
#######################################################
#                                                     #
#                        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 T0291TS393_3-D1
# Molecule2: number of CA atoms  100 (  781),  selected  100 , name T0291_D1.pdb
# PARAMETERS: T0291TS393_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          5.858
LGA    Y       2      Y       2          4.982
LGA    V       3      V       3          3.939
LGA    D       4      D       4          4.451
LGA    P       5      P       5          2.177
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          1.379
LGA    H      16      H      16          1.473
LGA    E      17      E      17          2.220
LGA    F      18      F      18          1.438
LGA    A      19      A      19          1.251
LGA    K      20      K      20          3.099
LGA    E      21      E      21          1.971
LGA    L      22      L      22          1.931
LGA    D      23      D      23          2.903
LGA    A      24      -       -           -
LGA    T      25      A      24          2.118
LGA    N      26      T      25          2.729
LGA    I      27      N      26          3.445
LGA    S      28      I      27          3.194
LGA    I      29      S      28          2.544
LGA    D      30      I      29          2.750
LGA    -       -      D      30           -
LGA    K      31      K      31          2.415
LGA    V      32      V      32          1.127
LGA    V      33      V      33          0.833
LGA    G      34      G      34          2.867
LGA    A      35      A      35          1.437
LGA    G      36      G      36          1.180
LGA    E      37      E      37          2.781
LGA    F      38      F      38          1.844
LGA    G      39      G      39          1.210
LGA    E      40      E      40          0.550
LGA    V      41      V      41          1.346
LGA    C      42      C      42          2.615
LGA    S      43      S      43          0.843
LGA    G      44      G      44          0.952
LGA    R      45      R      45          2.137
LGA    L      46      L      46          0.645
LGA    K      47      K      47          3.238
LGA    L      48      L      48          3.897
LGA    P      49      P      49          2.030
LGA    S      50      S      50          2.755
LGA    K      51      K      51          1.633
LGA    K      52      K      52          1.868
LGA    E      53      E      53          1.128
LGA    I      54      I      54          2.131
LGA    S      55      S      55          2.472
LGA    V      56      V      56          2.133
LGA    A      57      A      57          2.126
LGA    I      58      I      58          1.824
LGA    K      59      K      59          1.907
LGA    T      60      T      60          0.659
LGA    L      61      L      61          2.946
LGA    K      62      K      62          2.602
LGA    V      63      V      63          2.147
LGA    G      64      G      64          1.487
LGA    Y      65      Y      65          1.473
LGA    T      66      T      66          2.768
LGA    E      67      E      67          2.036
LGA    K      68      K      68          1.553
LGA    Q      69      Q      69          1.142
LGA    R      70      R      70          1.224
LGA    R      71      R      71          0.939
LGA    D      72      D      72          0.674
LGA    F      73      F      73          0.565
LGA    L      74      L      74          0.816
LGA    G      75      G      75          0.953
LGA    E      76      E      76          1.360
LGA    A      77      A      77          1.396
LGA    S      78      S      78          1.635
