
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0363TS168_1
# Molecule2: number of CA atoms   80 (  645),  selected   80 , name T0363.pdb
# PARAMETERS: T0363TS168_1.T0363.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    A       2      -       -           -
LGA    H       3      -       -           -
LGA    H       4      -       -           -
LGA    H       5      -       -           -
LGA    H       6      -       -           -
LGA    H       7      -       -           -
LGA    H       8      -       -           -
LGA    S       9      -       -           -
LGA    L      10      -       -           -
LGA    N      11      L      10           #
LGA    Q      12      N      11           #
LGA    -       -      Q      12           -
LGA    I      13      I      13          2.092
LGA    N      14      N      14          2.749
LGA    I      15      I      15          2.053
LGA    E      16      E      16          0.619
LGA    I      17      I      17          3.092
LGA    A      18      A      18          1.501
LGA    Y      19      Y      19          1.263
LGA    A      20      A      20          4.408
LGA    F      21      F      21          2.198
LGA    P      22      P      22          3.817
LGA    E      23      E      23          1.850
LGA    R      24      R      24           #
LGA    Y      25      -       -           -
LGA    Y      26      Y      25          4.348
LGA    L      27      Y      26          3.995
LGA    K      28      L      27          5.439
LGA    S      29      K      28           -
LGA    F      30      S      29           #
LGA    Q      31      F      30           -
LGA    -       -      Q      31           -
LGA    V      32      V      32           #
LGA    D      33      D      33           -
LGA    E      34      E      34          3.632
LGA    G      35      G      35          1.343
LGA    I      36      I      36          2.153
LGA    T      37      T      37          4.379
LGA    V      38      V      38          2.954
LGA    Q      39      Q      39          2.478
LGA    T      40      T      40          0.682
LGA    A      41      A      41          0.690
LGA    I      42      I      42          1.163
LGA    T      43      T      43          2.241
LGA    Q      44      Q      44          2.341
LGA    S      45      S      45          3.780
LGA    G      46      G      46          0.581
LGA    I      47      I      47          3.509
LGA    L      48      L      48          3.053
LGA    S      49      S      49          2.327
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    Q      50      P      52          4.560
LGA    F      51      E      53           -
LGA    P      52      I      54           -
LGA    E      53      D      55           -
LGA    I      54      L      56           -
LGA    D      55      S      57           -
LGA    L      56      T      58           -
LGA    S      57      N      59           -
LGA    T      58      K      60           -
LGA    N      59      -       -           -
LGA    K      60      -       -           -
LGA    I      61      -       -           -
LGA    G      62      -       -           -
LGA    I      63      -       -           -
LGA    F      64      -       -           -
LGA    S      65      I      61          3.857
LGA    R      66      G      62          3.997
LGA    P      67      I      63          0.867
LGA    I      68      F      64           -
LGA    -       -      S      65           -
LGA    -       -      R      66           -
LGA    -       -      P      67           -
LGA    -       -      I      68           -
LGA    -       -      K      69           -
LGA    -       -      L      70           -
LGA    -       -      T      71           -
LGA    -       -      D      72           -
LGA    -       -      V      73           -
LGA    -       -      L      74           -
LGA    -       -      K      75           -
LGA    -       -      E      76           -
LGA    -       -      G      77           -
LGA    K      69      D      78          5.259
LGA    L      70      R      79           #
LGA    T      71      I      80           -
LGA    D      72      E      81           -
LGA    V      73      I      82           -
LGA    L      74      Y      83           -
LGA    K      75      R      84           -
LGA    E      76      -       -           -
LGA    G      77      -       -           -
LGA    D      78      -       -           -
LGA    R      79      -       -           -
LGA    I      80      -       -           -
LGA    E      81      -       -           -
LGA    I      82      -       -           -
LGA    Y      83      -       -           -
