
#######################################################
#                                                     #
#                        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  117 (  117),  selected  117 , name T0351TS168_1
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351TS168_1.T0351.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      I       2           -
LGA    L       3      L       3           -
LGA    Y       4      Y       4           -
LGA    D       5      D       5           -
LGA    A       6      A       6           -
LGA    -       -      I       7           -
LGA    I       7      M       8          4.571
LGA    -       -      Y       9           -
LGA    -       -      K      10           -
LGA    -       -      Y      11           -
LGA    -       -      P      12           -
LGA    -       -      N      13           -
LGA    M       8      A      14           #
LGA    Y       9      V      15          4.988
LGA    K      10      -       -           -
LGA    Y      11      -       -           -
LGA    P      12      -       -           -
LGA    N      13      -       -           -
LGA    A      14      -       -           -
LGA    V      15      -       -           -
LGA    S      16      -       -           -
LGA    R      17      -       -           -
LGA    K      18      -       -           -
LGA    D      19      S      16           #
LGA    -       -      R      17           -
LGA    -       -      K      18           -
LGA    -       -      D      19           -
LGA    -       -      F      20           -
LGA    F      20      E      21          4.319
LGA    E      21      L      22          4.179
LGA    L      22      R      23          0.682
LGA    R      23      N      24          1.256
LGA    N      24      D      25          3.190
LGA    D      25      G      26          2.969
LGA    G      26      N      27          3.336
LGA    N      27      G      28          1.432
LGA    G      28      S      29           #
LGA    S      29      Y      30          3.572
LGA    Y      30      -       -           -
LGA    I      31      -       -           -
LGA    E      32      -       -           -
LGA    K      33      I      31          4.443
LGA    W      34      E      32           -
LGA    N      35      K      33           -
LGA    L      36      W      34           -
LGA    R      37      N      35           #
LGA    A      38      L      36          2.216
LGA    P      39      R      37          0.839
LGA    L      40      A      38          1.955
LGA    P      41      P      39          3.056
LGA    T      42      L      40          4.018
LGA    Q      43      P      41          2.750
LGA    A      44      -       -           -
LGA    E      45      -       -           -
LGA    L      46      -       -           -
LGA    E      47      T      42           #
LGA    T      48      -       -           -
LGA    W      49      -       -           -
LGA    W      50      -       -           -
LGA    E      51      -       -           -
LGA    E      52      -       -           -
LGA    L      53      -       -           -
LGA    Q      54      -       -           -
LGA    K      55      -       -           -
LGA    N      56      -       -           -
LGA    P      57      -       -           -
LGA    P      58      -       -           -
LGA    Y      59      -       -           -
LGA    E      60      -       -           -
LGA    P      61      -       -           -
LGA    P      62      -       -           -
LGA    D      63      -       -           -
LGA    Q      64      -       -           -
LGA    V      65      -       -           -
LGA    E      66      -       -           -
LGA    L      67      -       -           -
LGA    L      68      -       -           -
LGA    A      69      -       -           -
LGA    Q      70      -       -           -
LGA    E      71      -       -           -
LGA    L      72      -       -           -
LGA    S      73      -       -           -
LGA    Q      74      -       -           -
