
#######################################################
#                                                     #
#                        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_4
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351TS168_4.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      -       -           -
LGA    I       7      -       -           -
LGA    M       8      -       -           -
LGA    Y       9      -       -           -
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      -       -           -
LGA    F      20      -       -           -
LGA    E      21      -       -           -
LGA    L      22      -       -           -
LGA    R      23      -       -           -
LGA    N      24      -       -           -
LGA    D      25      -       -           -
LGA    G      26      -       -           -
LGA    N      27      -       -           -
LGA    G      28      -       -           -
LGA    S      29      -       -           -
LGA    Y      30      -       -           -
LGA    I      31      A       6          4.403
LGA    -       -      I       7           -
LGA    -       -      M       8           -
LGA    E      32      Y       9          1.812
LGA    K      33      K      10          3.870
LGA    W      34      Y      11          2.220
LGA    N      35      P      12          2.669
LGA    L      36      N      13          3.629
LGA    R      37      A      14          4.122
LGA    A      38      V      15          2.594
LGA    P      39      S      16          3.017
LGA    L      40      R      17          4.802
LGA    P      41      K      18          4.721
LGA    -       -      D      19           -
LGA    -       -      F      20           -
LGA    -       -      E      21           -
LGA    T      42      L      22          2.773
LGA    Q      43      R      23           #
LGA    -       -      N      24           -
LGA    -       -      D      25           -
LGA    -       -      G      26           -
LGA    -       -      N      27           -
LGA    -       -      G      28           -
LGA    -       -      S      29           -
LGA    -       -      Y      30           -
LGA    -       -      I      31           -
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    A      44      W      34          1.989
LGA    E      45      N      35          4.735
LGA    L      46      -       -           -
LGA    E      47      L      36           #
LGA    T      48      R      37          5.232
LGA    W      49      A      38          2.143
LGA    W      50      P      39          1.861
LGA    E      51      L      40          4.826
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      P      41           #
LGA    L      72      T      42          0.655
LGA    S      73      Q      43          0.730
LGA    Q      74      A      44          0.821
LGA    E      75      E      45          0.443
LGA    K      76      L      46          0.436
LGA    L      77      E      47          0.735
LGA    A      78      T      48          0.451
LGA    R      79      W      49          0.797
LGA    K      80      W      50          0.908
LGA    Q      81      E      51          0.237
LGA    L      82      E      52          0.819
LGA    E      83      L      53          1.236
LGA    E      84      Q      54          0.869
LGA    L      85      K      55          1.022
LGA    N      86      N      56          1.839
LGA    K      87      -       -           -
LGA    T      88      -       -           -
LGA    L      89      -       -           -
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     33    2.73     9.09     41.041     1.167

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.958358 * X  +  -0.067711 * Y  +   0.277425 * Z  +   6.367302
  Y_new =  -0.153238 * X  +  -0.697831 * Y  +  -0.699678 * Z  +  -2.826992
  Z_new =   0.240972 * X  +  -0.713054 * Y  +   0.658397 * Z  +   0.547842 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.825231    2.316361  [ DEG:   -47.2823    132.7177 ]
  Theta =  -0.243367   -2.898226  [ DEG:   -13.9439   -166.0561 ]
  Phi   =  -2.983038    0.158554  [ DEG:  -170.9155      9.0845 ]
 
# 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_4                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351TS168_4.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   33   2.73    9.09  41.041
REMARK  ---------------------------------------------------------- 
MOLECULE T0351TS168_4
PFRMAT TS
TARGET T0351
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1       9.230 -17.904  -0.244  1.00 25.00           C
