
#######################################################
#                                                     #
#                        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   16 (  121),  selected   16 , name T0335TS389_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS389_3-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          1.147
LGA    K       6      K       6          1.171
LGA    I       7      I       7          1.392
LGA    A       8      A       8          1.024
LGA    R       9      R       9          0.267
LGA    I      10      I      10          1.154
LGA    G      20      N      11          0.370
LGA    V      21      E      12          1.260
LGA    I      22      L      13          2.406
LGA    -       -      A      14           -
LGA    -       -      A      15           -
LGA    T      23      K      16          1.344
LGA    -       -      A      17           -
LGA    E      24      K      18          2.780
LGA    E      25      A      19          2.803
LGA    E      26      G      20          4.136
LGA    K      27      -       -           -
LGA    K      39      V      21          3.639
LGA    G      40      I      22          2.444
LGA    -       -      T      23           -
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    -       -      K      27           -
LGA    -       -      A      28           -
LGA    -       -      E      29           -
LGA    -       -      Q      30           -
LGA    -       -      Q      31           -
LGA    -       -      K      32           -
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      Q      35           -
LGA    -       -      E      36           -
LGA    -       -      Y      37           -
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16   36    5.0     15    2.13    40.00     35.785     0.671

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.074365 * X  +  -0.776411 * Y  +  -0.625824 * Z  +   5.499812
  Y_new =  -0.270140 * X  +  -0.619782 * Y  +   0.736814 * Z  +  -2.033622
  Z_new =  -0.959945 * X  +   0.114267 * Y  +  -0.255829 * Z  +  10.184742 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.721525   -0.420067  [ DEG:   155.9319    -24.0681 ]
  Theta =   1.286806    1.854787  [ DEG:    73.7285    106.2715 ]
  Phi   =  -1.302168    1.839425  [ DEG:   -74.6087    105.3913 ]
 
# 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: T0335TS389_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS389_3-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16   36   5.0   15   2.13   40.00  35.785
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS389_3-D1
PFRMAT TS
TARGET T0335
MODEL  3
PARENT N/A
ATOM     16  N   ALA     5       0.072  -9.731  -7.667  1.00  0.00
ATOM     17  CA  ALA     5      -0.521 -10.294  -6.420  1.00  0.00
ATOM     18  CB  ALA     5       0.216 -11.558  -6.006  1.00  0.00
ATOM     19  O   ALA     5      -1.411  -8.891  -4.691  1.00  0.00
ATOM     20  C   ALA     5      -0.422  -9.274  -5.280  1.00  0.00
ATOM     21  N   LYS     6       0.767  -8.837  -4.968  1.00  0.00
ATOM     22  CA  LYS     6       0.931  -7.844  -3.866  1.00  0.00
ATOM     23  CB  LYS     6       2.408  -7.496  -3.673  1.00  0.00
ATOM     24  CG  LYS     6       2.673  -6.519  -2.539  1.00  0.00
ATOM     25  CD  LYS     6       4.162  -6.275  -2.358  1.00  0.00
ATOM     26  CE  LYS     6       4.425  -5.258  -1.257  1.00  0.00
ATOM     27  NZ  LYS     6       5.879  -4.990  -1.085  1.00  0.00
ATOM     28  O   LYS     6      -0.540  -6.018  -3.366  1.00  0.00
ATOM     29  C   LYS     6       0.165  -6.560  -4.194  1.00  0.00