LGA    E      75      -       -           -
LGA    K      76      -       -           -
LGA    L      77      Q      43           #
LGA    -       -      A      44           -
LGA    A      78      E      45          5.436
LGA    R      79      L      46          4.067
LGA    K      80      E      47          4.096
LGA    Q      81      T      48          3.477
LGA    L      82      W      49          2.158
LGA    E      83      W      50          1.514
LGA    E      84      E      51          1.328
LGA    L      85      E      52          1.114
LGA    N      86      L      53          1.122
LGA    K      87      Q      54          2.498
LGA    T      88      K      55          3.111
LGA    L      89      N      56          3.667
LGA    G      90      -       -           -
LGA    N      91      -       -           -
LGA    E      92      -       -           -
LGA    L      93      -       -           -
LGA    S      94      -       -           -
LGA    D      95      -       -           -
LGA    I      96      -       -           -
LGA    K      97      -       -           -
LGA    L      98      -       -           -
LGA    S      99      -       -           -
LGA    L     100      -       -           -
LGA    L     101      -       -           -
LGA    S     102      -       -           -
LGA    L     103      -       -           -
LGA    K     104      -       -           -
LGA    G     105      -       -           -
LGA    D     106      -       -           -
LGA    Y     107      -       -           -
LGA    A     108      -       -           -
LGA    E     109      -       -           -
LGA    L     110      -       -           -
LGA    E     111      -       -           -
LGA    H     112      -       -           -
LGA    H     113      -       -           -
LGA    H     114      -       -           -
LGA    H     115      -       -           -
LGA    H     116      -       -           -
LGA    H     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  117   56    5.0     30    3.20     6.67     34.733     0.910

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.158339 * X  +  -0.684188 * Y  +   0.711910 * Z  +  -0.681064
  Y_new =  -0.372577 * X  +  -0.626305 * Y  +  -0.684783 * Z  +  -0.662061
  Z_new =   0.914393 * X  +  -0.373670 * Y  +  -0.155744 * Z  +   0.832307 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.965698    1.175895  [ DEG:  -112.6262     67.3738 ]
  Theta =  -1.154006   -1.987586  [ DEG:   -66.1197   -113.8803 ]
  Phi   =  -1.972654    1.168939  [ DEG:  -113.0247     66.9753 ]
 
# 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: T0351TS168_1                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351TS168_1.T0351.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117   56   5.0   30   3.20    6.67  34.733
REMARK  ---------------------------------------------------------- 
MOLECULE T0351TS168_1
PFRMAT TS
TARGET T0351
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      -1.308 -11.580  12.463  1.00 25.00           C
ATOM      2  CA  ILE     2       1.423  -9.086  11.507  1.00 25.00           C
ATOM      3  CA  LEU     3       2.726  -5.612  12.501  1.00 25.00           C
ATOM      4  CA  TYR     4       6.193  -4.038  12.778  1.00 25.00           C
ATOM      5  CA  ASP     5       7.107  -0.483  13.767  1.00 25.00           C
ATOM      6  CA  ALA     6       5.767   1.620  10.956  1.00 25.00           C
ATOM      7  CA  ILE     7       4.224   3.372   8.001  1.00 25.00           C
ATOM      8  CA  MET     8       2.345   6.001   5.991  1.00 25.00           C
ATOM      9  CA  TYR     9       0.105   6.806   3.021  1.00 25.00           C
ATOM     10  CA  LYS    10      -3.566   6.014   3.068  1.00 25.00           C
ATOM     11  CA  TYR    11      -5.947   8.430   1.256  1.00 25.00           C
ATOM     12  CA  PRO    12      -8.294   8.971  -1.722  1.00 25.00           C
ATOM     13  CA  ASN    13      -8.331  12.607  -2.977  1.00 25.00           C
ATOM     14  CA  ALA    14      -6.442  13.720   0.097  1.00 25.00           C
