
#######################################################
#                                                     #
#                        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   68 (   68),  selected   68 , name T0348TS393_3
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS393_3.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      D       2           -
LGA    D       2      A       3           -
LGA    A       3      K       4           -
LGA    K       4      F       5           -
LGA    F       5      L       6           -
LGA    L       6      E       7           -
LGA    E       7      I       8           -
LGA    I       8      -       -           -
LGA    L       9      -       -           -
LGA    V      10      -       -           -
LGA    C      11      L       9          4.138
LGA    P      12      V      10          2.032
LGA    L      13      C      11          0.819
LGA    C      14      P      12          3.372
LGA    -       -      L      13           -
LGA    K      15      C      14          1.927
LGA    G      16      K      15          3.064
LGA    P      17      G      16          3.111
LGA    L      18      P      17           #
LGA    -       -      L      18           -
LGA    -       -      V      19           -
LGA    -       -      F      20           -
LGA    -       -      D      21           -
LGA    -       -      K      22           -
LGA    -       -      S      23           -
LGA    -       -      K      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      L      27           -
LGA    -       -      I      28           -
LGA    -       -      C      29           -
LGA    -       -      K      30           -
LGA    -       -      G      31           -
LGA    V      19      D      32          3.128
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    F      20      A      35          4.635
LGA    D      21      F      36          3.575
LGA    -       -      P      37           -
LGA    -       -      I      38           -
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    -       -      M      44           -
LGA    K      22      M      45          0.608
LGA    S      23      L      46          4.489
LGA    K      24      E      47           #
LGA    D      25      S      48           -
LGA    E      26      -       -           -
LGA    L      27      -       -           -
LGA    I      28      -       -           -
LGA    C      29      E      49           #
LGA    K      30      A      50          0.546
LGA    G      31      -       -           -
LGA    D      32      R      51          2.450
LGA    R      33      E      52          2.336
LGA    L      34      L      53          3.692
LGA    A      35      A      54           -
LGA    F      36      P      55           -
LGA    -       -      E      56           -
LGA    P      37      E      57          4.678
LGA    I      38      E      58           #
LGA    K      39      V      59          2.720
LGA    D      40      K      60          4.700
LGA    -       -      L      61           -
LGA    G      41      E      62          1.566
LGA    I      42      -       -           -
LGA    P      43      -       -           -
LGA    M      44      -       -           -
LGA    M      45      -       -           -
LGA    L      46      -       -           -
LGA    E      47      -       -           -
LGA    S      48      -       -           -
LGA    E      49      -       -           -
LGA    A      50      -       -           -
LGA    R      51      -       -           -
LGA    E      52      -       -           -
LGA    L      53      -       -           -
LGA    A      54      -       -           -
LGA    P      55      -       -           -
LGA    E      56      -       -           -
LGA    E      57      -       -           -
LGA    E      58      -       -           -
LGA    V      59      -       -           -
LGA    K      60      -       -           -
LGA    L      61      -       -           -
LGA    E      62      -       -           -
LGA    H      63      -       -           -
LGA    H      64      -       -           -
LGA    H      65      -       -           -
LGA    H      66      -       -           -
LGA    H      67      -       -           -
LGA    H      68      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   68   61    5.0     20    3.16     5.00     20.788     0.613

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.094002 * X  +   0.776209 * Y  +  -0.623428 * Z  +  21.131287
  Y_new =  -0.993330 * X  +  -0.115124 * Y  +   0.006439 * Z  +  26.663195
  Z_new =  -0.066774 * X  +   0.619875 * Y  +   0.781854 * Z  +  56.999298 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.670352   -2.471241  [ DEG:    38.4084   -141.5916 ]
  Theta =   0.066823    3.074769  [ DEG:     3.8287    176.1713 ]
  Phi   =  -1.665148    1.476444  [ DEG:   -95.4060     84.5940 ]
 
# 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: T0348TS393_3                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS393_3.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   68   61   5.0   20   3.16    5.00  20.788
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS393_3
PFRMAT TS
TARGET T0348
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      21.537  25.594  46.738  1.00 25.00           C
