
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms  100 (  781),  selected  100 , name T0291_D1.pdb
# PARAMETERS: T0291TS168_1-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          3.837
LGA    Y       2      Y       2          3.158
LGA    V       3      V       3          4.760
LGA    D       4      D       4          5.260
LGA    P       5      -       -           -
LGA    H       6      -       -           -
LGA    T       7      -       -           -
LGA    Y       8      -       -           -
LGA    E       9      -       -           -
LGA    D      10      P       5           #
LGA    P      11      H       6           #
LGA    T      12      -       -           -
LGA    Q      13      -       -           -
LGA    A      14      -       -           -
LGA    V      15      V      15          1.129
LGA    H      16      H      16          2.442
LGA    E      17      E      17          3.593
LGA    F      18      F      18          2.953
LGA    A      19      A      19          2.332
LGA    K      20      K      20          4.430
LGA    E      21      E      21          2.698
LGA    L      22      L      22          1.622
LGA    D      23      D      23          0.947
LGA    A      24      A      24          3.835
LGA    T      25      T      25          1.077
LGA    N      26      N      26          1.469
LGA    I      27      I      27          4.089
LGA    S      28      S      28          1.927
LGA    I      29      I      29          1.924
LGA    D      30      D      30          2.256
LGA    K      31      K      31          1.457
LGA    V      32      V      32          2.096
LGA    V      33      V      33          1.879
LGA    G      34      G      34          1.627
LGA    A      35      A      35          2.979
LGA    G      36      G      36          4.579
LGA    E      37      E      37          3.876
LGA    F      38      F      38          3.487
LGA    G      39      G      39          2.961
LGA    E      40      E      40          0.803
LGA    V      41      V      41          0.718
LGA    C      42      C      42          0.650
LGA    S      43      S      43          0.630
LGA    G      44      G      44          0.914
LGA    R      45      R      45          0.849
LGA    L      46      L      46          0.840
LGA    K      47      K      47          1.085
LGA    L      48      L      48          1.790
LGA    P      49      P      49          2.307
LGA    S      50      S      50          0.449
LGA    K      51      K      51          2.001
LGA    K      52      K      52          2.511
LGA    E      53      E      53          2.219
LGA    I      54      I      54          0.959
LGA    S      55      S      55          1.170
LGA    V      56      V      56          0.730
LGA    A      57      A      57          1.625
LGA    I      58      I      58          1.489
LGA    K      59      K      59          0.422
LGA    T      60      T      60          1.478
LGA    L      61      L      61          1.263
LGA    K      62      K      62          2.397
LGA    V      63      V      63          1.430
LGA    G      64      G      64          1.410
LGA    Y      65      Y      65          1.821
LGA    T      66      T      66          1.691
LGA    E      67      E      67          1.418
LGA    K      68      K      68          1.034
LGA    Q      69      Q      69          0.189
LGA    R      70      R      70          0.626
LGA    R      71      R      71          0.857
LGA    D      72      D      72          0.721
LGA    F      73      F      73          0.560
LGA    L      74      L      74          0.874
LGA    G      75      G      75          0.744
LGA    E      76      E      76          1.206