ATOM     15  CA  VAL    15      -6.354  17.536  -0.477  1.00 25.00           C
ATOM     16  CA  SER    16      -5.147  21.013   0.602  1.00 25.00           C
ATOM     17  CA  ARG    17      -5.643  19.640   4.053  1.00 25.00           C
ATOM     18  CA  LYS    18      -4.393  17.733   7.153  1.00 25.00           C
ATOM     19  CA  ASP    19      -3.550  14.101   6.406  1.00 25.00           C
ATOM     20  CA  PHE    20      -7.151  13.651   5.263  1.00 25.00           C
ATOM     21  CA  GLU    21      -8.788  10.613   6.722  1.00 25.00           C
ATOM     22  CA  LEU    22      -9.812   7.267   5.278  1.00 25.00           C
ATOM     23  CA  ARG    23     -12.394   5.455   7.450  1.00 25.00           C
ATOM     24  CA  ASN    24     -12.111   2.561   4.971  1.00 25.00           C
ATOM     25  CA  ASP    25     -14.202   0.604   7.560  1.00 25.00           C
ATOM     26  CA  GLY    26     -12.567  -2.362   5.811  1.00 25.00           C
ATOM     27  CA  ASN    27      -9.303  -2.068   7.746  1.00 25.00           C
ATOM     28  CA  GLY    28      -7.361  -2.650   4.553  1.00 25.00           C
ATOM     29  CA  SER    29      -6.307   1.016   4.719  1.00 25.00           C
ATOM     30  CA  TYR    30      -2.863   0.673   3.176  1.00 25.00           C
ATOM     31  CA  ILE    31      -0.983  -1.100   0.349  1.00 25.00           C
ATOM     32  CA  GLU    32      -3.946  -0.536  -2.010  1.00 25.00           C
ATOM     33  CA  LYS    33      -4.029   3.173  -1.059  1.00 25.00           C
ATOM     34  CA  TRP    34      -0.268   3.453  -1.724  1.00 25.00           C
ATOM     35  CA  ASN    35       2.761   4.187  -3.934  1.00 25.00           C
ATOM     36  CA  LEU    36       3.950   6.138  -0.834  1.00 25.00           C
ATOM     37  CA  ARG    37       3.943   9.882  -1.685  1.00 25.00           C
ATOM     38  CA  ALA    38       2.500   9.198  -5.148  1.00 25.00           C
ATOM     39  CA  PRO    39       3.004  10.074  -8.856  1.00 25.00           C
ATOM     40  CA  LEU    40       0.361   7.743 -10.286  1.00 25.00           C
ATOM     41  CA  PRO    41       0.034   5.620 -13.434  1.00 25.00           C
ATOM     42  CA  THR    42      -2.560   3.080 -12.401  1.00 25.00           C
ATOM     43  CA  GLN    43      -2.966   2.131  -8.782  1.00 25.00           C
ATOM     44  CA  ALA    44      -3.227   5.671  -7.343  1.00 25.00           C
ATOM     45  CA  GLU    45      -5.312   6.770 -10.362  1.00 25.00           C
ATOM     46  CA  LEU    46      -7.621   3.750  -9.898  1.00 25.00           C
ATOM     47  CA  GLU    47      -8.030   4.602  -6.187  1.00 25.00           C
ATOM     48  CA  THR    48      -8.873   8.228  -7.087  1.00 25.00           C
ATOM     49  CA  TRP    49     -11.466   7.018  -9.632  1.00 25.00           C
ATOM     50  CA  TRP    50     -13.017   4.715  -6.995  1.00 25.00           C
ATOM     51  CA  GLU    51     -13.180   7.625  -4.512  1.00 25.00           C
ATOM     52  CA  GLU    52     -14.868   9.820  -7.158  1.00 25.00           C
ATOM     53  CA  LEU    53     -17.413   7.049  -7.868  1.00 25.00           C
ATOM     54  CA  GLN    54     -18.136   6.719  -4.122  1.00 25.00           C
ATOM     55  CA  LYS    55     -18.822  10.443  -3.993  1.00 25.00           C
ATOM     56  CA  ASN    56     -20.870  11.849  -1.155  1.00 25.00           C
ATOM     57  CA  PRO    57     -24.597  12.773  -1.351  1.00 25.00           C
ATOM     58  CA  PRO    58     -26.605   9.552  -0.780  1.00 25.00           C
ATOM     59  CA  TYR    59     -28.013   9.596  -4.314  1.00 25.00           C
ATOM     60  CA  GLU    60     -29.563   6.106  -4.007  1.00 25.00           C
ATOM     61  CA  PRO    61     -29.453   2.429  -5.000  1.00 25.00           C
ATOM     62  CA  PRO    62     -29.428  -0.857  -6.861  1.00 25.00           C
ATOM     63  CA  ASP    63     -27.035  -1.797  -9.699  1.00 25.00           C
ATOM     64  CA  GLN    64     -24.742   1.125  -8.765  1.00 25.00           C
ATOM     65  CA  VAL    65     -24.770   0.010  -5.102  1.00 25.00           C
ATOM     66  CA  GLU    66     -23.892  -3.566  -6.158  1.00 25.00           C
