
#######################################################
#                                                     #
#                        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   88 (   88),  selected   88 , name T0288TS393_4-D1
# Molecule2: number of CA atoms   86 (  617),  selected   86 , name T0288_D1.pdb
# PARAMETERS: T0288TS393_4-D1.T0288_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           -
LGA    M       2      M       2           -
LGA    V       3      -       -           -
LGA    P       4      V       3          6.235
LGA    -       -      P       4           -
LGA    G       5      G       5          1.220
LGA    K       6      K       6          3.017
LGA    V       7      V       7          0.897
LGA    T       8      T       8          2.619
LGA    L       9      L       9          2.457
LGA    Q      10      Q      10          2.279
LGA    K      11      K      11          2.205
LGA    D      12      D      12          2.118
LGA    A      13      A      13          2.215
LGA    Q      14      Q      14          2.045
LGA    N      15      N      15          0.368
LGA    L      16      L      16          0.916
LGA    I      17      I      17          1.716
LGA    G      18      G      18          1.393
LGA    I      19      I      19          2.462
LGA    S      20      S      20          2.074
LGA    I      21      I      21          1.933
LGA    G      22      G      22          1.085
LGA    G      23      G      23          2.924
LGA    G      24      G      24          1.545
LGA    A      25      A      25          4.051
LGA    Q      26      Q      26          2.548
LGA    Y      27      -       -           -
LGA    C      28      -       -           -
LGA    P      29      P      29          3.322
LGA    C      30      C      30          2.162
LGA    L      31      L      31          1.183
LGA    Y      32      Y      32          1.376
LGA    I      33      I      33          1.318
LGA    V      34      V      34          0.382
LGA    Q      35      Q      35          0.445
LGA    V      36      V      36          1.390
LGA    F      37      F      37          1.345
LGA    D      38      D      38          1.576
LGA    N      39      N      39          1.846
LGA    T      40      T      40          1.824
LGA    P      41      P      41          1.558
LGA    A      42      A      42          0.621
LGA    A      43      A      43          0.551
LGA    L      44      L      44          0.459
LGA    D      45      D      45          2.291
LGA    G      46      G      46          2.566
LGA    T      47      T      47          1.849
LGA    V      48      V      48          1.471
LGA    A      49      A      49          1.409
LGA    A      50      A      50          1.547
LGA    G      51      G      51          1.378
LGA    D      52      D      52          0.699
LGA    E      53      E      53          0.495
LGA    I      54      I      54          1.260
LGA    T      55      T      55          2.241
LGA    G      56      G      56          2.351
LGA    V      57      V      57          2.284
LGA    N      58      N      58          0.588
LGA    G      59      G      59          3.250
LGA    R      60      R      60          2.760
LGA    S      61      S      61          3.059
LGA    I      62      I      62          2.147
LGA    K      63      K      63          2.778
LGA    G      64      G      64          1.110
LGA    K      65      K      65          1.264
LGA    T      66      T      66          1.727
LGA    K      67      K      67          0.817
LGA    V      68      V      68          0.879
LGA    E      69      E      69          0.527
LGA    V      70      V      70          1.048
LGA    A      71      A      71          0.813
LGA    K      72      K      72          0.647
LGA    M      73      M      73          1.323
LGA    I      74      I      74          1.502
LGA    Q      75      Q      75          0.335
LGA    E      76      E      76          1.747
LGA    V      77      V      77          2.517
LGA    K      78      K      78          2.606
LGA    G      79      G      79          2.569
LGA    E      80      E      80          2.972
