
#######################################################
#                                                     #
#                        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   75 (   75),  selected   75 , name T0330TS168_3-D2
# Molecule2: number of CA atoms   72 (  556),  selected   72 , name T0330_D2.pdb
# PARAMETERS: T0330TS168_3-D2.T0330_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      V      17          0.865
LGA    E      18      E      18          2.182
LGA    S      19      -       -           -
LGA    M      20      S      19          3.984
LGA    N      21      M      20          2.612
LGA    R      22      N      21          2.276
LGA    R      23      R      22          2.086
LGA    V      24      R      23          2.586
LGA    L      25      V      24          3.751
LGA    A      26      L      25          3.252
LGA    D      27      A      26          2.403
LGA    A      28      D      27          4.155
LGA    L      29      A      28          5.106
LGA    I      30      L      29          4.255
LGA    E      31      I      30          4.251
LGA    V      32      -       -           -
LGA    Y      33      -       -           -
LGA    G      34      -       -           -
LGA    T      35      -       -           -
LGA    E      36      -       -           -
LGA    G      37      E      31          3.935
LGA    S      38      V      32           -
LGA    T      39      Y      33           -
LGA    G      40      G      34           -
LGA    S      41      T      35           -
LGA    H      42      E      36           -
LGA    D      43      G      37           -
LGA    F      44      S      38           -
LGA    S      45      T      39           -
LGA    G      46      D      43           -
LGA    K      47      F      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      K      47           -
LGA    M      48      M      48          3.940
LGA    D      49      D      49          1.021
LGA    G      50      G      50          1.313
LGA    A      51      A      51          1.693
LGA    I      52      I      52          1.476
LGA    I      53      I      53          0.681
LGA    Y      54      Y      54          0.691
LGA    E      55      E      55          1.588
LGA    V      56      V      56          1.562
LGA    L      57      L      57          1.454
LGA    S      58      S      58          1.836
LGA    N      59      N      59          2.152
LGA    V      60      V      60          2.137
LGA    G      61      G      61          0.973
LGA    L      62      L      62          1.157
LGA    E      63      E      63          2.994
LGA    R      64      R      64          2.774
LGA    A      65      A      65          0.941
LGA    E      66      E      66          2.506
LGA    I      67      I      67          1.486
LGA    A      68      A      68          2.399
LGA    D      69      D      69          3.112
LGA    K      70      K      70          1.709
LGA    F      71      F      71          3.112
LGA    D      72      D      72          3.449
LGA    K      73      K      73          2.164
LGA    A      74      A      74          0.980
LGA    K      75      K      75          1.409
LGA    E      76      E      76          2.610
LGA    T      77      T      77          2.825
LGA    Y      78      Y      78          2.326
LGA    I      79      I      79          2.547
LGA    A      80      A      80          4.237
LGA    L      81      -       -           -
LGA    F      82      L      81           #
LGA    R      83      F      82           -
LGA    E      84      R      83          5.528
LGA    R      85      E      84          5.109
LGA    A      86      R      85           -
LGA    R      87      A      86           -
LGA    R      88      R      87           -
LGA    E      89      R      88           -
LGA    D      90      E      89           -
LGA    I      91      D      90           -
LGA    -       -      I      91           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   75   72    5.0     50    2.80    72.00     48.109     1.726

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.725577 * X  +  -0.555630 * Y  +  -0.405973 * Z  +  12.469335
  Y_new =   0.026695 * X  +   0.612238 * Y  +  -0.790223 * Z  +  29.284132
  Z_new =   0.687623 * X  +   0.562530 * Y  +   0.459058 * Z  +  10.227012 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.886339   -2.255254  [ DEG:    50.7835   -129.2165 ]
  Theta =  -0.758211   -2.383382  [ DEG:   -43.4423   -136.5577 ]
  Phi   =   0.036774   -3.104818  [ DEG:     2.1070   -177.8930 ]
 
# 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: T0330TS168_3-D2                               
REMARK     2: T0330_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS168_3-D2.T0330_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   75   72   5.0   50   2.80   72.00  48.109
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS168_3-D2
PFRMAT TS
TARGET T0330
MODEL 3
PARENT N/A
ATOM     17  CA  VAL    17      15.782  35.935  11.422  1.00 25.00           C
ATOM     18  CA  GLU    18      16.072  33.585   8.465  1.00 25.00           C
ATOM     19  CA  SER    19      19.015  35.819   7.457  1.00 25.00           C
ATOM     20  CA  MET    20      20.434  33.008   5.276  1.00 25.00           C
ATOM     21  CA  ASN    21      17.017  32.544   3.611  1.00 25.00           C
ATOM     22  CA  ARG    22      16.803  36.308   2.940  1.00 25.00           C