ATOM      2  CA  ILE     2      11.148 -14.680   0.397  1.00 25.00           C
ATOM      3  CA  LEU     3      13.265 -12.470   2.644  1.00 25.00           C
ATOM      4  CA  TYR     4      16.742 -12.324   4.237  1.00 25.00           C
ATOM      5  CA  ASP     5      19.246 -10.461   2.175  1.00 25.00           C
ATOM      6  CA  ALA     6      16.580  -7.825   2.010  1.00 25.00           C
ATOM      7  CA  ILE     7      15.278  -4.741   0.238  1.00 25.00           C
ATOM      8  CA  MET     8      14.315  -1.087   0.662  1.00 25.00           C
ATOM      9  CA  TYR     9      12.386   0.046  -2.427  1.00 25.00           C
ATOM     10  CA  LYS    10      11.084   3.345  -3.755  1.00 25.00           C
ATOM     11  CA  TYR    11       7.851   3.815  -5.700  1.00 25.00           C
ATOM     12  CA  PRO    12       6.366   5.762  -8.566  1.00 25.00           C
ATOM     13  CA  ASN    13       6.495   9.414  -9.555  1.00 25.00           C
ATOM     14  CA  ALA    14       9.288  11.658  -8.363  1.00 25.00           C
ATOM     15  CA  VAL    15      10.337  15.348  -8.495  1.00 25.00           C
ATOM     16  CA  SER    16      13.935  16.511  -7.721  1.00 25.00           C
ATOM     17  CA  ARG    17      15.768  13.206  -7.024  1.00 25.00           C
ATOM     18  CA  LYS    18      16.737  11.846 -10.475  1.00 25.00           C
ATOM     19  CA  ASP    19      15.701   8.323  -9.569  1.00 25.00           C
ATOM     20  CA  PHE    20      12.247   7.350  -8.289  1.00 25.00           C
ATOM     21  CA  GLU    21      12.095   3.823  -9.768  1.00 25.00           C
ATOM     22  CA  LEU    22      10.213   0.559 -10.252  1.00 25.00           C
ATOM     23  CA  ARG    23       6.427   0.032 -10.611  1.00 25.00           C
ATOM     24  CA  ASN    24       7.009  -3.306 -12.370  1.00 25.00           C
ATOM     25  CA  ASP    25       4.419  -5.975 -13.154  1.00 25.00           C
ATOM     26  CA  GLY    26       4.667  -7.544  -9.750  1.00 25.00           C
ATOM     27  CA  ASN    27       7.362  -7.176  -7.143  1.00 25.00           C
ATOM     28  CA  GLY    28       5.384  -4.950  -4.772  1.00 25.00           C
ATOM     29  CA  SER    29       8.179  -2.444  -4.147  1.00 25.00           C
ATOM     30  CA  TYR    30       5.402   0.001  -3.497  1.00 25.00           C
ATOM     31  CA  ILE    31       3.377  -0.510  -0.287  1.00 25.00           C
ATOM     32  CA  GLU    32       6.613  -0.887   1.725  1.00 25.00           C
ATOM     33  CA  LYS    33       7.984   2.333   0.169  1.00 25.00           C
ATOM     34  CA  TRP    34       4.740   4.169   1.049  1.00 25.00           C
ATOM     35  CA  ASN    35       6.486   4.858   4.406  1.00 25.00           C
ATOM     36  CA  LEU    36      10.166   5.922   4.449  1.00 25.00           C
ATOM     37  CA  ARG    37       8.948   9.129   2.706  1.00 25.00           C
ATOM     38  CA  ALA    38       5.302   9.864   2.056  1.00 25.00           C
ATOM     39  CA  PRO    39       2.475  11.120   4.364  1.00 25.00           C
ATOM     40  CA  LEU    40      -0.342  10.353   1.876  1.00 25.00           C
ATOM     41  CA  PRO    41      -3.111  10.666   4.382  1.00 25.00           C
ATOM     42  CA  THR    42      -5.485   8.660   2.115  1.00 25.00           C
ATOM     43  CA  GLN    43      -6.342   6.198  -0.653  1.00 25.00           C
ATOM     44  CA  ALA    44      -5.839   9.221  -2.950  1.00 25.00           C
ATOM     45  CA  GLU    45      -2.065   8.571  -3.021  1.00 25.00           C
ATOM     46  CA  LEU    46      -2.692   4.895  -3.896  1.00 25.00           C
ATOM     47  CA  GLU    47      -5.060   5.944  -6.717  1.00 25.00           C
ATOM     48  CA  THR    48      -2.425   8.377  -8.059  1.00 25.00           C
ATOM     49  CA  TRP    49       0.216   5.605  -7.968  1.00 25.00           C
ATOM     50  CA  TRP    50      -2.149   3.256  -9.854  1.00 25.00           C
ATOM     51  CA  GLU    51      -2.781   5.966 -12.485  1.00 25.00           C
ATOM     52  CA  GLU    52       0.992   6.495 -12.882  1.00 25.00           C
ATOM     53  CA  LEU    53       1.501   2.723 -13.309  1.00 25.00           C
ATOM     54  CA  GLN    54      -1.261   2.625 -15.960  1.00 25.00           C
ATOM     55  CA  LYS    55       0.451   4.677 -18.669  1.00 25.00           C
ATOM     56  CA  ASN    56       1.295   6.862 -21.593  1.00 25.00           C
ATOM     57  CA  PRO    57      -1.760   8.531 -23.082  1.00 25.00           C
ATOM     58  CA  PRO    58      -5.384   7.536 -23.827  1.00 25.00           C
ATOM     59  CA  TYR    59      -8.399   5.835 -25.445  1.00 25.00           C
