
#######################################################
#                                                     #
#                        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   85 (   85),  selected   85 , name T0353TS168_5
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353TS168_5.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    Q       2      Q       2           -
LGA    I       3      I       3           -
LGA    -       -      H       4           -
LGA    -       -      V       5           -
LGA    -       -      Y       6           -
LGA    H       4      D       7          3.349
LGA    V       5      T       8          2.240
LGA    Y       6      Y       9           #
LGA    D       7      -       -           -
LGA    T       8      -       -           -
LGA    Y       9      -       -           -
LGA    V      10      -       -           -
LGA    K      11      -       -           -
LGA    A      12      -       -           -
LGA    K      13      -       -           -
LGA    D      14      -       -           -
LGA    G      15      -       -           -
LGA    H      16      -       -           -
LGA    V      17      -       -           -
LGA    M      18      -       -           -
LGA    H      19      -       -           -
LGA    F      20      -       -           -
LGA    D      21      -       -           -
LGA    V      22      -       -           -
LGA    F      23      -       -           -
LGA    T      24      V      10          3.658
LGA    D      25      K      11          0.549
LGA    V      26      A      12           #
LGA    R      27      K      13           -
LGA    -       -      D      14           -
LGA    -       -      G      15           -
LGA    D      28      H      16          2.425
LGA    D      29      V      17          3.105
LGA    K      30      M      18          3.326
LGA    K      31      H      19          2.862
LGA    A      32      -       -           -
LGA    I      33      F      20          2.434
LGA    E      34      D      21          3.502
LGA    F      35      -       -           -
LGA    A      36      -       -           -
LGA    K      37      V      22          2.628
LGA    Q      38      -       -           -
LGA    W      39      -       -           -
LGA    L      40      F      23          3.926
LGA    S      41      -       -           -
LGA    S      42      -       -           -
LGA    I      43      -       -           -
LGA    G      44      -       -           -
LGA    E      45      T      24           #
LGA    E      46      D      25          3.195
LGA    G      47      V      26          2.586
LGA    A      48      R      27          1.744
LGA    T      49      D      28          2.149
LGA    V      50      D      29          3.910
LGA    T      51      K      30          2.378
LGA    S      52      K      31           -
LGA    E      53      A      32           -
LGA    E      54      I      33           -
LGA    -       -      E      34           -
LGA    -       -      F      35           -
LGA    -       -      A      36           -
LGA    -       -      K      37           -
LGA    -       -      Q      38           -
LGA    -       -      W      39           -
LGA    -       -      L      40           -
LGA    -       -      S      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      E      45           -
LGA    -       -      E      46           -
LGA    -       -      G      47           -
LGA    C      55      A      48           #
LGA    R      56      T      49          1.274
LGA    F      57      V      50           #
LGA    C      58      T      51          5.252
LGA    H      59      -       -           -
LGA    S      60      -       -           -
LGA    Q      61      S      52          2.828
LGA    K      62      E      53          4.630
LGA    A      63      E      54          4.048
LGA    P      64      C      55          4.421
LGA    D      65      R      56          4.531
LGA    E      66      F      57          2.586
LGA    V      67      C      58          1.942
LGA    I      68      H      59           #
LGA    E      69      -       -           -
LGA    A      70      -       -           -
LGA    I      71      S      60           #
LGA    K      72      Q      61           #
LGA    Q      73      K      62          4.799