ATOM     30  N   ILE     7       0.296  -6.069  -5.397  1.00  0.00
ATOM     31  CA  ILE     7      -0.432  -4.823  -5.770  1.00  0.00
ATOM     32  CB  ILE     7      -0.437  -4.607  -7.295  1.00  0.00
ATOM     33  CG1 ILE     7       0.975  -4.290  -7.792  1.00  0.00
ATOM     34  CG2 ILE     7      -1.350  -3.448  -7.666  1.00  0.00
ATOM     35  CD1 ILE     7       1.114  -4.327  -9.299  1.00  0.00
ATOM     36  O   ILE     7      -2.453  -3.940  -4.827  1.00  0.00
ATOM     37  C   ILE     7      -1.884  -4.908  -5.294  1.00  0.00
ATOM     38  N   ALA     8      -2.486  -6.060  -5.405  1.00  0.00
ATOM     39  CA  ALA     8      -3.897  -6.212  -4.954  1.00  0.00
ATOM     40  CB  ALA     8      -4.527  -7.444  -5.586  1.00  0.00
ATOM     41  O   ALA     8      -4.936  -6.053  -2.799  1.00  0.00
ATOM     42  C   ALA     8      -3.946  -6.360  -3.431  1.00  0.00
ATOM     43  N   ARG     9      -2.880  -6.825  -2.840  1.00  0.00
ATOM     44  CA  ARG     9      -2.861  -6.993  -1.359  1.00  0.00
ATOM     45  CB  ARG     9      -1.578  -7.702  -0.916  1.00  0.00
ATOM     46  CG  ARG     9      -1.518  -9.171  -1.297  1.00  0.00
ATOM     47  CD  ARG     9      -0.185  -9.788  -0.902  1.00  0.00
ATOM     48  NE  ARG     9      -0.106 -11.200  -1.270  1.00  0.00
ATOM     49  CZ  ARG     9       0.991 -11.941  -1.157  1.00  0.00
ATOM     50  NH1 ARG     9       0.970 -13.218  -1.516  1.00  0.00
ATOM     51  NH2 ARG     9       2.107 -11.405  -0.684  1.00  0.00
ATOM     52  O   ARG     9      -3.518  -5.473   0.375  1.00  0.00
ATOM     53  C   ARG     9      -2.927  -5.625  -0.676  1.00  0.00
ATOM     54  N   ILE    10      -2.327  -4.628  -1.265  1.00  0.00
ATOM     55  CA  ILE    10      -2.360  -3.269  -0.650  1.00  0.00
ATOM     56  CB  ILE    10      -1.298  -2.342  -1.270  1.00  0.00
ATOM     57  CG1 ILE    10       0.109  -2.832  -0.917  1.00  0.00
ATOM     58  CG2 ILE    10      -1.458  -0.923  -0.745  1.00  0.00
ATOM     59  CD1 ILE    10       1.208  -2.132  -1.684  1.00  0.00
ATOM     60  O   ILE    10      -4.191  -1.835  -0.068  1.00  0.00
ATOM     61  C   ILE    10      -3.733  -2.632  -0.865  1.00  0.00
ATOM     62  N   GLY    20      -4.394  -2.977  -1.935  1.00  0.00
ATOM     63  CA  GLY    20      -5.739  -2.394  -2.201  1.00  0.00
ATOM     64  O   GLY    20      -7.775  -2.597  -0.950  1.00  0.00
ATOM     65  C   GLY    20      -6.807  -3.163  -1.418  1.00  0.00
ATOM     66  N   VAL    21      -6.634  -4.448  -1.271  1.00  0.00
ATOM     67  CA  VAL    21      -7.634  -5.255  -0.519  1.00  0.00
ATOM     68  CB  VAL    21      -7.186  -6.722  -0.379  1.00  0.00
ATOM     69  CG1 VAL    21      -8.118  -7.478   0.555  1.00  0.00
ATOM     70  CG2 VAL    21      -7.195  -7.415  -1.733  1.00  0.00
ATOM     71  O   VAL    21      -8.873  -4.825   1.489  1.00  0.00
ATOM     72  C   VAL    21      -7.827  -4.680   0.886  1.00  0.00
ATOM     73  N   ILE    22      -6.825  -4.032   1.413  1.00  0.00
ATOM     74  CA  ILE    22      -6.952  -3.449   2.781  1.00  0.00
ATOM     75  CB  ILE    22      -5.837  -2.425   3.063  1.00  0.00
ATOM     76  CG1 ILE    22      -5.920  -1.260   2.075  1.00  0.00
ATOM     77  CG2 ILE    22      -4.470  -3.076   2.927  1.00  0.00
ATOM     78  CD1 ILE    22      -4.993  -0.111   2.408  1.00  0.00
ATOM     79  O   ILE    22      -8.898  -2.319   1.953  1.00  0.00
ATOM     80  C   ILE    22      -8.300  -2.738   2.924  1.00  0.00
ATOM     81  N   THR    23      -8.784  -2.600   4.129  1.00  0.00
ATOM     82  CA  THR    23     -10.093  -1.918   4.332  1.00  0.00
