
#######################################################
#                                                     #
#                        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  108 (  108),  selected  108 , name T0291TS168_3-D1
# Molecule2: number of CA atoms  100 (  781),  selected  100 , name T0291_D1.pdb
# PARAMETERS: T0291TS168_3-D1.T0291_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T       1      T       1          3.586
LGA    Y       2      Y       2          3.421
LGA    V       3      V       3          2.594
LGA    D       4      D       4          3.572
LGA    P       5      P       5          2.426
LGA    H       6      H       6           #
LGA    T       7      -       -           -
LGA    Y       8      -       -           -
LGA    E       9      -       -           -
LGA    D      10      -       -           -
LGA    P      11      -       -           -
LGA    T      12      -       -           -
LGA    Q      13      -       -           -
LGA    A      14      -       -           -
LGA    V      15      V      15          2.307
LGA    H      16      H      16          1.482
LGA    E      17      E      17          3.925
LGA    F      18      F      18          2.790
LGA    A      19      A      19          1.089
LGA    K      20      K      20          2.231
LGA    E      21      E      21          0.852
LGA    L      22      L      22          3.595
LGA    D      23      D      23          1.962
LGA    A      24      A      24           #
LGA    T      25      T      25           -
LGA    N      26      N      26           #
LGA    I      27      I      27           -
LGA    S      28      -       -           -
LGA    I      29      S      28           #
LGA    D      30      I      29           #
LGA    K      31      D      30          1.074
LGA    V      32      K      31          0.787
LGA    V      33      V      32          4.111
LGA    G      34      V      33          0.859
LGA    A      35      G      34          1.684
LGA    G      36      A      35          3.507
LGA    E      37      G      36          2.513
LGA    F      38      E      37          2.147
LGA    -       -      F      38           -
LGA    G      39      G      39          2.664
LGA    E      40      E      40          2.907
LGA    V      41      V      41          2.879
LGA    C      42      C      42          1.599
LGA    S      43      S      43          1.384
LGA    G      44      G      44          2.585
LGA    R      45      R      45          4.428
LGA    L      46      L      46          4.420
LGA    K      47      K      47          3.129
LGA    L      48      L      48           #
LGA    P      49      P      49          3.519
LGA    S      50      S      50          1.568
LGA    K      51      K      51          1.561
LGA    K      52      K      52          3.335
LGA    E      53      E      53          2.665
LGA    I      54      I      54          5.131
LGA    S      55      S      55          5.535
LGA    V      56      V      56          2.148
LGA    A      57      A      57          2.170
LGA    I      58      I      58          2.425
LGA    K      59      K      59          1.801
LGA    T      60      T      60          1.668
LGA    L      61      L      61          1.508
LGA    K      62      K      62          1.425
LGA    V      63      V      63          1.356
LGA    G      64      G      64          1.970
LGA    Y      65      Y      65          2.804
LGA    T      66      T      66          1.818
LGA    E      67      E      67          1.553
LGA    K      68      K      68          1.491
LGA    Q      69      Q      69          0.884
LGA    R      70      R      70          0.588
LGA    R      71      R      71          0.751