LGA    A      77      A      77          1.216
LGA    S      78      S      78          0.848
LGA    I      79      I      79          1.063
LGA    M      80      M      80          1.499
LGA    G      81      G      81          1.456
LGA    Q      82      Q      82          1.803
LGA    F      83      F      83          2.493
LGA    D      84      D      84          2.254
LGA    H      85      H      85          1.851
LGA    P      86      P      86          2.458
LGA    N      87      N      87          1.819
LGA    I      88      I      88          2.454
LGA    I      89      I      89          1.450
LGA    R      90      R      90          1.444
LGA    L      91      L      91          1.110
LGA    E      92      E      92          0.674
LGA    G      93      G      93          1.271
LGA    V      94      V      94          0.655
LGA    V      95      V      95          0.553
LGA    T      96      T      96          1.046
LGA    K      97      K      97          2.857
LGA    S      98      S      98          3.184
LGA    K      99      K      99          2.186
LGA    P     100      P     100          1.704
LGA    V     101      V     101          0.457
LGA    M     102      M     102          2.316
LGA    I     103      I     103          1.907
LGA    V     104      V     104          1.826
LGA    T     105      T     105          1.391
LGA    E     106      E     106          1.168
LGA    Y     107      Y     107          2.361
LGA    M     108      M     108          0.700

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  108  100    5.0     98    2.09   100.00     83.994     4.473

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.304660 * X  +   0.660523 * Y  +   0.686215 * Z  +  -0.805567
  Y_new =  -0.722406 * X  +   0.309293 * Y  +  -0.618440 * Z  +  10.485114
  Z_new =  -0.620735 * X  +  -0.684140 * Y  +   0.382937 * Z  +  54.985641 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.060510    2.081083  [ DEG:   -60.7627    119.2373 ]
  Theta =   0.669680    2.471912  [ DEG:    38.3699    141.6301 ]
  Phi   =  -1.969893    1.171699  [ DEG:  -112.8666     67.1334 ]
 
# 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_1-D1                               
REMARK     2: T0291_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS168_1-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   2.09  100.00  83.994
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS168_1-D1
PFRMAT TS
TARGET T0291
MODEL 1
PARENT N/A
ATOM      1  CA  THR     1      -2.938  32.794  45.756  1.00 25.00           C
ATOM      2  CA  TYR     2      -3.379  30.148  48.419  1.00 25.00           C
ATOM      3  CA  VAL     3      -7.045  30.870  47.925  1.00 25.00           C
ATOM      4  CA  ASP     4      -7.906  28.646  50.867  1.00 25.00           C
ATOM      5  CA  PRO     5     -11.631  28.411  50.302  1.00 25.00           C
ATOM      6  CA  HIS     6     -12.176  31.628  52.323  1.00 25.00           C
ATOM      7  CA  THR     7     -12.245  35.002  54.196  1.00 25.00           C
ATOM      8  CA  TYR     8     -16.081  35.143  54.003  1.00 25.00           C
ATOM      9  CA  GLU     9     -18.151  35.874  57.146  1.00 25.00           C
ATOM     10  CA  ASP    10     -18.863  32.175  57.481  1.00 25.00           C
ATOM     11  CA  PRO    11     -17.250  29.058  55.997  1.00 25.00           C
ATOM     12  CA  THR    12     -19.779  26.378  54.955  1.00 25.00           C
ATOM     13  CA  GLN    13     -21.310  28.782  52.397  1.00 25.00           C
ATOM     14  CA  ALA    14     -17.829  29.554  51.002  1.00 25.00           C
ATOM     15  CA  VAL    15     -17.086  25.807  50.717  1.00 25.00           C
