
#######################################################
#                                                     #
#                        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  103 (  103),  selected  103 , name T0314TS168_3-D1
# Molecule2: number of CA atoms  103 ( 1643),  selected  103 , name T0314_D1.pdb
# PARAMETERS: T0314TS168_3-D1.T0314_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    S       2      S       2           -
LGA    I       3      I       3           -
LGA    T       4      T       4           -
LGA    -       -      S       5           -
LGA    -       -      T       6           -
LGA    -       -      D       7           -
LGA    -       -      I       8           -
LGA    -       -      C       9           -
LGA    -       -      Q      10           -
LGA    S       5      A      11           #
LGA    -       -      A      12           -
LGA    T       6      D      13          3.075
LGA    D       7      A      14           #
LGA    I       8      L      15          4.727
LGA    C       9      K      16          1.854
LGA    Q      10      -       -           -
LGA    A      11      G      17          3.315
LGA    A      12      F      18          2.354
LGA    D      13      -       -           -
LGA    A      14      -       -           -
LGA    L      15      V      19           #
LGA    K      16      -       -           -
LGA    G      17      -       -           -
LGA    F      18      G      20          3.183
LGA    V      19      F      21          4.373
LGA    G      20      N      22          2.140
LGA    F      21      R      23          2.491
LGA    N      22      K      24          1.818
LGA    R      23      T      25          5.019
LGA    K      24      G      26          4.230
LGA    T      25      -       -           -
LGA    G      26      R      27          3.235
LGA    R      27      Y      28           #
LGA    Y      28      I      29          3.208
LGA    I      29      V      30           #
LGA    -       -      R      31           -
LGA    -       -      F      32           -
LGA    -       -      S      33           -
LGA    -       -      E      34           -
LGA    -       -      D      35           -
LGA    -       -      S      36           -
LGA    -       -      F      37           -
LGA    -       -      G      38           -
LGA    -       -      M      39           -
LGA    -       -      D      40           -
LGA    V      30      V      41           #
LGA    R      31      A      42          4.122
LGA    -       -      D      43           -
LGA    F      32      D      44          0.983
LGA    S      33      S      45          4.878
LGA    E      34      -       -           -
LGA    D      35      -       -           -
LGA    S      36      -       -           -
LGA    F      37      I      46           #
LGA    G      38      T      47          1.900
LGA    M      39      P      48           #
LGA    -       -      T      49           -
LGA    -       -      S      50           -
LGA    -       -      E      51           -
LGA    -       -      F      52           -
LGA    -       -      V      53           -
LGA    -       -      W      54           -
LGA    D      40      S      55           #
LGA    V      41      S      56           -
LGA    A      42      V      57           -
LGA    D      43      R      58           -
LGA    D      44      D      59           -
LGA    S      45      D      60           -
LGA    I      46      V      61           -
LGA    T      47      M      62           -
LGA    P      48      R      63           -
LGA    T      49      L      64           -
LGA    S      50      G      65           -
LGA    E      51      R      66           -
LGA    F      52      E      67           -
LGA    V      53      Q      68           -
LGA    W      54      L      69           -