LGA    D      72      D      72          0.862
LGA    F      73      F      73          0.543
LGA    L      74      L      74          1.288
LGA    G      75      G      75          1.140
LGA    E      76      E      76          1.753
LGA    A      77      A      77          1.611
LGA    S      78      S      78          1.834
LGA    I      79      I      79          2.577
LGA    M      80      M      80          2.520
LGA    G      81      G      81          2.696
LGA    Q      82      Q      82          3.823
LGA    F      83      F      83          2.564
LGA    D      84      D      84          4.362
LGA    H      85      H      85          4.154
LGA    P      86      P      86          2.748
LGA    N      87      N      87          2.314
LGA    I      88      I      88          2.451
LGA    I      89      I      89          2.216
LGA    R      90      R      90          2.231
LGA    L      91      L      91          1.444
LGA    E      92      E      92          1.274
LGA    G      93      G      93          1.184
LGA    V      94      V      94          0.765
LGA    V      95      V      95          1.542
LGA    T      96      T      96          1.493
LGA    K      97      K      97          0.833
LGA    S      98      S      98          0.787
LGA    K      99      K      99          1.495
LGA    P     100      P     100          2.291
LGA    V     101      V     101          1.575
LGA    M     102      M     102          2.203
LGA    I     103      I     103          2.032
LGA    V     104      V     104          2.052
LGA    T     105      T     105          2.411
LGA    E     106      E     106          1.988
LGA    Y     107      Y     107          2.169
LGA    M     108      M     108          1.430

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  108  100    5.0     91    2.45    92.31     64.512     3.570

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.074343 * X  +   0.742244 * Y  +   0.665993 * Z  +  -1.419816
  Y_new =  -0.950561 * X  +  -0.254662 * Y  +   0.177711 * Z  +   9.905242
  Z_new =   0.301508 * X  +  -0.619855 * Y  +   0.724481 * Z  +  55.471924 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.707728    2.433865  [ DEG:   -40.5498    139.4502 ]
  Theta =  -0.306274   -2.835319  [ DEG:   -17.5482   -162.4518 ]
  Phi   =  -1.648847    1.492746  [ DEG:   -94.4720     85.5280 ]
 
# 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: T0291TS168_3-D1                               
REMARK     2: T0291_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS168_3-D1.T0291_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  108  100   5.0   91   2.45   92.31  64.512
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS168_3-D1
PFRMAT TS
TARGET T0291
MODEL 3
PARENT N/A
ATOM      1  CA  THR     1      -2.400  33.475  46.590  1.00 25.00           C
ATOM      2  CA  TYR     2      -3.622  30.208  48.067  1.00 25.00           C
ATOM      3  CA  VAL     3      -6.826  29.984  50.147  1.00 25.00           C
ATOM      4  CA  ASP     4      -9.534  29.424  52.665  1.00 25.00           C
ATOM      5  CA  PRO     5     -12.884  29.952  54.275  1.00 25.00           C
ATOM      6  CA  HIS     6     -12.912  33.299  56.048  1.00 25.00           C
ATOM      7  CA  THR     7     -11.962  34.971  52.768  1.00 25.00           C
ATOM      8  CA  TYR     8     -15.719  35.084  52.117  1.00 25.00           C
ATOM      9  CA  GLU     9     -18.960  36.431  53.537  1.00 25.00           C
ATOM     10  CA  ASP    10     -21.371  33.914  52.012  1.00 25.00           C
ATOM     11  CA  PRO    11     -19.156  31.371  53.694  1.00 25.00           C
ATOM     12  CA  THR    12     -20.821  27.953  53.230  1.00 25.00           C
ATOM     13  CA  GLN    13     -22.300  29.101  49.888  1.00 25.00           C