ATOM     83  CB  THR    23     -10.768  -2.368   5.640  1.00  0.00
ATOM     84  CG2 THR    23     -10.967  -3.876   5.647  1.00  0.00
ATOM     85  OG1 THR    23      -9.945  -2.004   6.755  1.00  0.00
ATOM     86  O   THR    23      -8.817   0.083   4.681  1.00  0.00
ATOM     87  C   THR    23      -9.895  -0.401   4.396  1.00  0.00
ATOM     88  N   GLU    24     -10.928   0.354   4.137  1.00  0.00
ATOM     89  CA  GLU    24     -10.799   1.837   4.188  1.00  0.00
ATOM     90  CB  GLU    24     -12.118   2.503   3.792  1.00  0.00
ATOM     91  CG  GLU    24     -12.461   2.373   2.317  1.00  0.00
ATOM     92  CD  GLU    24     -13.816   2.963   1.980  1.00  0.00
ATOM     93  OE1 GLU    24     -14.518   3.410   2.912  1.00  0.00
ATOM     94  OE2 GLU    24     -14.177   2.977   0.784  1.00  0.00
ATOM     95  O   GLU    24      -9.805   3.308   5.802  1.00  0.00
ATOM     96  C   GLU    24     -10.429   2.284   5.605  1.00  0.00
ATOM     97  N   GLU    25     -10.810   1.522   6.595  1.00  0.00
ATOM     98  CA  GLU    25     -10.480   1.903   7.996  1.00  0.00
ATOM     99  CB  GLU    25     -11.389   1.163   8.980  1.00  0.00
ATOM    100  CG  GLU    25     -12.855   1.559   8.888  1.00  0.00
ATOM    101  CD  GLU    25     -13.728   0.791   9.861  1.00  0.00
ATOM    102  OE1 GLU    25     -13.180  -0.015  10.642  1.00  0.00
ATOM    103  OE2 GLU    25     -14.960   0.994   9.842  1.00  0.00
ATOM    104  O   GLU    25      -8.427   2.087   9.221  1.00  0.00
ATOM    105  C   GLU    25      -9.025   1.545   8.315  1.00  0.00
ATOM    106  N   GLU    26      -8.454   0.637   7.572  1.00  0.00
ATOM    107  CA  GLU    26      -7.038   0.243   7.829  1.00  0.00
ATOM    108  CB  GLU    26      -6.667  -0.992   7.007  1.00  0.00
ATOM    109  CG  GLU    26      -5.256  -1.500   7.254  1.00  0.00
ATOM    110  CD  GLU    26      -4.937  -2.745   6.449  1.00  0.00
ATOM    111  OE1 GLU    26      -5.818  -3.208   5.694  1.00  0.00
ATOM    112  OE2 GLU    26      -3.804  -3.257   6.572  1.00  0.00
ATOM    113  O   GLU    26      -5.221   1.766   8.203  1.00  0.00
ATOM    114  C   GLU    26      -6.093   1.384   7.446  1.00  0.00
ATOM    115  N   LYS    27      -6.261   1.938   6.275  1.00  0.00
ATOM    116  CA  LYS    27      -5.372   3.055   5.843  1.00  0.00
ATOM    117  CB  LYS    27      -5.460   3.255   4.328  1.00  0.00
ATOM    118  CG  LYS    27      -4.970   2.069   3.516  1.00  0.00
ATOM    119  CD  LYS    27      -3.475   1.856   3.697  1.00  0.00
ATOM    120  CE  LYS    27      -2.960   0.748   2.792  1.00  0.00
ATOM    121  NZ  LYS    27      -1.499   0.525   2.963  1.00  0.00
ATOM    122  O   LYS    27      -5.024   5.291   6.638  1.00  0.00
ATOM    123  C   LYS    27      -5.792   4.354   6.535  1.00  0.00
ATOM    124  N   LYS    39      -7.003   4.417   7.012  1.00  0.00
ATOM    125  CA  LYS    39      -7.472   5.654   7.700  1.00  0.00
ATOM    126  CB  LYS    39      -8.979   5.588   7.955  1.00  0.00
ATOM    127  CG  LYS    39      -9.554   6.832   8.611  1.00  0.00
ATOM    128  CD  LYS    39     -11.063   6.733   8.755  1.00  0.00
ATOM    129  CE  LYS    39     -11.635   7.964   9.442  1.00  0.00
ATOM    130  NZ  LYS    39     -13.106   7.859   9.640  1.00  0.00
ATOM    131  O   LYS    39      -6.258   6.872   9.370  1.00  0.00
ATOM    132  C   LYS    39      -6.757   5.813   9.044  1.00  0.00
ATOM    133  N   GLY    40      -6.703   4.769   9.826  1.00  0.00
ATOM    134  CA  GLY    40      -6.019   4.863  11.148  1.00  0.00
ATOM    135  O   GLY    40      -3.779   5.585  11.608  1.00  0.00
ATOM    136  C   GLY    40      -4.500   4.853  10.960  1.00  0.00
TER
END