LGA    I      79      I      79          2.117
LGA    M      80      M      80          1.913
LGA    G      81      G      81          2.165
LGA    Q      82      Q      82          3.084
LGA    F      83      F      83          2.828
LGA    D      84      D      84          3.192
LGA    H      85      H      85          4.207
LGA    P      86      P      86          3.477
LGA    N      87      N      87          2.496
LGA    I      88      I      88          2.965
LGA    I      89      I      89          1.318
LGA    R      90      R      90          1.921
LGA    L      91      L      91          2.439
LGA    E      92      E      92          1.807
LGA    G      93      G      93          0.404
LGA    V      94      V      94          1.176
LGA    V      95      V      95          1.484
LGA    T      96      T      96          1.446
LGA    K      97      K      97          1.618
LGA    S      98      S      98          2.409
LGA    K      99      K      99          1.156
LGA    P     100      P     100          1.130
LGA    V     101      V     101          1.157
LGA    M     102      M     102          1.255
LGA    I     103      I     103          0.914
LGA    V     104      V     104          1.349
LGA    T     105      T     105          0.952
LGA    E     106      E     106          0.828
LGA    Y     107      Y     107          1.757
LGA    M     108      M     108          1.909

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  108  100    5.0     98    2.23    93.88     81.388     4.208

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.135628 * X  +  -0.078437 * Y  +   0.987650 * Z  +  -1.987300
  Y_new =  -0.638629 * X  +  -0.769054 * Y  +   0.026623 * Z  +   9.688962
  Z_new =   0.757468 * X  +  -0.634353 * Y  +  -0.154398 * Z  +  55.782860 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.809548    1.332045  [ DEG:  -103.6795     76.3205 ]
  Theta =  -0.859426   -2.282166  [ DEG:   -49.2415   -130.7585 ]
  Phi   =  -1.361531    1.780061  [ DEG:   -78.0100    101.9900 ]
 
# 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: T0291TS393_3-D1                               
REMARK     2: T0291_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS393_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   98   2.23   93.88  81.388
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS393_3-D1
PFRMAT TS
TARGET T0291
MODEL 3
PARENT N/A
ATOM      1  CA  THR     1      -3.607  35.598  46.005  1.00 25.00           C
ATOM      2  CA  TYR     2      -3.922  32.072  47.450  1.00 25.00           C
ATOM      3  CA  VAL     3      -7.095  30.407  48.729  1.00 25.00           C
ATOM      4  CA  ASP     4      -9.264  29.757  51.714  1.00 25.00           C
ATOM      5  CA  PRO     5     -12.130  28.584  53.892  1.00 25.00           C
ATOM      6  CA  HIS     6     -13.667  32.068  53.478  1.00 25.00           C
ATOM      7  CA  THR     7     -12.397  34.874  55.740  1.00 25.00           C
ATOM      8  CA  TYR     8     -15.294  33.730  58.022  1.00 25.00           C
ATOM      9  CA  GLU     9     -17.912  36.355  57.139  1.00 25.00           C
ATOM     10  CA  ASP    10     -20.073  33.792  55.337  1.00 25.00           C
ATOM     11  CA  PRO    11     -18.418  30.402  55.053  1.00 25.00           C
ATOM     12  CA  THR    12     -21.036  28.004  53.617  1.00 25.00           C
ATOM     13  CA  GLN    13     -21.179  30.057  50.387  1.00 25.00           C
ATOM     14  CA  ALA    14     -17.359  29.968  50.132  1.00 25.00           C
ATOM     15  CA  VAL    15     -17.390  26.172  50.636  1.00 25.00           C
ATOM     16  CA  HIS    16     -20.046  25.805  47.901  1.00 25.00           C