ATOM     23  CA  ARG    23      20.313  36.259   1.408  1.00 25.00           C
ATOM     24  CA  VAL    24      19.326  33.304  -0.820  1.00 25.00           C
ATOM     25  CA  LEU    25      16.177  35.171  -1.945  1.00 25.00           C
ATOM     26  CA  ALA    26      18.276  38.270  -2.757  1.00 25.00           C
ATOM     27  CA  ASP    27      20.714  36.118  -4.781  1.00 25.00           C
ATOM     28  CA  ALA    28      17.787  34.561  -6.696  1.00 25.00           C
ATOM     29  CA  LEU    29      16.384  38.046  -7.438  1.00 25.00           C
ATOM     30  CA  ILE    30      19.817  39.186  -8.694  1.00 25.00           C
ATOM     31  CA  GLU    31      20.047  36.097 -10.947  1.00 25.00           C
ATOM     32  CA  VAL    32      16.553  36.822 -12.338  1.00 25.00           C
ATOM     33  CA  TYR    33      16.261  40.585 -12.932  1.00 25.00           C
ATOM     34  CA  GLY    34      13.405  39.614 -15.325  1.00 25.00           C
ATOM     35  CA  THR    35      10.809  40.637 -12.688  1.00 25.00           C
ATOM     36  CA  GLU    36      11.827  44.283 -13.158  1.00 25.00           C
ATOM     37  CA  GLY    37      14.347  44.507 -10.266  1.00 25.00           C
ATOM     38  CA  SER    38      11.852  46.358  -8.072  1.00 25.00           C
ATOM     39  CA  THR    39       8.625  44.765  -9.327  1.00 25.00           C
ATOM     40  CA  GLY    40       8.258  41.285  -7.771  1.00 25.00           C
ATOM     41  CA  SER    41      10.927  42.145  -5.161  1.00 25.00           C
ATOM     42  CA  HIS    42      13.564  41.631  -2.509  1.00 25.00           C
ATOM     43  CA  ASP    43      15.368  40.829   0.694  1.00 25.00           C
ATOM     44  CA  PHE    44      17.872  42.183   3.196  1.00 25.00           C
ATOM     45  CA  SER    45      19.297  43.685   6.349  1.00 25.00           C
ATOM     46  CA  GLY    46      18.187  46.790   8.324  1.00 25.00           C
ATOM     47  CA  LYS    47      21.227  49.107   8.663  1.00 25.00           C
ATOM     48  CA  MET    48      23.279  46.017   9.507  1.00 25.00           C
ATOM     49  CA  ASP    49      23.954  45.934   5.736  1.00 25.00           C
ATOM     50  CA  GLY    50      25.506  48.021   2.925  1.00 25.00           C
ATOM     51  CA  ALA    51      29.016  47.206   4.225  1.00 25.00           C
ATOM     52  CA  ILE    52      28.140  43.478   4.324  1.00 25.00           C
ATOM     53  CA  ILE    53      26.830  43.665   0.730  1.00 25.00           C
ATOM     54  CA  TYR    54      30.057  45.404  -0.381  1.00 25.00           C
ATOM     55  CA  GLU    55      32.141  42.691   1.340  1.00 25.00           C
ATOM     56  CA  VAL    56      30.086  39.972  -0.407  1.00 25.00           C
ATOM     57  CA  LEU    57      30.611  41.707  -3.780  1.00 25.00           C
ATOM     58  CA  SER    58      34.380  41.901  -3.122  1.00 25.00           C
ATOM     59  CA  ASN    59      34.441  38.175  -2.237  1.00 25.00           C
ATOM     60  CA  VAL    60      33.152  37.903  -5.813  1.00 25.00           C
ATOM     61  CA  GLY    61      34.724  40.213  -8.352  1.00 25.00           C
ATOM     62  CA  LEU    62      31.942  42.763  -9.135  1.00 25.00           C
ATOM     63  CA  GLU    63      32.708  46.208 -10.537  1.00 25.00           C
ATOM     64  CA  ARG    64      33.732  48.968  -8.122  1.00 25.00           C
ATOM     65  CA  ALA    65      32.171  52.289  -7.024  1.00 25.00           C
ATOM     66  CA  GLU    66      29.164  51.660  -9.310  1.00 25.00           C
ATOM     67  CA  ILE    67      28.754  48.145  -7.844  1.00 25.00           C
ATOM     68  CA  ALA    68      28.889  49.583  -4.296  1.00 25.00           C
ATOM     69  CA  ASP    69      26.236  52.185  -5.224  1.00 25.00           C
ATOM     70  CA  LYS    70      24.007  49.432  -6.678  1.00 25.00           C
ATOM     71  CA  PHE    71      24.419  47.374  -3.475  1.00 25.00           C
ATOM     72  CA  ASP    72      23.489  50.430  -1.362  1.00 25.00           C
ATOM     73  CA  LYS    73      20.386  51.015  -3.529  1.00 25.00           C
ATOM     74  CA  ALA    74      19.377  47.343  -3.118  1.00 25.00           C
ATOM     75  CA  LYS    75      19.816  47.622   0.677  1.00 25.00           C
ATOM     76  CA  GLU    76      17.657  50.784   0.719  1.00 25.00           C
ATOM     77  CA  THR    77      14.953  48.996  -1.320  1.00 25.00           C
ATOM     78  CA  TYR    78      15.036  46.042   1.116  1.00 25.00           C
ATOM     79  CA  ILE    79      14.695  48.445   4.079  1.00 25.00           C
ATOM     80  CA  ALA    80      11.715  50.151   2.384  1.00 25.00           C
ATOM     81  CA  LEU    81      10.075  46.745   1.781  1.00 25.00           C
ATOM     82  CA  PHE    82      10.610  45.808   5.456  1.00 25.00           C
ATOM     83  CA  ARG    83       9.049  49.129   6.553  1.00 25.00           C
ATOM     84  CA  GLU    84       6.041  48.499   4.268  1.00 25.00           C
ATOM     85  CA  ARG    85       5.631  44.986   5.735  1.00 25.00           C
ATOM     86  CA  ALA    86       5.767  46.424   9.282  1.00 25.00           C
ATOM     87  CA  ARG    87       3.114  49.026   8.354  1.00 25.00           C
ATOM     88  CA  ARG    88       1.105  48.244   5.158  1.00 25.00           C
ATOM     89  CA  GLU    89       1.017  44.675   3.827  1.00 25.00           C
ATOM     90  CA  ASP    90       2.349  41.132   3.911  1.00 25.00           C
ATOM     91  CA  ILE    91       5.370  39.401   5.408  1.00 25.00           C
TER
END