ATOM     67  CA  LEU    67     -21.008  -2.249  -8.306  1.00 25.00           C
ATOM     68  CA  LEU    68     -19.726  -0.172  -5.354  1.00 25.00           C
ATOM     69  CA  ALA    69     -19.895  -3.251  -3.083  1.00 25.00           C
ATOM     70  CA  GLN    70     -17.957  -5.299  -5.674  1.00 25.00           C
ATOM     71  CA  GLU    71     -15.300  -2.549  -5.896  1.00 25.00           C
ATOM     72  CA  LEU    72     -15.000  -2.496  -2.078  1.00 25.00           C
ATOM     73  CA  SER    73     -14.600  -6.306  -2.032  1.00 25.00           C
ATOM     74  CA  GLN    74     -11.878  -6.076  -4.717  1.00 25.00           C
ATOM     75  CA  GLU    75     -10.061  -3.388  -2.681  1.00 25.00           C
ATOM     76  CA  LYS    76     -10.253  -5.591   0.445  1.00 25.00           C
ATOM     77  CA  LEU    77      -8.841  -8.555  -1.526  1.00 25.00           C
ATOM     78  CA  ALA    78      -5.979  -6.363  -2.819  1.00 25.00           C
ATOM     79  CA  ARG    79      -5.224  -5.201   0.751  1.00 25.00           C
ATOM     80  CA  LYS    80      -5.187  -8.838   1.953  1.00 25.00           C
ATOM     81  CA  GLN    81      -2.794  -9.777  -0.885  1.00 25.00           C
ATOM     82  CA  LEU    82      -0.500  -6.855   0.048  1.00 25.00           C
ATOM     83  CA  GLU    83      -0.529  -7.971   3.712  1.00 25.00           C
ATOM     84  CA  GLU    84       0.349 -11.547   2.655  1.00 25.00           C
ATOM     85  CA  LEU    85       3.234 -10.229   0.508  1.00 25.00           C
ATOM     86  CA  ASN    86       4.515  -8.152   3.459  1.00 25.00           C
ATOM     87  CA  LYS    87       4.347 -11.231   5.731  1.00 25.00           C
ATOM     88  CA  THR    88       6.285 -13.279   3.140  1.00 25.00           C
ATOM     89  CA  LEU    89       8.941 -10.530   2.917  1.00 25.00           C
ATOM     90  CA  GLY    90       9.241 -10.477   6.735  1.00 25.00           C
ATOM     91  CA  ASN    91       9.642 -14.286   6.780  1.00 25.00           C
ATOM     92  CA  GLU    92      12.364 -14.056   4.096  1.00 25.00           C
ATOM     93  CA  LEU    93      14.180 -11.369   6.132  1.00 25.00           C
ATOM     94  CA  SER    94      13.988 -13.571   9.259  1.00 25.00           C
ATOM     95  CA  ASP    95      15.400 -16.535   7.286  1.00 25.00           C
ATOM     96  CA  ILE    96      18.262 -14.344   5.994  1.00 25.00           C
ATOM     97  CA  LYS    97      19.017 -13.182   9.564  1.00 25.00           C
ATOM     98  CA  LEU    98      19.054 -16.818  10.766  1.00 25.00           C
ATOM     99  CA  SER    99      21.448 -17.757   7.927  1.00 25.00           C
ATOM    100  CA  LEU   100      23.741 -14.836   8.861  1.00 25.00           C
ATOM    101  CA  LEU   101      23.712 -15.952  12.525  1.00 25.00           C
ATOM    102  CA  SER   102      24.590 -19.527  11.467  1.00 25.00           C
ATOM    103  CA  LEU   103      27.587 -18.003   9.585  1.00 25.00           C
ATOM    104  CA  LYS   104      29.805 -15.629   7.618  1.00 25.00           C
ATOM    105  CA  GLY   105      32.381 -13.532   5.756  1.00 25.00           C
ATOM    106  CA  ASP   106      32.255 -11.203   2.687  1.00 25.00           C
ATOM    107  CA  TYR   107      31.089  -8.311   4.877  1.00 25.00           C
ATOM    108  CA  ALA   108      32.377  -5.056   3.324  1.00 25.00           C
ATOM    109  CA  GLU   109      28.933  -4.402   1.780  1.00 25.00           C
ATOM    110  CA  LEU   110      27.268  -5.017   5.173  1.00 25.00           C
ATOM    111  CA  GLU   111      29.715  -2.590   6.842  1.00 25.00           C
ATOM    112  CA  HIS   112      28.957   0.049   4.173  1.00 25.00           C
ATOM    113  CA  HIS   113      26.078   2.248   3.072  1.00 25.00           C
ATOM    114  CA  HIS   114      25.507  -0.106   0.157  1.00 25.00           C
ATOM    115  CA  HIS   115      21.747  -0.330  -0.270  1.00 25.00           C
ATOM    116  CA  HIS   116      21.488  -0.417  -4.041  1.00 25.00           C
ATOM    117  CA  HIS   117      17.746  -1.087  -3.884  1.00 25.00           C
TER
END