LGA    V      81      V      81          1.385
LGA    T      82      T      82          0.325
LGA    I      83      I      83          0.661
LGA    H      84      H      84          0.853
LGA    Y      85      Y      85          1.468
LGA    N      86      N      86          1.375
LGA    K      87      K      87          1.903
LGA    L      88      L      88          0.802

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   88   86    5.0     83    1.96    98.80     85.159     4.034

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.966426 * X  +   0.251639 * Y  +   0.051945 * Z  +  27.424690
  Y_new =   0.071767 * X  +  -0.458475 * Y  +   0.885805 * Z  +  17.296318
  Z_new =   0.246719 * X  +  -0.852337 * Y  +  -0.461141 * Z  +  13.378402 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.066728    1.074865  [ DEG:  -118.4148     61.5852 ]
  Theta =  -0.249293   -2.892299  [ DEG:   -14.2834   -165.7166 ]
  Phi   =   0.074124   -3.067469  [ DEG:     4.2470   -175.7530 ]
 
# 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: T0288TS393_4-D1                               
REMARK     2: T0288_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0288TS393_4-D1.T0288_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   88   86   5.0   83   1.96   98.80  85.159
REMARK  ---------------------------------------------------------- 
MOLECULE T0288TS393_4-D1
PFRMAT TS
TARGET T0288
MODEL 4
PARENT N/A
ATOM      1  CA  SER     1      22.647   6.595  30.877  1.00 25.00           C
ATOM      2  CA  MET     2      23.972  10.037  29.984  1.00 25.00           C
ATOM      3  CA  VAL     3      21.957   9.812  26.715  1.00 25.00           C
ATOM      4  CA  PRO     4      24.051  12.606  25.140  1.00 25.00           C
ATOM      5  CA  GLY     5      21.793  15.356  23.679  1.00 25.00           C
ATOM      6  CA  LYS     6      20.076  18.381  22.210  1.00 25.00           C
ATOM      7  CA  VAL     7      20.875  19.723  18.681  1.00 25.00           C
ATOM      8  CA  THR     8      17.673  21.699  17.941  1.00 25.00           C
ATOM      9  CA  LEU     9      19.835  23.700  15.625  1.00 25.00           C
ATOM     10  CA  GLN    10      18.707  25.466  12.398  1.00 25.00           C
ATOM     11  CA  LYS    11      18.100  26.648   8.836  1.00 25.00           C
ATOM     12  CA  ASP    12      19.828  29.890   7.844  1.00 25.00           C
ATOM     13  CA  ALA    13      18.585  29.361   4.350  1.00 25.00           C
ATOM     14  CA  GLN    14      22.128  28.971   3.073  1.00 25.00           C
ATOM     15  CA  ASN    15      21.350  25.300   2.303  1.00 25.00           C
ATOM     16  CA  LEU    16      23.204  24.644   5.580  1.00 25.00           C
ATOM     17  CA  ILE    17      24.792  23.359   8.856  1.00 25.00           C
ATOM     18  CA  GLY    18      28.155  25.090   8.377  1.00 25.00           C
ATOM     19  CA  ILE    19      29.565  21.585   7.916  1.00 25.00           C
ATOM     20  CA  SER    20      32.590  19.634   6.756  1.00 25.00           C
ATOM     21  CA  ILE    21      32.050  15.952   7.616  1.00 25.00           C
ATOM     22  CA  GLY    22      35.743  15.126   7.817  1.00 25.00           C
ATOM     23  CA  GLY    23      36.701  11.440   7.518  1.00 25.00           C
ATOM     24  CA  GLY    24      36.550   8.359   9.825  1.00 25.00           C
ATOM     25  CA  ALA    25      38.196   5.238   8.311  1.00 25.00           C
ATOM     26  CA  GLN    26      41.323   5.733  10.437  1.00 25.00           C
ATOM     27  CA  TYR    27      40.248   8.113  13.257  1.00 25.00           C
ATOM     28  CA  CYS    28      38.752   6.144  16.147  1.00 25.00           C
ATOM     29  CA  PRO    29      35.408   6.727  14.414  1.00 25.00           C
ATOM     30  CA  CYS    30      32.561   9.172  14.827  1.00 25.00           C
ATOM     31  CA  LEU    31      34.117  11.837  12.672  1.00 25.00           C
ATOM     32  CA  TYR    32      33.780  15.607  12.482  1.00 25.00           C
ATOM     33  CA  ILE    33      32.248  19.042  12.212  1.00 25.00           C
ATOM     34  CA  VAL    34      35.817  20.312  11.554  1.00 25.00           C
ATOM     35  CA  GLN    35      34.494  23.910  11.386  1.00 25.00           C