LGA    N      74      A      63           #
LGA    G      75      P      64           -
LGA    -       -      D      65           -
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    -       -      I      68           -
LGA    -       -      E      69           -
LGA    -       -      A      70           -
LGA    Y      76      I      71           #
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    -       -      G      75           -
LGA    F      77      Y      76          5.138
LGA    I      78      F      77           -
LGA    Y      79      I      78           -
LGA    K      80      Y      79           -
LGA    M      81      K      80           -
LGA    E      82      M      81           -
LGA    G      83      E      82           -
LGA    C      84      G      83           -
LGA    N      85      C      84           -
LGA    -       -      N      85           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   85   85    5.0     29    3.35     0.00     19.129     0.840

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.686754 * X  +   0.640960 * Y  +   0.342840 * Z  +  -1.795660
  Y_new =   0.582615 * X  +  -0.203339 * Y  +  -0.786901 * Z  +   3.243263
  Z_new =  -0.434659 * X  +   0.740152 * Y  +  -0.513076 * Z  +   0.160055 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.176947   -0.964646  [ DEG:   124.7299    -55.2701 ]
  Theta =   0.449660    2.691933  [ DEG:    25.7636    154.2364 ]
  Phi   =   0.703541   -2.438052  [ DEG:    40.3099   -139.6901 ]
 
# 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: T0353TS168_5                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353TS168_5.T0353.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   85   85   5.0   29   3.35    0.00  19.129
REMARK  ---------------------------------------------------------- 
MOLECULE T0353TS168_5
PFRMAT TS
TARGET T0353
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1       6.810  15.591  11.782  1.00 25.00           C
ATOM      2  CA  GLN     2       5.530  13.313   8.983  1.00 25.00           C
ATOM      3  CA  ILE     3       3.698  10.792   6.865  1.00 25.00           C
ATOM      4  CA  HIS     4       1.654   7.662   6.253  1.00 25.00           C
ATOM      5  CA  VAL     5      -0.360   5.274   4.134  1.00 25.00           C
ATOM      6  CA  TYR     6      -2.077   3.068   1.504  1.00 25.00           C
ATOM      7  CA  ASP     7      -3.587   0.050  -0.368  1.00 25.00           C
ATOM      8  CA  THR     8      -6.475   2.536  -0.863  1.00 25.00           C
ATOM      9  CA  TYR     9      -8.265  -0.392  -2.572  1.00 25.00           C
ATOM     10  CA  VAL    10      -5.854   0.268  -5.411  1.00 25.00           C
ATOM     11  CA  LYS    11      -8.895   0.531  -7.692  1.00 25.00           C
ATOM     12  CA  ALA    12      -9.321  -3.184  -6.874  1.00 25.00           C
ATOM     13  CA  LYS    13     -10.462  -6.802  -6.667  1.00 25.00           C
ATOM     14  CA  ASP    14     -10.518 -10.313  -8.222  1.00 25.00           C
ATOM     15  CA  GLY    15      -9.420 -10.292 -11.879  1.00 25.00           C
ATOM     16  CA  HIS    16      -7.592  -7.067 -11.038  1.00 25.00           C
ATOM     17  CA  VAL    17      -4.173  -5.578 -10.584  1.00 25.00           C
ATOM     18  CA  MET    18      -4.230  -5.851  -6.826  1.00 25.00           C
ATOM     19  CA  HIS    19      -3.762  -4.368  -3.353  1.00 25.00           C
ATOM     20  CA  PHE    20      -3.944  -4.881   0.412  1.00 25.00           C
ATOM     21  CA  ASP    21      -4.613  -3.881   3.971  1.00 25.00           C
ATOM     22  CA  VAL    22      -7.031  -0.989   3.207  1.00 25.00           C
ATOM     23  CA  PHE    23      -7.702   1.720   5.832  1.00 25.00           C
ATOM     24  CA  THR    24     -10.323   0.481   8.361  1.00 25.00           C
ATOM     25  CA  ASP    25      -9.618   3.023  11.062  1.00 25.00           C
ATOM     26  CA  VAL    26      -7.348   4.598  13.757  1.00 25.00           C
ATOM     27  CA  ARG    27      -3.937   3.474  15.084  1.00 25.00           C
ATOM     28  CA  ASP    28      -4.771  -0.163  14.218  1.00 25.00           C
ATOM     29  CA  ASP    29      -5.810   0.891  10.686  1.00 25.00           C
ATOM     30  CA  LYS    30      -2.532   2.827  10.273  1.00 25.00           C