ATOM     60  CA  GLU    60     -11.754   4.722 -23.891  1.00 25.00           C
ATOM     61  CA  PRO    61     -13.965   3.132 -21.223  1.00 25.00           C
ATOM     62  CA  PRO    62     -16.148   1.330 -18.680  1.00 25.00           C
ATOM     63  CA  ASP    63     -14.512  -2.059 -19.392  1.00 25.00           C
ATOM     64  CA  GLN    64     -11.041  -0.455 -19.188  1.00 25.00           C
ATOM     65  CA  VAL    65     -11.965   1.176 -15.848  1.00 25.00           C
ATOM     66  CA  GLU    66     -13.198  -2.195 -14.514  1.00 25.00           C
ATOM     67  CA  LEU    67      -9.929  -3.856 -15.620  1.00 25.00           C
ATOM     68  CA  LEU    68      -7.913  -1.108 -13.871  1.00 25.00           C
ATOM     69  CA  ALA    69      -9.965  -1.602 -10.675  1.00 25.00           C
ATOM     70  CA  GLN    70      -9.350  -5.380 -10.836  1.00 25.00           C
ATOM     71  CA  GLU    71      -5.594  -4.774 -11.278  1.00 25.00           C
ATOM     72  CA  LEU    72      -5.596  -2.408  -8.266  1.00 25.00           C
ATOM     73  CA  SER    73      -7.433  -5.037  -6.172  1.00 25.00           C
ATOM     74  CA  GLN    74      -4.876  -7.690  -7.214  1.00 25.00           C
ATOM     75  CA  GLU    75      -2.009  -5.342  -6.248  1.00 25.00           C
ATOM     76  CA  LYS    76      -3.645  -4.704  -2.845  1.00 25.00           C
ATOM     77  CA  LEU    77      -4.026  -8.474  -2.294  1.00 25.00           C
ATOM     78  CA  ALA    78      -0.340  -9.003  -3.191  1.00 25.00           C
ATOM     79  CA  ARG    79       0.679  -6.250  -0.732  1.00 25.00           C
ATOM     80  CA  LYS    80      -1.444  -7.878   2.009  1.00 25.00           C
ATOM     81  CA  GLN    81       0.192 -11.268   1.296  1.00 25.00           C
ATOM     82  CA  LEU    82       3.663  -9.662   1.500  1.00 25.00           C
ATOM     83  CA  GLU    83       2.740  -8.031   4.840  1.00 25.00           C
ATOM     84  CA  GLU    84       1.507 -11.404   6.173  1.00 25.00           C
ATOM     85  CA  LEU    85       4.776 -13.064   5.068  1.00 25.00           C
ATOM     86  CA  ASN    86       6.791 -10.316   6.817  1.00 25.00           C
ATOM     87  CA  LYS    87       4.740 -10.811  10.012  1.00 25.00           C
ATOM     88  CA  THR    88       5.354 -14.588   9.852  1.00 25.00           C
ATOM     89  CA  LEU    89       9.111 -13.982   9.410  1.00 25.00           C
ATOM     90  CA  GLY    90       9.109 -11.616  12.422  1.00 25.00           C
ATOM     91  CA  ASN    91       7.271 -14.244  14.516  1.00 25.00           C
ATOM     92  CA  GLU    92       9.829 -16.898  13.475  1.00 25.00           C
ATOM     93  CA  LEU    93      12.695 -14.550  14.440  1.00 25.00           C
ATOM     94  CA  SER    94      11.059 -13.912  17.844  1.00 25.00           C
ATOM     95  CA  ASP    95      10.678 -17.683  18.394  1.00 25.00           C
ATOM     96  CA  ILE    96      14.364 -18.211  17.497  1.00 25.00           C
ATOM     97  CA  LYS    97      15.382 -15.458  19.957  1.00 25.00           C
ATOM     98  CA  LEU    98      13.261 -17.086  22.697  1.00 25.00           C
ATOM     99  CA  SER    99      14.896 -20.476  21.984  1.00 25.00           C
ATOM    100  CA  LEU   100      18.367 -18.870  22.188  1.00 25.00           C
ATOM    101  CA  LEU   101      17.444 -17.239  25.528  1.00 25.00           C
ATOM    102  CA  SER   102      16.211 -20.611  26.861  1.00 25.00           C
ATOM    103  CA  LEU   103      19.856 -21.547  26.483  1.00 25.00           C
ATOM    104  CA  LYS   104      22.423 -18.903  27.484  1.00 25.00           C
ATOM    105  CA  GLY   105      25.956 -17.539  27.611  1.00 25.00           C
ATOM    106  CA  ASP   106      27.624 -14.377  26.264  1.00 25.00           C
ATOM    107  CA  TYR   107      26.577 -10.695  25.837  1.00 25.00           C
ATOM    108  CA  ALA   108      28.399  -8.042  23.764  1.00 25.00           C
ATOM    109  CA  GLU   109      25.746  -8.329  21.018  1.00 25.00           C
ATOM    110  CA  LEU   110      22.969  -7.932  23.625  1.00 25.00           C
ATOM    111  CA  GLU   111      24.712  -4.833  25.046  1.00 25.00           C
ATOM    112  CA  HIS   112      25.008  -3.355  21.524  1.00 25.00           C
ATOM    113  CA  HIS   113      27.934  -2.897  19.082  1.00 25.00           C
ATOM    114  CA  HIS   114      26.012   0.281  18.214  1.00 25.00           C
ATOM    115  CA  HIS   115      22.787  -1.431  17.018  1.00 25.00           C
ATOM    116  CA  HIS   116      21.109   1.142  19.260  1.00 25.00           C
ATOM    117  CA  HIS   117      18.124   1.175  16.890  1.00 25.00           C
TER
END