LGA    S      55      Q      70           -
LGA    S      56      I      71           -
LGA    V      57      L      72           -
LGA    R      58      L      73           -
LGA    D      59      -       -           -
LGA    D      60      -       -           -
LGA    V      61      -       -           -
LGA    M      62      E      74           #
LGA    R      63      Q      75          4.307
LGA    L      64      -       -           -
LGA    G      65      -       -           -
LGA    R      66      N      76          2.562
LGA    E      67      I      77          2.196
LGA    Q      68      N      78          3.878
LGA    L      69      E      79           -
LGA    Q      70      R      80           -
LGA    -       -      L      81           -
LGA    -       -      N      82           -
LGA    I      71      I      83          3.681
LGA    L      72      G      84           #
LGA    L      73      E      85           -
LGA    E      74      P      86           #
LGA    Q      75      L      87          0.863
LGA    -       -      L      88           -
LGA    -       -      V      89           -
LGA    N      76      Y      90          2.401
LGA    I      77      L      91          3.097
LGA    N      78      R      92           #
LGA    E      79      -       -           -
LGA    R      80      R      93          3.651
LGA    L      81      Q      94          3.077
LGA    N      82      D      95          2.038
LGA    I      83      L      96          2.300
LGA    G      84      P      97          4.846
LGA    E      85      E      98          4.176
LGA    P      86      I      99          3.156
LGA    L      87      T     100          1.720
LGA    L      88      -       -           -
LGA    V      89      -       -           -
LGA    Y      90      A     101          1.317
LGA    L      91      Q     102          3.945
LGA    R      92      -       -           -
LGA    R      93      R     103          3.208
LGA    Q      94      -       -           -
LGA    D      95      -       -           -
LGA    L      96      -       -           -
LGA    P      97      -       -           -
LGA    E      98      -       -           -
LGA    I      99      -       -           -
LGA    T     100      -       -           -
LGA    A     101      -       -           -
LGA    Q     102      -       -           -
LGA    R     103      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  103  103    5.0     37    3.26    13.51     20.165     1.102

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.902501 * X  +  -0.084305 * Y  +  -0.422357 * Z  +  18.373928
  Y_new =   0.327855 * X  +   0.770411 * Y  +   0.546788 * Z  +   7.232782
  Z_new =   0.279292 * X  +  -0.631948 * Y  +   0.722937 * Z  + -18.105736 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.718343    2.423249  [ DEG:   -41.1580    138.8420 ]
  Theta =  -0.283056   -2.858536  [ DEG:   -16.2179   -163.7821 ]
  Phi   =   0.348451   -2.793142  [ DEG:    19.9648   -160.0352 ]
 
# 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: T0314TS168_3-D1                               
REMARK     2: T0314_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0314TS168_3-D1.T0314_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  103  103   5.0   37   3.26   13.51  20.165
REMARK  ---------------------------------------------------------- 
MOLECULE T0314TS168_3-D1
PFRMAT TS
TARGET T0314
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      21.644  16.027  -5.028  1.00 25.00           C
ATOM      2  CA  SER     2      22.411  17.155  -8.598  1.00 25.00           C
ATOM      3  CA  ILE     3      21.907  14.931 -11.621  1.00 25.00           C
ATOM      4  CA  THR     4      18.389  13.617 -11.027  1.00 25.00           C
ATOM      5  CA  SER     5      16.030  10.892 -12.278  1.00 25.00           C