ATOM     31  CA  LYS    31      -0.549  -0.233  11.443  1.00 25.00           C
ATOM     32  CA  ALA    32      -2.433  -2.440   8.944  1.00 25.00           C
ATOM     33  CA  ILE    33      -1.679   0.053   6.136  1.00 25.00           C
ATOM     34  CA  GLU    34       2.026   0.060   7.105  1.00 25.00           C
ATOM     35  CA  PHE    35       2.068  -3.769   7.070  1.00 25.00           C
ATOM     36  CA  ALA    36       0.432  -3.780   3.608  1.00 25.00           C
ATOM     37  CA  LYS    37       3.041  -1.280   2.338  1.00 25.00           C
ATOM     38  CA  GLN    38       5.855  -3.471   3.735  1.00 25.00           C
ATOM     39  CA  TRP    39       4.351  -6.544   2.014  1.00 25.00           C
ATOM     40  CA  LEU    40       4.142  -4.620  -1.291  1.00 25.00           C
ATOM     41  CA  SER    41       7.802  -3.549  -0.927  1.00 25.00           C
ATOM     42  CA  SER    42       8.822  -7.179  -0.254  1.00 25.00           C
ATOM     43  CA  ILE    43       8.493  -6.621  -4.035  1.00 25.00           C
ATOM     44  CA  GLY    44       8.215  -3.789  -6.473  1.00 25.00           C
ATOM     45  CA  GLU    45       8.110  -1.299  -9.403  1.00 25.00           C
ATOM     46  CA  GLU    46       6.511   1.468 -11.465  1.00 25.00           C
ATOM     47  CA  GLY    47       3.810   3.996 -10.577  1.00 25.00           C
ATOM     48  CA  ALA    48       1.264   5.104  -8.061  1.00 25.00           C
ATOM     49  CA  THR    49      -2.368   4.414  -8.873  1.00 25.00           C
ATOM     50  CA  VAL    50      -5.786   5.341  -7.411  1.00 25.00           C
ATOM     51  CA  THR    51      -7.376   7.707  -4.866  1.00 25.00           C
ATOM     52  CA  SER    52      -9.970   9.488  -2.628  1.00 25.00           C
ATOM     53  CA  GLU    53     -13.727   8.878  -2.417  1.00 25.00           C
ATOM     54  CA  GLU    54     -14.331   9.188   1.328  1.00 25.00           C
ATOM     55  CA  CYS    55     -12.547   5.910   1.946  1.00 25.00           C
ATOM     56  CA  ARG    56     -14.015   4.940   5.334  1.00 25.00           C
ATOM     57  CA  PHE    57     -12.250   6.720   8.176  1.00 25.00           C
ATOM     58  CA  CYS    58      -8.876   6.778   6.383  1.00 25.00           C
ATOM     59  CA  HIS    59      -5.750   9.013   6.122  1.00 25.00           C
ATOM     60  CA  SER    60      -6.246  11.964   3.717  1.00 25.00           C
ATOM     61  CA  GLN    61      -9.666  10.773   2.517  1.00 25.00           C
ATOM     62  CA  LYS    62      -7.732   7.593   1.562  1.00 25.00           C
ATOM     63  CA  ALA    63      -3.937   7.858   1.598  1.00 25.00           C
ATOM     64  CA  PRO    64      -0.861  10.069   1.185  1.00 25.00           C
ATOM     65  CA  ASP    65       0.777   9.445  -2.219  1.00 25.00           C
ATOM     66  CA  GLU    66       4.125  10.724  -0.871  1.00 25.00           C
ATOM     67  CA  VAL    67       3.812   8.415   2.169  1.00 25.00           C
ATOM     68  CA  ILE    68       3.061   5.448  -0.134  1.00 25.00           C
ATOM     69  CA  GLU    69       6.122   6.298  -2.271  1.00 25.00           C
ATOM     70  CA  ALA    70       8.298   6.481   0.876  1.00 25.00           C
ATOM     71  CA  ILE    71       6.968   3.077   2.023  1.00 25.00           C
ATOM     72  CA  LYS    72       7.742   1.588  -1.419  1.00 25.00           C
ATOM     73  CA  GLN    73      11.291   3.019  -1.268  1.00 25.00           C
ATOM     74  CA  ASN    74      10.585   4.046  -4.831  1.00 25.00           C
ATOM     75  CA  GLY    75       7.412   3.284  -6.705  1.00 25.00           C
ATOM     76  CA  TYR    76       4.349   1.588  -5.255  1.00 25.00           C
ATOM     77  CA  PHE    77       0.790   0.562  -4.545  1.00 25.00           C
ATOM     78  CA  ILE    78      -0.854   3.914  -3.635  1.00 25.00           C
ATOM     79  CA  TYR    79      -1.943   7.394  -4.834  1.00 25.00           C
ATOM     80  CA  LYS    80      -1.861  10.524  -6.995  1.00 25.00           C
ATOM     81  CA  MET    81      -4.364  13.405  -6.658  1.00 25.00           C
ATOM     82  CA  GLU    82      -4.442  15.261  -3.330  1.00 25.00           C
ATOM     83  CA  GLY    83      -3.681  18.851  -2.445  1.00 25.00           C
ATOM     84  CA  CYS    84      -0.430  19.256  -0.415  1.00 25.00           C
ATOM     85  CA  ASN    85      -0.296  22.978  -1.274  1.00 25.00           C
TER
END