ATOM      2  CA  ASP     2      18.196  26.556  45.258  1.00 25.00           C
ATOM      3  CA  ALA     3      17.430  29.726  47.161  1.00 25.00           C
ATOM      4  CA  LYS     4      15.781  32.623  49.046  1.00 25.00           C
ATOM      5  CA  PHE     5      12.965  30.300  50.203  1.00 25.00           C
ATOM      6  CA  LEU     6      15.542  27.734  51.404  1.00 25.00           C
ATOM      7  CA  GLU     7      17.413  30.474  53.319  1.00 25.00           C
ATOM      8  CA  ILE     8      14.137  31.612  54.941  1.00 25.00           C
ATOM      9  CA  LEU     9      13.353  28.002  55.952  1.00 25.00           C
ATOM     10  CA  VAL    10       9.804  27.665  54.474  1.00 25.00           C
ATOM     11  CA  CYS    11       8.872  31.186  55.678  1.00 25.00           C
ATOM     12  CA  PRO    12       9.679  31.417  59.332  1.00 25.00           C
ATOM     13  CA  LEU    13       6.520  29.314  59.964  1.00 25.00           C
ATOM     14  CA  CYS    14       4.357  26.936  61.995  1.00 25.00           C
ATOM     15  CA  LYS    15       6.928  26.788  64.796  1.00 25.00           C
ATOM     16  CA  GLY    16       9.297  29.649  64.305  1.00 25.00           C
ATOM     17  CA  PRO    17      12.702  28.872  62.847  1.00 25.00           C
ATOM     18  CA  LEU    18      10.799  26.572  60.445  1.00 25.00           C
ATOM     19  CA  VAL    19       8.323  23.702  60.929  1.00 25.00           C
ATOM     20  CA  PHE    20       6.814  24.904  57.584  1.00 25.00           C
ATOM     21  CA  ASP    21       4.833  27.101  55.178  1.00 25.00           C
ATOM     22  CA  LYS    22       3.300  30.583  55.133  1.00 25.00           C
ATOM     23  CA  SER    23       2.395  30.024  51.455  1.00 25.00           C
ATOM     24  CA  LYS    24       5.951  30.985  50.407  1.00 25.00           C
ATOM     25  CA  ASP    25       6.665  27.272  50.509  1.00 25.00           C
ATOM     26  CA  GLU    26       7.218  24.262  48.226  1.00 25.00           C
ATOM     27  CA  LEU    27      10.891  23.680  48.959  1.00 25.00           C
ATOM     28  CA  ILE    28      10.302  20.238  50.532  1.00 25.00           C
ATOM     29  CA  CYS    29       7.697  21.742  52.905  1.00 25.00           C
ATOM     30  CA  LYS    30       4.127  22.163  54.198  1.00 25.00           C
ATOM     31  CA  GLY    31       4.309  19.691  57.147  1.00 25.00           C
ATOM     32  CA  ASP    32       4.669  16.976  54.458  1.00 25.00           C
ATOM     33  CA  ARG    33       8.481  17.077  54.536  1.00 25.00           C
ATOM     34  CA  LEU    34       9.302  19.466  57.431  1.00 25.00           C
ATOM     35  CA  ALA    35      11.195  22.662  56.608  1.00 25.00           C
ATOM     36  CA  PHE    36      13.340  23.112  53.490  1.00 25.00           C
ATOM     37  CA  PRO    37      15.110  19.918  54.446  1.00 25.00           C
ATOM     38  CA  ILE    38      18.857  20.074  54.144  1.00 25.00           C
ATOM     39  CA  LYS    39      19.689  17.178  56.444  1.00 25.00           C
ATOM     40  CA  ASP    40      20.110  17.427  60.183  1.00 25.00           C
ATOM     41  CA  GLY    41      23.863  18.018  60.764  1.00 25.00           C
ATOM     42  CA  ILE    42      26.542  19.027  58.207  1.00 25.00           C
ATOM     43  CA  PRO    43      28.499  16.464  56.189  1.00 25.00           C
ATOM     44  CA  MET    44      31.588  17.581  54.215  1.00 25.00           C
ATOM     45  CA  MET    45      31.969  20.160  56.993  1.00 25.00           C
ATOM     46  CA  LEU    46      31.862  23.045  54.559  1.00 25.00           C
ATOM     47  CA  GLU    47      34.216  22.468  51.563  1.00 25.00           C
ATOM     48  CA  SER    48      35.338  26.010  52.349  1.00 25.00           C
ATOM     49  CA  GLU    49      38.495  26.912  50.419  1.00 25.00           C
ATOM     50  CA  ALA    50      40.115  23.926  48.597  1.00 25.00           C
ATOM     51  CA  ARG    51      42.703  23.036  51.249  1.00 25.00           C
ATOM     52  CA  GLU    52      43.751  26.366  52.716  1.00 25.00           C
ATOM     53  CA  LEU    53      45.089  28.950  55.144  1.00 25.00           C
ATOM     54  CA  ALA    54      48.203  30.364  56.781  1.00 25.00           C
ATOM     55  CA  PRO    55      46.900  30.525  60.327  1.00 25.00           C
ATOM     56  CA  GLU    56      47.777  27.673  62.700  1.00 25.00           C
ATOM     57  CA  GLU    57      44.855  27.684  65.092  1.00 25.00           C
ATOM     58  CA  GLU    58      44.107  30.902  67.073  1.00 25.00           C
ATOM     59  CA  VAL    59      40.586  32.166  66.458  1.00 25.00           C
ATOM     60  CA  LYS    60      38.084  29.862  68.244  1.00 25.00           C
ATOM     61  CA  LEU    61      37.473  32.421  71.049  1.00 25.00           C
ATOM     62  CA  GLU    62      34.293  34.085  69.889  1.00 25.00           C
ATOM     63  CA  HIS    63      30.732  33.139  70.941  1.00 25.00           C
ATOM     64  CA  HIS    64      29.399  35.483  68.305  1.00 25.00           C
ATOM     65  CA  HIS    65      28.753  38.547  66.177  1.00 25.00           C
ATOM     66  CA  HIS    66      30.082  38.149  62.618  1.00 25.00           C
ATOM     67  CA  HIS    67      27.468  40.764  61.598  1.00 25.00           C
ATOM     68  CA  HIS    68      24.568  38.586  62.705  1.00 25.00           C
TER
END