ATOM     16  CA  HIS    16     -20.405  25.263  48.886  1.00 25.00           C
ATOM     17  CA  GLU    17     -19.574  28.124  46.479  1.00 25.00           C
ATOM     18  CA  PHE    18     -16.122  26.601  45.820  1.00 25.00           C
ATOM     19  CA  ALA    19     -17.731  23.194  45.128  1.00 25.00           C
ATOM     20  CA  LYS    20     -20.203  24.826  42.701  1.00 25.00           C
ATOM     21  CA  GLU    21     -22.036  21.717  41.424  1.00 25.00           C
ATOM     22  CA  LEU    22     -21.461  17.973  41.142  1.00 25.00           C
ATOM     23  CA  ASP    23     -24.226  15.365  40.592  1.00 25.00           C
ATOM     24  CA  ALA    24     -27.963  14.731  41.053  1.00 25.00           C
ATOM     25  CA  THR    25     -27.483  11.146  39.887  1.00 25.00           C
ATOM     26  CA  ASN    26     -24.649   9.643  37.933  1.00 25.00           C
ATOM     27  CA  ILE    27     -23.415   6.101  38.288  1.00 25.00           C
ATOM     28  CA  SER    28     -22.673   6.554  41.993  1.00 25.00           C
ATOM     29  CA  ILE    29     -22.910   3.967  44.772  1.00 25.00           C
ATOM     30  CA  ASP    30     -21.288   0.622  45.315  1.00 25.00           C
ATOM     31  CA  LYS    31     -19.542  -1.374  48.099  1.00 25.00           C
ATOM     32  CA  VAL    32     -16.802  -1.579  50.769  1.00 25.00           C
ATOM     33  CA  VAL    33     -13.586  -0.595  52.637  1.00 25.00           C
ATOM     34  CA  GLY    34     -15.081   0.033  56.047  1.00 25.00           C
ATOM     35  CA  ALA    35     -15.797   0.666  59.786  1.00 25.00           C
ATOM     36  CA  GLY    36     -12.811   2.943  60.569  1.00 25.00           C
ATOM     37  CA  GLU    37     -12.884   6.689  60.664  1.00 25.00           C
ATOM     38  CA  PHE    38     -16.091   8.672  61.427  1.00 25.00           C
ATOM     39  CA  GLY    39     -18.299   6.196  59.569  1.00 25.00           C
ATOM     40  CA  GLU    40     -18.846   5.552  55.859  1.00 25.00           C
ATOM     41  CA  VAL    41     -16.178   4.564  53.421  1.00 25.00           C
ATOM     42  CA  CYS    42     -17.552   3.504  50.056  1.00 25.00           C
ATOM     43  CA  SER    43     -16.200   2.899  46.523  1.00 25.00           C
ATOM     44  CA  GLY    44     -17.923   4.161  43.355  1.00 25.00           C
ATOM     45  CA  ARG    45     -17.398   4.595  39.554  1.00 25.00           C
ATOM     46  CA  LEU    46     -18.765   8.133  39.161  1.00 25.00           C
ATOM     47  CA  LYS    47     -20.216   9.012  35.753  1.00 25.00           C
ATOM     48  CA  LEU    48     -19.079  12.619  35.733  1.00 25.00           C
ATOM     49  CA  PRO    49     -17.326  15.255  33.599  1.00 25.00           C
ATOM     50  CA  SER    50     -17.206  14.322  29.928  1.00 25.00           C
ATOM     51  CA  LYS    51     -17.049  10.509  29.741  1.00 25.00           C
ATOM     52  CA  LYS    52     -16.423   7.074  31.366  1.00 25.00           C
ATOM     53  CA  GLU    53     -15.029   5.169  34.393  1.00 25.00           C
ATOM     54  CA  ILE    54     -13.621   7.856  36.706  1.00 25.00           C
ATOM     55  CA  SER    55     -12.584   6.025  39.921  1.00 25.00           C
ATOM     56  CA  VAL    56     -14.145   7.537  43.044  1.00 25.00           C
ATOM     57  CA  ALA    57     -14.926   7.740  46.768  1.00 25.00           C
ATOM     58  CA  ILE    58     -18.175   8.694  48.438  1.00 25.00           C
ATOM     59  CA  LYS    59     -17.279   9.008  52.079  1.00 25.00           C
ATOM     60  CA  THR    60     -19.844  10.537  54.413  1.00 25.00           C
ATOM     61  CA  LEU    61     -21.307  11.940  57.594  1.00 25.00           C
ATOM     62  CA  LYS    62     -25.126  11.589  57.857  1.00 25.00           C