ATOM     14  CA  ALA    14     -18.853  30.331  48.759  1.00 25.00           C
ATOM     15  CA  VAL    15     -17.303  26.968  49.737  1.00 25.00           C
ATOM     16  CA  HIS    16     -20.020  25.117  47.772  1.00 25.00           C
ATOM     17  CA  GLU    17     -19.358  27.335  44.720  1.00 25.00           C
ATOM     18  CA  PHE    18     -15.604  26.627  44.990  1.00 25.00           C
ATOM     19  CA  ALA    19     -16.302  22.867  45.192  1.00 25.00           C
ATOM     20  CA  LYS    20     -18.547  23.092  42.097  1.00 25.00           C
ATOM     21  CA  GLU    21     -20.709  20.388  43.629  1.00 25.00           C
ATOM     22  CA  LEU    22     -22.463  19.798  40.338  1.00 25.00           C
ATOM     23  CA  ASP    23     -23.421  16.080  40.303  1.00 25.00           C
ATOM     24  CA  ALA    24     -20.316  14.695  38.475  1.00 25.00           C
ATOM     25  CA  THR    25     -17.159  14.998  36.306  1.00 25.00           C
ATOM     26  CA  ASN    26     -16.479  11.430  35.082  1.00 25.00           C
ATOM     27  CA  ILE    27     -13.849   8.757  35.591  1.00 25.00           C
ATOM     28  CA  SER    28     -13.577   5.211  36.955  1.00 25.00           C
ATOM     29  CA  ILE    29     -15.847   3.393  39.444  1.00 25.00           C
ATOM     30  CA  ASP    30     -18.281   0.862  40.894  1.00 25.00           C
ATOM     31  CA  LYS    31     -18.594  -0.972  44.253  1.00 25.00           C
ATOM     32  CA  VAL    32     -17.341  -1.468  47.825  1.00 25.00           C
ATOM     33  CA  VAL    33     -14.563  -0.886  50.352  1.00 25.00           C
ATOM     34  CA  GLY    34     -14.792   0.477  53.846  1.00 25.00           C
ATOM     35  CA  ALA    35     -14.947   0.889  57.587  1.00 25.00           C
ATOM     36  CA  GLY    36     -13.717   4.348  58.590  1.00 25.00           C
ATOM     37  CA  GLU    37     -14.839   6.159  61.742  1.00 25.00           C
ATOM     38  CA  PHE    38     -16.629   9.084  60.209  1.00 25.00           C
ATOM     39  CA  GLY    39     -18.310   6.597  57.804  1.00 25.00           C
ATOM     40  CA  GLU    40     -17.177   4.816  54.609  1.00 25.00           C
ATOM     41  CA  VAL    41     -15.164   4.931  51.333  1.00 25.00           C
ATOM     42  CA  CYS    42     -17.860   3.556  49.075  1.00 25.00           C
ATOM     43  CA  SER    43     -16.229   3.226  45.592  1.00 25.00           C
ATOM     44  CA  GLY    44     -19.779   4.150  44.471  1.00 25.00           C
ATOM     45  CA  ARG    45     -21.647   5.802  41.674  1.00 25.00           C
ATOM     46  CA  LEU    46     -22.293   9.398  40.472  1.00 25.00           C
ATOM     47  CA  LYS    47     -22.309   9.532  36.671  1.00 25.00           C
ATOM     48  CA  LEU    48     -21.875   9.013  32.927  1.00 25.00           C
ATOM     49  CA  PRO    49     -21.302  12.691  32.499  1.00 25.00           C
ATOM     50  CA  SER    50     -18.441  14.370  30.676  1.00 25.00           C
ATOM     51  CA  LYS    51     -18.034  11.005  28.891  1.00 25.00           C
ATOM     52  CA  LYS    52     -17.805   7.315  29.856  1.00 25.00           C
ATOM     53  CA  GLU    53     -17.174   5.074  32.936  1.00 25.00           C
ATOM     54  CA  ILE    54     -18.501   6.265  36.305  1.00 25.00           C
ATOM     55  CA  SER    55     -17.522   8.261  39.394  1.00 25.00           C
ATOM     56  CA  VAL    56     -15.561   7.620  42.565  1.00 25.00           C
ATOM     57  CA  ALA    57     -15.181   8.130  46.331  1.00 25.00           C
ATOM     58  CA  ILE    58     -18.827   8.200  47.362  1.00 25.00           C
ATOM     59  CA  LYS    59     -17.568   9.729  50.630  1.00 25.00           C
ATOM     60  CA  THR    60     -20.221   8.573  53.172  1.00 25.00           C
ATOM     61  CA  LEU    61     -21.540  11.373  55.443  1.00 25.00           C