LGA    R      84      -       -           -
LGA    P      85      -       -           -
LGA    L      86      -       -           -
LGA    L      87      -       -           -
LGA    A      88      -       -           -
LGA    D      89      -       -           -
LGA    P      90      -       -           -
LGA    K      91      -       -           -
LGA    E      92      -       -           -
LGA    I      93      -       -           -
LGA    R      94      P      85           #
LGA    R      95      L      86           -
LGA    E      96      L      87           -
LGA    G      97      A      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   80    5.0     35    3.05    80.00     27.500     1.112

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.102944 * X  +   0.972328 * Y  +   0.209716 * Z  +  22.983498
  Y_new =   0.986874 * X  +  -0.126214 * Y  +   0.100745 * Z  +  13.605800
  Z_new =   0.124426 * X  +   0.196593 * Y  +  -0.972558 * Z  +   4.910561 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.942141   -0.199452  [ DEG:   168.5722    -11.4278 ]
  Theta =  -0.124750   -3.016843  [ DEG:    -7.1476   -172.8524 ]
  Phi   =   1.466859   -1.674734  [ DEG:    84.0448    -95.9552 ]
 
# 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: T0363TS168_1                                  
REMARK     2: T0363.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS168_1.T0363.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   80   5.0   35   3.05   80.00  27.500
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS168_1
PFRMAT TS
TARGET T0363
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      -9.418  -3.620   7.444  1.00 25.00           C
ATOM      2  CA  ALA     2      -7.161  -4.064  10.494  1.00 25.00           C
ATOM      3  CA  HIS     3      -4.197  -4.410  12.850  1.00 25.00           C
ATOM      4  CA  HIS     4      -2.249  -1.673  14.636  1.00 25.00           C
ATOM      5  CA  HIS     5       1.063  -0.194  15.571  1.00 25.00           C
ATOM      6  CA  HIS     6       2.910  -1.123  12.398  1.00 25.00           C
ATOM      7  CA  HIS     7       4.667   0.119   9.229  1.00 25.00           C
ATOM      8  CA  HIS     8       5.963  -1.842   6.216  1.00 25.00           C
ATOM      9  CA  SER     9       9.211  -2.373   4.196  1.00 25.00           C
ATOM     10  CA  LEU    10      12.613  -0.853   4.999  1.00 25.00           C
ATOM     11  CA  ASN    11      11.554   2.066   7.199  1.00 25.00           C
ATOM     12  CA  GLN    12      13.823   5.033   7.800  1.00 25.00           C
ATOM     13  CA  ILE    13      16.344   7.895   7.984  1.00 25.00           C
ATOM     14  CA  ASN    14      19.953   7.658   6.858  1.00 25.00           C
ATOM     15  CA  ILE    15      21.906  10.852   6.095  1.00 25.00           C
ATOM     16  CA  GLU    16      21.698  14.008   3.896  1.00 25.00           C
ATOM     17  CA  ILE    17      23.470  16.453   1.525  1.00 25.00           C
ATOM     18  CA  ALA    18      26.328  18.300   3.246  1.00 25.00           C
ATOM     19  CA  TYR    19      28.686  21.333   3.340  1.00 25.00           C
ATOM     20  CA  ALA    20      31.120  20.884   0.452  1.00 25.00           C
ATOM     21  CA  PHE    21      30.380  22.415  -2.960  1.00 25.00           C
ATOM     22  CA  PRO    22      29.104  24.731  -5.653  1.00 25.00           C
ATOM     23  CA  GLU    23      31.475  27.160  -7.278  1.00 25.00           C
ATOM     24  CA  ARG    24      29.945  29.691  -4.909  1.00 25.00           C
ATOM     25  CA  TYR    25      29.786  27.752  -1.679  1.00 25.00           C
ATOM     26  CA  TYR    26      26.608  25.672  -1.087  1.00 25.00           C
ATOM     27  CA  LEU    27      25.382  22.062  -0.651  1.00 25.00           C
ATOM     28  CA  LYS    28      22.985  21.900   2.299  1.00 25.00           C
ATOM     29  CA  SER    29      21.869  19.697   5.228  1.00 25.00           C
ATOM     30  CA  PHE    30      20.863  17.101   7.829  1.00 25.00           C
ATOM     31  CA  GLN    31      21.499  14.316  10.300  1.00 25.00           C
ATOM     32  CA  VAL    32      20.296  10.699  10.861  1.00 25.00           C
ATOM     33  CA  ASP    33      21.185  10.604  14.553  1.00 25.00           C
ATOM     34  CA  GLU    34      21.019   6.803  14.711  1.00 25.00           C
ATOM     35  CA  GLY    35      23.837   4.272  15.426  1.00 25.00           C
ATOM     36  CA  ILE    36      26.105   7.253  14.725  1.00 25.00           C
ATOM     37  CA  THR    37      24.640   7.387  11.236  1.00 25.00           C
ATOM     38  CA  VAL    38      25.338  11.110  11.372  1.00 25.00           C
