43.163  1.00  0.00
ATOM     61  N   LYS    73      17.634  26.940  48.706  1.00  0.00
ATOM     62  CA  LYS    73      19.020  27.382  48.706  1.00  0.00
ATOM     63  C   LYS    73      19.825  26.340  49.472  1.00  0.00
ATOM     64  O   LYS    73      20.896  25.909  49.043  1.00  0.00
ATOM     65  CB  LYS    73      19.137  28.735  49.412  1.00  0.00
ATOM     66  CG  LYS    73      20.517  29.371  49.352  1.00  0.00
ATOM     67  CD  LYS    73      20.690  30.231  48.104  1.00  0.00
ATOM     68  CE  LYS    73      19.732  31.419  48.108  1.00  0.00
ATOM     69  NZ  LYS    73      19.929  32.313  46.929  1.00  0.00
ATOM     70  N   ARG    74      19.285  25.934  50.615  1.00  0.00
ATOM     71  CA  ARG    74      19.935  24.948  51.462  1.00  0.00
ATOM     72  C   ARG    74      19.959  23.590  50.770  1.00  0.00
ATOM     73  O   ARG    74      20.931  22.843  50.882  1.00  0.00
ATOM     74  CB  ARG    74      19.192  24.861  52.798  1.00  0.00
ATOM     75  CG  ARG    74      19.978  24.207  53.917  1.00  0.00
ATOM     76  CD  ARG    74      19.453  24.671  55.265  1.00  0.00
ATOM     77  NE  ARG    74      19.508  26.128  55.368  1.00  0.00
ATOM     78  CZ  ARG    74      19.104  26.826  56.426  1.00  0.00
ATOM     79  NH1 ARG    74      18.608  26.203  57.488  1.00  0.00
ATOM     80  NH2 ARG    74      19.198  28.149  56.420  1.00  0.00
ATOM     81  N   ILE    75      18.888  23.282  50.047  1.00  0.00
ATOM     82  CA  ILE    75      18.781  22.017  49.333  1.00  0.00
ATOM     83  C   ILE    75      19.894  21.963  48.288  1.00  0.00
ATOM     84  O   ILE    75      20.521  20.930  48.078  1.00  0.00
ATOM     85  CB  ILE    75      17.419  21.881  48.626  1.00  0.00
ATOM     86  CG1 ILE    75      16.295  21.752  49.655  1.00  0.00
ATOM     87  CG2 ILE    75      17.401  20.647  47.737  1.00  0.00
ATOM     88  CD1 ILE    75      14.908  21.881  49.065  1.00  0.00
TER
END