ATOM     62  CA  LYS    62     -24.233   9.986  57.759  1.00 25.00           C
ATOM     63  CA  VAL    63     -27.723  11.254  58.749  1.00 25.00           C
ATOM     64  CA  GLY    64     -27.997  10.682  62.499  1.00 25.00           C
ATOM     65  CA  TYR    65     -26.520  13.484  64.619  1.00 25.00           C
ATOM     66  CA  THR    66     -26.381  16.905  63.026  1.00 25.00           C
ATOM     67  CA  GLU    67     -25.643  20.362  61.736  1.00 25.00           C
ATOM     68  CA  LYS    68     -22.390  20.511  63.753  1.00 25.00           C
ATOM     69  CA  GLN    69     -21.265  17.181  62.232  1.00 25.00           C
ATOM     70  CA  ARG    70     -22.043  18.494  58.719  1.00 25.00           C
ATOM     71  CA  ARG    71     -20.033  21.674  59.436  1.00 25.00           C
ATOM     72  CA  ASP    72     -17.088  19.563  60.675  1.00 25.00           C
ATOM     73  CA  PHE    73     -17.256  17.422  57.505  1.00 25.00           C
ATOM     74  CA  LEU    74     -17.278  20.583  55.342  1.00 25.00           C
ATOM     75  CA  GLY    75     -14.238  21.933  57.240  1.00 25.00           C
ATOM     76  CA  GLU    76     -12.407  18.609  56.719  1.00 25.00           C
ATOM     77  CA  ALA    77     -13.219  18.720  52.978  1.00 25.00           C
ATOM     78  CA  SER    78     -11.903  22.311  52.774  1.00 25.00           C
ATOM     79  CA  ILE    79      -8.684  21.259  54.562  1.00 25.00           C
ATOM     80  CA  MET    80      -8.253  18.340  52.122  1.00 25.00           C
ATOM     81  CA  GLY    81      -8.757  20.712  49.157  1.00 25.00           C
ATOM     82  CA  GLN    82      -6.149  23.114  50.604  1.00 25.00           C
ATOM     83  CA  PHE    83      -3.744  21.351  48.264  1.00 25.00           C
ATOM     84  CA  ASP    84      -2.214  18.818  45.926  1.00 25.00           C
ATOM     85  CA  HIS    85       1.551  18.137  45.563  1.00 25.00           C
ATOM     86  CA  PRO    86       1.191  14.771  43.755  1.00 25.00           C
ATOM     87  CA  ASN    87       0.972  13.442  47.313  1.00 25.00           C
ATOM     88  CA  ILE    88      -1.838  15.028  49.382  1.00 25.00           C
ATOM     89  CA  ILE    89      -5.019  12.943  49.156  1.00 25.00           C
ATOM     90  CA  ARG    90      -6.447  14.719  46.145  1.00 25.00           C
ATOM     91  CA  LEU    91     -10.192  15.626  46.139  1.00 25.00           C
ATOM     92  CA  GLU    92     -12.660  15.542  43.254  1.00 25.00           C
ATOM     93  CA  GLY    93     -16.388  16.074  43.820  1.00 25.00           C
ATOM     94  CA  VAL    94     -18.823  16.524  46.773  1.00 25.00           C
ATOM     95  CA  VAL    95     -22.476  15.891  45.892  1.00 25.00           C
ATOM     96  CA  THR    96     -24.074  18.234  48.401  1.00 25.00           C
ATOM     97  CA  LYS    97     -27.810  18.851  48.539  1.00 25.00           C
ATOM     98  CA  SER    98     -29.482  15.618  49.607  1.00 25.00           C
ATOM     99  CA  LYS    99     -28.892  12.249  51.218  1.00 25.00           C
ATOM    100  CA  PRO   100     -25.099  12.569  51.461  1.00 25.00           C
ATOM    101  CA  VAL   101     -22.984  15.397  52.799  1.00 25.00           C
ATOM    102  CA  MET   102     -19.598  14.401  51.256  1.00 25.00           C
ATOM    103  CA  ILE   103     -15.864  14.719  50.683  1.00 25.00           C
ATOM    104  CA  VAL   104     -14.379  13.113  47.525  1.00 25.00           C
ATOM    105  CA  THR   105     -11.184  11.127  48.315  1.00 25.00           C
ATOM    106  CA  GLU   106      -8.705   9.922  45.741  1.00 25.00           C
ATOM    107  CA  TYR   107      -8.556   7.361  42.893  1.00 25.00           C
ATOM    108  CA  MET   108      -7.017   4.424  44.688  1.00 25.00           C
TER
END