ATOM      6  CA  THR     6      16.847   8.938  -9.086  1.00 25.00           C
ATOM      7  CA  ASP     7      16.073   5.643 -10.877  1.00 25.00           C
ATOM      8  CA  ILE     8      18.346   6.661 -13.786  1.00 25.00           C
ATOM      9  CA  CYS     9      21.151   7.523 -11.325  1.00 25.00           C
ATOM     10  CA  GLN    10      20.724   4.125  -9.611  1.00 25.00           C
ATOM     11  CA  ALA    11      20.888   2.364 -13.007  1.00 25.00           C
ATOM     12  CA  ALA    12      24.078   4.294 -13.882  1.00 25.00           C
ATOM     13  CA  ASP    13      25.628   3.305 -10.522  1.00 25.00           C
ATOM     14  CA  ALA    14      24.720  -0.362 -11.154  1.00 25.00           C
ATOM     15  CA  LEU    15      26.306  -0.180 -14.635  1.00 25.00           C
ATOM     16  CA  LYS    16      29.391   1.997 -14.342  1.00 25.00           C
ATOM     17  CA  GLY    17      28.392   3.738 -17.572  1.00 25.00           C
ATOM     18  CA  PHE    18      26.374   1.409 -19.741  1.00 25.00           C
ATOM     19  CA  VAL    19      27.501   0.088 -23.107  1.00 25.00           C
ATOM     20  CA  GLY    20      28.102  -2.649 -25.636  1.00 25.00           C
ATOM     21  CA  PHE    21      26.762  -6.238 -25.890  1.00 25.00           C
ATOM     22  CA  ASN    22      28.329  -9.754 -25.614  1.00 25.00           C
ATOM     23  CA  ARG    23      27.322  -9.907 -29.320  1.00 25.00           C
ATOM     24  CA  LYS    24      23.557 -10.607 -29.144  1.00 25.00           C
ATOM     25  CA  THR    25      22.291 -10.784 -25.584  1.00 25.00           C
ATOM     26  CA  GLY    26      20.112  -8.443 -23.513  1.00 25.00           C
ATOM     27  CA  ARG    27      23.401  -7.075 -22.111  1.00 25.00           C
ATOM     28  CA  TYR    28      24.701  -3.682 -21.002  1.00 25.00           C
ATOM     29  CA  ILE    29      22.476  -1.117 -22.797  1.00 25.00           C
ATOM     30  CA  VAL    30      23.259   2.235 -24.447  1.00 25.00           C
ATOM     31  CA  ARG    31      25.409   5.286 -25.166  1.00 25.00           C
ATOM     32  CA  PHE    32      24.624   8.187 -27.421  1.00 25.00           C
ATOM     33  CA  SER    33      24.437  10.161 -24.219  1.00 25.00           C
ATOM     34  CA  GLU    34      27.032  12.939 -24.408  1.00 25.00           C
ATOM     35  CA  ASP    35      29.997  11.174 -22.805  1.00 25.00           C
ATOM     36  CA  SER    36      27.701   9.494 -20.353  1.00 25.00           C
ATOM     37  CA  PHE    37      24.494  11.315 -19.262  1.00 25.00           C
ATOM     38  CA  GLY    38      21.221   9.460 -19.981  1.00 25.00           C
ATOM     39  CA  MET    39      21.379   5.915 -21.469  1.00 25.00           C
ATOM     40  CA  ASP    40      19.260   6.820 -24.460  1.00 25.00           C
ATOM     41  CA  VAL    41      18.166   4.680 -27.480  1.00 25.00           C
ATOM     42  CA  ALA    42      17.134   1.487 -29.338  1.00 25.00           C
ATOM     43  CA  ASP    43      15.178   3.583 -31.752  1.00 25.00           C
ATOM     44  CA  ASP    44      16.058   5.843 -34.738  1.00 25.00           C
ATOM     45  CA  SER    45      19.353   4.684 -36.242  1.00 25.00           C
ATOM     46  CA  ILE    46      21.488   3.750 -33.235  1.00 25.00           C
ATOM     47  CA  THR    47      24.948   3.313 -31.864  1.00 25.00           C
ATOM     48  CA  PRO    48      28.468   1.929 -32.018  1.00 25.00           C
ATOM     49  CA  THR    49      29.631   2.797 -28.472  1.00 25.00           C
ATOM     50  CA  SER    50      30.270   6.057 -26.583  1.00 25.00           C
ATOM     51  CA  GLU    51      32.286   6.355 -23.303  1.00 25.00           C
ATOM     52  CA  PHE    52      31.440   2.951 -21.809  1.00 25.00           C
ATOM     53  CA  VAL    53      32.422  -0.339 -20.167  1.00 25.00           C
ATOM     54  CA  TRP    54      32.198  -4.115 -20.097  1.00 25.00           C