ATOM     39  CA  GLN    39      28.787  11.552  12.975  1.00 25.00           C
ATOM     40  CA  THR    40      29.962   8.257  11.417  1.00 25.00           C
ATOM     41  CA  ALA    41      28.677   9.391   7.992  1.00 25.00           C
ATOM     42  CA  ILE    42      30.524  12.725   8.376  1.00 25.00           C
ATOM     43  CA  THR    43      33.741  10.865   9.304  1.00 25.00           C
ATOM     44  CA  GLN    44      33.351   8.609   6.234  1.00 25.00           C
ATOM     45  CA  SER    45      32.843  11.685   4.008  1.00 25.00           C
ATOM     46  CA  GLY    46      33.134   9.578   0.869  1.00 25.00           C
ATOM     47  CA  ILE    47      33.002  12.186  -1.866  1.00 25.00           C
ATOM     48  CA  LEU    48      35.292  14.558   0.050  1.00 25.00           C
ATOM     49  CA  SER    49      39.119  14.632  -0.043  1.00 25.00           C
ATOM     50  CA  GLN    50      39.254  13.530   3.623  1.00 25.00           C
ATOM     51  CA  PHE    51      37.877  10.114   2.786  1.00 25.00           C
ATOM     52  CA  PRO    52      40.830   9.803   0.331  1.00 25.00           C
ATOM     53  CA  GLU    53      41.384  10.552  -3.343  1.00 25.00           C
ATOM     54  CA  ILE    54      37.702   9.864  -4.197  1.00 25.00           C
ATOM     55  CA  ASP    55      38.269   6.359  -2.722  1.00 25.00           C
ATOM     56  CA  LEU    56      34.998   5.377  -1.122  1.00 25.00           C
ATOM     57  CA  SER    57      32.070   2.977  -1.708  1.00 25.00           C
ATOM     58  CA  THR    58      29.738   5.357  -3.475  1.00 25.00           C
ATOM     59  CA  ASN    59      27.928   6.614  -0.396  1.00 25.00           C
ATOM     60  CA  LYS    60      28.279  10.309  -1.305  1.00 25.00           C
ATOM     61  CA  ILE    61      25.199  11.224   0.791  1.00 25.00           C
ATOM     62  CA  GLY    62      26.745  12.573   4.025  1.00 25.00           C
ATOM     63  CA  ILE    63      26.076  14.914   6.953  1.00 25.00           C
ATOM     64  CA  PHE    64      25.806  18.502   8.237  1.00 25.00           C
ATOM     65  CA  SER    65      25.777  22.219   9.279  1.00 25.00           C
ATOM     66  CA  ARG    66      21.989  21.979   9.715  1.00 25.00           C
ATOM     67  CA  PRO    67      22.370  19.402  12.511  1.00 25.00           C
ATOM     68  CA  ILE    68      24.012  20.373  15.803  1.00 25.00           C
ATOM     69  CA  LYS    69      22.284  23.508  17.092  1.00 25.00           C
ATOM     70  CA  LEU    70      21.714  26.446  14.793  1.00 25.00           C
ATOM     71  CA  THR    71      22.957  28.994  12.323  1.00 25.00           C
ATOM     72  CA  ASP    72      26.605  28.320  13.357  1.00 25.00           C
ATOM     73  CA  VAL    73      26.812  25.727  16.074  1.00 25.00           C
ATOM     74  CA  LEU    74      29.038  23.491  13.957  1.00 25.00           C
ATOM     75  CA  LYS    75      32.402  23.973  15.698  1.00 25.00           C
ATOM     76  CA  GLU    76      34.035  21.016  17.296  1.00 25.00           C
ATOM     77  CA  GLY    77      31.197  18.542  16.982  1.00 25.00           C
ATOM     78  CA  ASP    78      28.482  18.362  14.355  1.00 25.00           C
ATOM     79  CA  ARG    79      30.193  18.255  10.925  1.00 25.00           C
ATOM     80  CA  ILE    80      31.276  19.431   7.486  1.00 25.00           C
ATOM     81  CA  GLU    81      30.757  16.537   5.073  1.00 25.00           C
ATOM     82  CA  ILE    82      30.310  15.303   1.561  1.00 25.00           C
ATOM     83  CA  TYR    83      27.941  16.443  -1.122  1.00 25.00           C
ATOM     84  CA  ARG    84      24.986  15.329  -3.238  1.00 25.00           C
ATOM     85  CA  PRO    85      21.626  13.725  -2.478  1.00 25.00           C
ATOM     86  CA  LEU    86      18.376  12.669  -4.175  1.00 25.00           C
ATOM     87  CA  LEU    87      19.338  13.979  -7.551  1.00 25.00           C
ATOM     88  CA  ALA    88      18.585  17.555  -6.532  1.00 25.00           C
ATOM     89  CA  ASP    89      14.769  17.464  -6.968  1.00 25.00           C
ATOM     90  CA  PRO    90      13.233  19.752  -4.284  1.00 25.00           C
ATOM     91  CA  LYS    91       9.766  19.769  -5.910  1.00 25.00           C
ATOM     92  CA  GLU    92       9.814  15.945  -6.111  1.00 25.00           C
ATOM     93  CA  ILE    93      10.796  15.739  -2.415  1.00 25.00           C
ATOM     94  CA  ARG    94       7.937  18.117  -1.498  1.00 25.00           C
ATOM     95  CA  ARG    95       5.792  15.313  -2.908  1.00 25.00           C
ATOM     96  CA  GLU    96       2.034  15.422  -2.358  1.00 25.00           C
ATOM     97  CA  GLY    97       2.809  15.753   1.318  1.00 25.00           C
TER
END