ATOM     63  CA  VAL    63     -28.817  10.738  58.478  1.00 25.00           C
ATOM     64  CA  GLY    64     -29.581  13.193  61.282  1.00 25.00           C
ATOM     65  CA  TYR    65     -26.092  12.729  62.798  1.00 25.00           C
ATOM     66  CA  THR    66     -26.330  16.456  63.553  1.00 25.00           C
ATOM     67  CA  GLU    67     -25.270  19.783  62.116  1.00 25.00           C
ATOM     68  CA  LYS    68     -21.939  20.666  63.786  1.00 25.00           C
ATOM     69  CA  GLN    69     -20.441  17.343  62.610  1.00 25.00           C
ATOM     70  CA  ARG    70     -21.663  18.026  59.045  1.00 25.00           C
ATOM     71  CA  ARG    71     -20.106  21.523  59.155  1.00 25.00           C
ATOM     72  CA  ASP    72     -16.795  20.038  60.378  1.00 25.00           C
ATOM     73  CA  PHE    73     -16.871  17.468  57.539  1.00 25.00           C
ATOM     74  CA  LEU    74     -17.525  20.258  54.999  1.00 25.00           C
ATOM     75  CA  GLY    75     -14.591  22.270  56.416  1.00 25.00           C
ATOM     76  CA  GLU    76     -12.324  19.193  56.161  1.00 25.00           C
ATOM     77  CA  ALA    77     -13.416  18.661  52.528  1.00 25.00           C
ATOM     78  CA  SER    78     -12.672  22.335  51.741  1.00 25.00           C
ATOM     79  CA  ILE    79      -9.210  22.002  53.343  1.00 25.00           C
ATOM     80  CA  MET    80      -8.525  18.856  51.270  1.00 25.00           C
ATOM     81  CA  GLY    81      -9.595  20.692  48.084  1.00 25.00           C
ATOM     82  CA  GLN    82      -7.277  23.612  48.960  1.00 25.00           C
ATOM     83  CA  PHE    83      -3.959  21.740  48.385  1.00 25.00           C
ATOM     84  CA  ASP    84      -3.606  20.657  44.762  1.00 25.00           C
ATOM     85  CA  HIS    85      -0.459  18.574  44.254  1.00 25.00           C
ATOM     86  CA  PRO    86       1.386  15.381  43.131  1.00 25.00           C
ATOM     87  CA  ASN    87       0.174  12.438  45.229  1.00 25.00           C
ATOM     88  CA  ILE    88      -0.694  14.283  48.420  1.00 25.00           C
ATOM     89  CA  ILE    89      -4.218  13.157  47.599  1.00 25.00           C
ATOM     90  CA  ARG    90      -7.103  14.530  45.557  1.00 25.00           C
ATOM     91  CA  LEU    91     -10.379  16.353  45.064  1.00 25.00           C
ATOM     92  CA  GLU    92     -13.194  14.920  42.929  1.00 25.00           C
ATOM     93  CA  GLY    93     -16.721  16.066  43.649  1.00 25.00           C
ATOM     94  CA  VAL    94     -19.175  16.668  46.556  1.00 25.00           C
ATOM     95  CA  VAL    95     -22.881  15.928  46.848  1.00 25.00           C
ATOM     96  CA  THR    96     -25.296  18.164  48.832  1.00 25.00           C
ATOM     97  CA  LYS    97     -28.235  19.726  50.754  1.00 25.00           C
ATOM     98  CA  SER    98     -31.428  17.775  50.275  1.00 25.00           C
ATOM     99  CA  LYS    99     -30.637  14.064  50.806  1.00 25.00           C
ATOM    100  CA  PRO   100     -27.361  13.253  52.488  1.00 25.00           C
ATOM    101  CA  VAL   101     -23.797  14.409  51.940  1.00 25.00           C
ATOM    102  CA  MET   102     -20.010  14.726  51.547  1.00 25.00           C
ATOM    103  CA  ILE   103     -16.217  14.658  50.976  1.00 25.00           C
ATOM    104  CA  VAL   104     -15.050  13.488  47.521  1.00 25.00           C
ATOM    105  CA  THR   105     -11.537  12.020  47.465  1.00 25.00           C
ATOM    106  CA  GLU   106      -9.372   9.895  45.143  1.00 25.00           C
ATOM    107  CA  TYR   107      -9.520   6.419  46.818  1.00 25.00           C
ATOM    108  CA  MET   108      -6.559   4.157  45.980  1.00 25.00           C
TER
END