ATOM     55  CA  SER    55      30.964  -3.687 -16.508  1.00 25.00           C
ATOM     56  CA  SER    56      30.303  -5.772 -13.413  1.00 25.00           C
ATOM     57  CA  VAL    57      29.437  -9.493 -13.367  1.00 25.00           C
ATOM     58  CA  ARG    58      27.444  -8.634 -16.523  1.00 25.00           C
ATOM     59  CA  ASP    59      24.503 -10.743 -15.269  1.00 25.00           C
ATOM     60  CA  ASP    60      24.635  -8.958 -11.883  1.00 25.00           C
ATOM     61  CA  VAL    61      24.649  -5.559 -13.648  1.00 25.00           C
ATOM     62  CA  MET    62      21.630  -6.614 -15.756  1.00 25.00           C
ATOM     63  CA  ARG    63      19.783  -7.737 -12.595  1.00 25.00           C
ATOM     64  CA  LEU    64      20.561  -4.381 -10.920  1.00 25.00           C
ATOM     65  CA  GLY    65      19.257  -2.513 -13.998  1.00 25.00           C
ATOM     66  CA  ARG    66      16.050  -4.606 -13.939  1.00 25.00           C
ATOM     67  CA  GLU    67      15.587  -3.837 -10.216  1.00 25.00           C
ATOM     68  CA  GLN    68      16.072  -0.101 -10.902  1.00 25.00           C
ATOM     69  CA  LEU    69      13.485  -0.256 -13.722  1.00 25.00           C
ATOM     70  CA  GLN    70      11.016  -2.029 -11.391  1.00 25.00           C
ATOM     71  CA  ILE    71      11.579   0.654  -8.716  1.00 25.00           C
ATOM     72  CA  LEU    72      10.971   3.404 -11.312  1.00 25.00           C
ATOM     73  CA  LEU    73       7.737   1.677 -12.420  1.00 25.00           C
ATOM     74  CA  GLU    74       6.587   1.437  -8.775  1.00 25.00           C
ATOM     75  CA  GLN    75       7.338   5.159  -8.267  1.00 25.00           C
ATOM     76  CA  ASN    76       5.346   6.016 -11.423  1.00 25.00           C
ATOM     77  CA  ILE    77       2.405   3.908 -10.170  1.00 25.00           C
ATOM     78  CA  ASN    78       2.537   5.693  -6.784  1.00 25.00           C
ATOM     79  CA  GLU    79       2.550   9.091  -8.548  1.00 25.00           C
ATOM     80  CA  ARG    80      -0.468   8.037 -10.657  1.00 25.00           C
ATOM     81  CA  LEU    81      -2.316   6.915  -7.495  1.00 25.00           C
ATOM     82  CA  ASN    82      -1.883  10.450  -6.027  1.00 25.00           C
ATOM     83  CA  ILE    83      -1.546  12.736  -9.093  1.00 25.00           C
ATOM     84  CA  GLY    84      -1.712  15.867 -11.264  1.00 25.00           C
ATOM     85  CA  GLU    85       1.821  15.770 -12.771  1.00 25.00           C
ATOM     86  CA  PRO    86       5.376  16.692 -11.684  1.00 25.00           C
ATOM     87  CA  LEU    87       6.684  15.879 -15.191  1.00 25.00           C
ATOM     88  CA  LEU    88       3.946  18.058 -16.744  1.00 25.00           C
ATOM     89  CA  VAL    89       4.859  20.932 -14.383  1.00 25.00           C
ATOM     90  CA  TYR    90       8.551  20.572 -15.335  1.00 25.00           C
ATOM     91  CA  LEU    91       7.626  20.642 -19.051  1.00 25.00           C
ATOM     92  CA  ARG    92       5.526  23.796 -18.494  1.00 25.00           C
ATOM     93  CA  ARG    93       8.451  25.449 -16.657  1.00 25.00           C
ATOM     94  CA  GLN    94       7.897  29.185 -16.201  1.00 25.00           C
ATOM     95  CA  ASP    95       7.496  29.841 -19.934  1.00 25.00           C
ATOM     96  CA  LEU    96      10.209  27.528 -21.175  1.00 25.00           C
ATOM     97  CA  PRO    97      12.691  25.784 -23.402  1.00 25.00           C
ATOM     98  CA  GLU    98      13.172  28.517 -26.041  1.00 25.00           C
ATOM     99  CA  ILE    99      13.620  31.136 -23.283  1.00 25.00           C
ATOM    100  CA  THR   100      16.207  28.907 -21.552  1.00 25.00           C
ATOM    101  CA  ALA   101      18.086  28.475 -24.861  1.00 25.00           C
ATOM    102  CA  GLN   102      18.070  32.268 -25.393  1.00 25.00           C
ATOM    103  CA  ARG   103      19.422  32.796 -21.849  1.00 25.00           C
TER
END