ATOM     36  CA  VAL    36      32.791  26.818  13.151  1.00 25.00           C
ATOM     37  CA  PHE    37      32.498  28.550   9.745  1.00 25.00           C
ATOM     38  CA  ASP    38      31.400  32.189  10.022  1.00 25.00           C
ATOM     39  CA  ASN    39      28.110  33.766   9.049  1.00 25.00           C
ATOM     40  CA  THR    40      26.740  30.166   8.942  1.00 25.00           C
ATOM     41  CA  PRO    41      23.834  29.012  11.098  1.00 25.00           C
ATOM     42  CA  ALA    42      25.581  26.985  13.806  1.00 25.00           C
ATOM     43  CA  ALA    43      27.553  29.939  15.238  1.00 25.00           C
ATOM     44  CA  LEU    44      24.291  31.849  15.855  1.00 25.00           C
ATOM     45  CA  ASP    45      21.386  29.533  16.884  1.00 25.00           C
ATOM     46  CA  GLY    46      23.800  28.037  19.425  1.00 25.00           C
ATOM     47  CA  THR    47      24.328  24.328  19.973  1.00 25.00           C
ATOM     48  CA  VAL    48      27.495  23.766  17.969  1.00 25.00           C
ATOM     49  CA  ALA    49      31.013  23.466  19.350  1.00 25.00           C
ATOM     50  CA  ALA    50      34.062  22.986  17.165  1.00 25.00           C
ATOM     51  CA  GLY    51      35.243  19.366  16.954  1.00 25.00           C
ATOM     52  CA  ASP    52      32.076  17.756  18.235  1.00 25.00           C
ATOM     53  CA  GLU    53      31.570  14.118  17.074  1.00 25.00           C
ATOM     54  CA  ILE    54      29.082  14.096  14.214  1.00 25.00           C
ATOM     55  CA  THR    55      25.966  11.940  14.842  1.00 25.00           C
ATOM     56  CA  GLY    56      22.781  12.216  12.708  1.00 25.00           C
ATOM     57  CA  VAL    57      20.213  13.075  10.082  1.00 25.00           C
ATOM     58  CA  ASN    58      17.070  12.899  12.269  1.00 25.00           C
ATOM     59  CA  GLY    59      17.327   9.146  12.002  1.00 25.00           C
ATOM     60  CA  ARG    60      20.595   7.857  10.586  1.00 25.00           C
ATOM     61  CA  SER    61      23.982   6.179  11.136  1.00 25.00           C
ATOM     62  CA  ILE    62      27.291   7.792  12.216  1.00 25.00           C
ATOM     63  CA  LYS    63      29.895   5.112  13.060  1.00 25.00           C
ATOM     64  CA  GLY    64      29.056   2.506  10.413  1.00 25.00           C
ATOM     65  CA  LYS    65      29.079   5.481   8.016  1.00 25.00           C
ATOM     66  CA  THR    66      32.214   7.293   6.676  1.00 25.00           C
ATOM     67  CA  LYS    67      32.339  10.781   5.122  1.00 25.00           C
ATOM     68  CA  VAL    68      30.447  10.978   1.799  1.00 25.00           C
ATOM     69  CA  GLU    69      27.317   9.533   3.467  1.00 25.00           C
ATOM     70  CA  VAL    70      27.604  12.106   6.289  1.00 25.00           C
ATOM     71  CA  ALA    71      27.943  14.925   3.718  1.00 25.00           C
ATOM     72  CA  LYS    72      24.845  13.641   1.868  1.00 25.00           C
ATOM     73  CA  MET    73      22.891  13.537   5.160  1.00 25.00           C
ATOM     74  CA  ILE    74      23.975  17.124   5.946  1.00 25.00           C
ATOM     75  CA  GLN    75      22.861  18.251   2.459  1.00 25.00           C
ATOM     76  CA  GLU    76      19.472  16.540   2.962  1.00 25.00           C
ATOM     77  CA  VAL    77      18.700  19.335   5.453  1.00 25.00           C
ATOM     78  CA  LYS    78      14.922  19.437   5.889  1.00 25.00           C
ATOM     79  CA  GLY    79      15.069  22.290   8.399  1.00 25.00           C
ATOM     80  CA  GLU    80      15.251  19.677  11.116  1.00 25.00           C
ATOM     81  CA  VAL    81      18.969  20.091  10.742  1.00 25.00           C
ATOM     82  CA  THR    82      19.098  17.427  13.521  1.00 25.00           C
ATOM     83  CA  ILE    83      22.738  17.449  14.465  1.00 25.00           C
ATOM     84  CA  HIS    84      23.242  15.235  17.512  1.00 25.00           C
ATOM     85  CA  TYR    85      26.528  16.546  18.951  1.00 25.00           C
ATOM     86  CA  ASN    86      28.066  13.775  20.929  1.00 25.00           C
ATOM     87  CA  LYS    87      31.225  14.729  22.771  1.00 25.00           C
ATOM     88  CA  LEU    88      34.822  15.510  23.638  1.00 25.00           C
TER
END