ATOM     17  CA  GLU    17     -17.940  27.955  45.533  1.00 25.00           C
ATOM     18  CA  PHE    18     -14.862  25.800  46.275  1.00 25.00           C
ATOM     19  CA  ALA    19     -16.884  22.624  45.572  1.00 25.00           C
ATOM     20  CA  LYS    20     -18.107  24.108  42.260  1.00 25.00           C
ATOM     21  CA  GLU    21     -20.664  21.272  42.167  1.00 25.00           C
ATOM     22  CA  LEU    22     -20.630  17.687  40.939  1.00 25.00           C
ATOM     23  CA  ASP    23     -24.304  17.921  39.920  1.00 25.00           C
ATOM     24  CA  ALA    24     -26.343  15.617  42.236  1.00 25.00           C
ATOM     25  CA  THR    25     -27.610  12.079  41.494  1.00 25.00           C
ATOM     26  CA  ASN    26     -24.628  11.474  39.168  1.00 25.00           C
ATOM     27  CA  ILE    27     -25.697   7.794  38.929  1.00 25.00           C
ATOM     28  CA  SER    28     -24.830   6.811  42.511  1.00 25.00           C
ATOM     29  CA  ILE    29     -23.304   3.697  44.166  1.00 25.00           C
ATOM     30  CA  ASP    30     -22.246   0.135  44.979  1.00 25.00           C
ATOM     31  CA  LYS    31     -20.435  -2.135  47.447  1.00 25.00           C
ATOM     32  CA  VAL    32     -18.473  -1.177  50.527  1.00 25.00           C
ATOM     33  CA  VAL    33     -15.485  -0.237  52.612  1.00 25.00           C
ATOM     34  CA  GLY    34     -14.507   1.816  55.643  1.00 25.00           C
ATOM     35  CA  ALA    35     -16.098   2.188  59.042  1.00 25.00           C
ATOM     36  CA  GLY    36     -14.550   5.675  59.509  1.00 25.00           C
ATOM     37  CA  GLU    37     -15.828   6.960  62.893  1.00 25.00           C
ATOM     38  CA  PHE    38     -17.020   9.983  60.916  1.00 25.00           C
ATOM     39  CA  GLY    39     -19.500   7.548  59.301  1.00 25.00           C
ATOM     40  CA  GLU    40     -18.990   5.357  56.226  1.00 25.00           C
ATOM     41  CA  VAL    41     -17.518   4.815  52.790  1.00 25.00           C
ATOM     42  CA  CYS    42     -19.124   4.452  49.307  1.00 25.00           C
ATOM     43  CA  SER    43     -16.197   2.801  47.538  1.00 25.00           C
ATOM     44  CA  GLY    44     -17.942   3.765  44.294  1.00 25.00           C
ATOM     45  CA  ARG    45     -19.406   5.468  41.162  1.00 25.00           C
ATOM     46  CA  LEU    46     -18.749   8.519  38.974  1.00 25.00           C
ATOM     47  CA  LYS    47     -21.151   7.086  36.423  1.00 25.00           C
ATOM     48  CA  LEU    48     -20.689  10.457  34.755  1.00 25.00           C
ATOM     49  CA  PRO    49     -20.195  13.904  33.254  1.00 25.00           C
ATOM     50  CA  SER    50     -16.966  12.748  31.662  1.00 25.00           C
ATOM     51  CA  LYS    51     -18.278   9.470  30.222  1.00 25.00           C
ATOM     52  CA  LYS    52     -14.836   7.939  30.481  1.00 25.00           C
ATOM     53  CA  GLU    53     -15.633   6.165  33.806  1.00 25.00           C
ATOM     54  CA  ILE    54     -14.423   8.734  36.317  1.00 25.00           C
ATOM     55  CA  SER    55     -12.228   6.310  38.334  1.00 25.00           C
ATOM     56  CA  VAL    56     -14.336   7.334  41.382  1.00 25.00           C
ATOM     57  CA  ALA    57     -14.118   7.111  45.141  1.00 25.00           C
ATOM     58  CA  ILE    58     -17.161   8.508  47.002  1.00 25.00           C
ATOM     59  CA  LYS    59     -18.080   9.464  50.532  1.00 25.00           C
ATOM     60  CA  THR    60     -20.830   9.634  53.130  1.00 25.00           C
ATOM     61  CA  LEU    61     -19.390  12.061  55.705  1.00 25.00           C
ATOM     62  CA  LYS    62     -22.514  11.353  57.816  1.00 25.00           C
ATOM     63  CA  VAL    63     -26.180  11.221  58.918  1.00 25.00           C
ATOM     64  CA  GLY    64     -28.279  11.070  62.090  1.00 25.00           C
ATOM     65  CA  TYR    65     -25.861  13.712  63.417  1.00 25.00           C
ATOM     66  CA  THR    66     -27.830  17.023  63.684  1.00 25.00           C
ATOM     67  CA  GLU    67     -25.015  18.982  62.000  1.00 25.00           C
ATOM     68  CA  LYS    68     -21.685  19.337  63.857  1.00 25.00           C
ATOM     69  CA  GLN    69     -20.383  16.148  62.184  1.00 25.00           C
ATOM     70  CA  ARG    70     -21.441  17.485  58.755  1.00 25.00           C
ATOM     71  CA  ARG    71     -19.651  20.796  59.466  1.00 25.00           C
ATOM     72  CA  ASP    72     -16.491  18.895  60.496  1.00 25.00           C
ATOM     73  CA  PHE    73     -16.653  16.830  57.274  1.00 25.00           C
ATOM     74  CA  LEU    74     -17.034  20.034  55.211  1.00 25.00           C
ATOM     75  CA  GLY    75     -14.015  21.571  56.997  1.00 25.00           C
ATOM     76  CA  GLU    76     -11.959  18.419  56.287  1.00 25.00           C
ATOM     77  CA  ALA    77     -12.968  18.562  52.596  1.00 25.00           C
ATOM     78  CA  SER    78     -11.950  22.251  52.436  1.00 25.00           C
ATOM     79  CA  ILE    79      -8.570  21.412  54.031  1.00 25.00           C
ATOM     80  CA  MET    80      -8.038  18.601  51.484  1.00 25.00           C
ATOM     81  CA  GLY    81      -8.878  21.001  48.621  1.00 25.00           C
ATOM     82  CA  GLN    82      -6.394  23.565  50.009  1.00 25.00           C
ATOM     83  CA  PHE    83      -3.654  21.349  48.528  1.00 25.00           C
ATOM     84  CA  ASP    84      -2.855  19.629  45.230  1.00 25.00           C
ATOM     85  CA  HIS    85       0.732  18.918  46.272  1.00 25.00           C
ATOM     86  CA  PRO    86       1.332  15.646  44.492  1.00 25.00           C
ATOM     87  CA  ASN    87       0.274  13.721  47.544  1.00 25.00           C
ATOM     88  CA  ILE    88      -2.334  15.190  49.967  1.00 25.00           C
ATOM     89  CA  ILE    89      -5.110  13.266  48.309  1.00 25.00           C
ATOM     90  CA  ARG    90      -7.412  15.525  46.303  1.00 25.00           C
ATOM     91  CA  LEU    91      -9.890  17.931  44.673  1.00 25.00           C
ATOM     92  CA  GLU    92     -13.253  16.717  43.590  1.00 25.00           C
ATOM     93  CA  GLY    93     -16.959  16.841  44.326  1.00 25.00           C
ATOM     94  CA  VAL    94     -19.884  17.839  46.503  1.00 25.00           C
ATOM     95  CA  VAL    95     -23.664  17.559  47.089  1.00 25.00           C
ATOM     96  CA  THR    96     -24.040  19.754  50.159  1.00 25.00           C
ATOM     97  CA  LYS    97     -27.758  19.885  49.367  1.00 25.00           C
ATOM     98  CA  SER    98     -30.187  17.291  50.562  1.00 25.00           C
ATOM     99  CA  LYS    99     -29.909  13.786  51.881  1.00 25.00           C
ATOM    100  CA  PRO   100     -26.310  12.720  52.488  1.00 25.00           C
ATOM    101  CA  VAL   101     -23.022  14.625  52.573  1.00 25.00           C
ATOM    102  CA  MET   102     -20.707  13.855  49.642  1.00 25.00           C
ATOM    103  CA  ILE   103     -17.061  14.562  50.142  1.00 25.00           C
ATOM    104  CA  VAL   104     -15.159  13.092  47.207  1.00 25.00           C
ATOM    105  CA  THR   105     -11.570  12.501  45.969  1.00 25.00           C
ATOM    106  CA  GLU   106      -9.906  10.312  43.278  1.00 25.00           C
ATOM    107  CA  TYR   107      -9.470   6.574  42.734  1.00 25.00           C
ATOM    108  CA  MET   108      -8.233   4.512  45.677  1.00 25.00           C
TER
END
