
#######################################################
#                                                     #
#                        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   91 (   91),  selected   91 , name T0350TS599_1-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350TS599_1-D1.T0350_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    N       2      -       -           -
LGA    I       3      -       -           -
LGA    E       4      -       -           -
LGA    R       5      -       -           -
LGA    L       6      -       -           -
LGA    T       7      -       -           -
LGA    T       8      -       -           -
LGA    L       9      -       -           -
LGA    Q      10      -       -           -
LGA    P      11      -       -           -
LGA    V      12      -       -           -
LGA    W      13      -       -           -
LGA    D      14      -       -           -
LGA    R      15      -       -           -
LGA    Y      16      -       -           -
LGA    D      17      -       -           -
LGA    T      18      -       -           -
LGA    Q      19      -       -           -
LGA    I      20      -       -           -
LGA    H      21      -       -           -
LGA    S      36      -       -           -
LGA    Y      37      -       -           -
LGA    T      38      -       -           -
LGA    N      39      -       -           -
LGA    L      40      -       -           -
LGA    A      41      -       -           -
LGA    E      42      -       -           -
LGA    M      43      -       -           -
LGA    V      44      M       1           #
LGA    G      45      N       2           -
LGA    E      46      I       3           -
LGA    M      47      E       4           -
LGA    N      48      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    K      49      T       8          1.864
LGA    L      50      L       9          2.455
LGA    -       -      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      Q      19           -
LGA    -       -      I      20           -
LGA    -       -      H      21           -
LGA    -       -      S      36           -
LGA    -       -      Y      37           -
LGA    -       -      T      38           -
LGA    -       -      N      39           -
LGA    -       -      L      40           -
LGA    -       -      A      41           -
LGA    -       -      E      42           -
LGA    -       -      M      43           -
LGA    -       -      V      44           -
LGA    -       -      G      45           -
LGA    -       -      E      46           -
LGA    -       -      M      47           -
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      E      52           -
LGA    -       -      P      53           -
LGA    L      51      S      54           #
LGA    E      52      Q      55          4.396
LGA    P      53      V      56          4.067
LGA    S      54      -       -           -
LGA    Q      55      H      57          1.718
LGA    V      56      L      58          3.039
LGA    H      57      K      59          1.777
LGA    L      58      F      60          3.118
LGA    K      59      E      61          4.626
LGA    F      60      L      62           #
LGA    E      61      H      63           -
LGA    L      62      D      64           -
LGA    H      63      K      65           -
LGA    D      64      L      66           -
LGA    K      65      N      67           -
LGA    L      66      E      68           -
LGA    N      67      Y      69           -
LGA    E      68      -       -           -
LGA    Y      69      -       -           -
LGA    Y      70      -       -           -
LGA    V      71      Y      70           #
LGA    K      72      V      71          3.469
LGA    V      73      K      72          4.204
LGA    I      74      V      73          2.286
LGA    E      75      I      74          2.153
LGA    D      76      E      75          4.517
LGA    -       -      D      76           -
LGA    -       -      S      77           -
LGA    S      77      T      78          4.253
LGA    T      78      N      79           #
LGA    N      79      E      80          3.869
LGA    E      80      V      81          2.930
LGA    V      81      I      82          3.244
LGA    I      82      R      83          4.588
LGA    R      83      E      84          4.033
LGA    E      84      -       -           -
LGA    I      85      I      85          2.742
LGA    P      86      P      86          2.897
LGA    P      87      P      87          2.627
LGA    K      88      K      88          2.880
LGA    R      89      R      89          2.917
LGA    W      90      W      90          3.184
LGA    L      91      L      91          2.771
LGA    D      92      D      92          1.163
LGA    F      93      F      93          1.482
LGA    Y      94      Y      94          1.830
LGA    A      95      A      95          1.501
LGA    A      96      A      96          1.561
LGA    M      97      M      97          1.301
LGA    T      98      T      98          1.446
LGA    E      99      E      99          2.310
LGA    F     100      F     100          2.439
LGA    L     101      L     101          1.705
LGA    G     102      G     102          1.562
LGA    L     103      L     103          3.187
LGA    F     104      F     104          3.715
LGA    V     105      V     105          3.039

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   91   91    5.0     41    2.98    53.66     29.718     1.331

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.352715 * X  +   0.158936 * Y  +  -0.922134 * Z  +   0.189278
  Y_new =   0.909064 * X  +  -0.291789 * Y  +   0.297424 * Z  +   4.146347
  Z_new =  -0.221797 * X  +  -0.943185 * Y  +  -0.247401 * Z  + -13.349349 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.827321    1.314271  [ DEG:  -104.6978     75.3022 ]
  Theta =   0.223657    2.917936  [ DEG:    12.8146    167.1854 ]
  Phi   =   1.200679   -1.940913  [ DEG:    68.7938   -111.2062 ]
 
# 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: T0350TS599_1-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS599_1-D1.T0350_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   91   91   5.0   41   2.98   53.66  29.718
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS599_1-D1
PFRMAT TS                                                                       
TARGET T0350                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       2.128  13.695 -20.154  1.00  0.00              
ATOM      2  CA  ASN     2       3.339   9.681 -19.804  1.00  0.00              
ATOM      3  CA  ILE     3      -0.401  10.744 -19.124  1.00  0.00              
ATOM      4  CA  GLU     4      -2.670   8.662 -17.116  1.00  0.00              
ATOM      5  CA  ARG     5      -2.755  10.996 -14.093  1.00  0.00              
ATOM      6  CA  LEU     6      -3.965  14.072 -15.981  1.00  0.00              
ATOM      7  CA  THR     7      -6.870  12.275 -17.730  1.00  0.00              
ATOM      8  CA  THR     8      -8.095  10.755 -14.450  1.00  0.00              
ATOM      9  CA  LEU     9      -8.078  14.026 -12.486  1.00  0.00              
ATOM     10  CA  GLN    10     -10.128  15.908 -15.095  1.00  0.00              
ATOM     11  CA  PRO    11     -12.865  13.236 -14.950  1.00  0.00              
ATOM     12  CA  VAL    12     -12.836  13.337 -11.128  1.00  0.00              
ATOM     13  CA  TRP    13     -13.091  17.175 -10.977  1.00  0.00              
ATOM     14  CA  ASP    14     -16.166  16.987 -13.130  1.00  0.00              
ATOM     15  CA  ARG    15     -17.802  14.231 -11.082  1.00  0.00              
ATOM     16  CA  TYR    16     -17.959  15.897  -7.731  1.00  0.00              
ATOM     17  CA  ASP    17     -15.015  15.081  -5.578  1.00  0.00              
ATOM     18  CA  THR    18     -16.939  13.008  -2.960  1.00  0.00              
ATOM     19  CA  GLN    19     -18.457  10.778  -5.673  1.00  0.00              
ATOM     20  CA  ILE    20     -15.024  10.176  -7.271  1.00  0.00              
ATOM     21  CA  HIS    21     -13.378   9.248  -3.994  1.00  0.00              
ATOM     36  CA  SER    36      -6.034 -12.271  -2.780  1.00  0.00              
ATOM     37  CA  TYR    37      -4.315  -9.994  -0.297  1.00  0.00              
ATOM     38  CA  THR    38      -0.947 -11.650  -0.664  1.00  0.00              
ATOM     39  CA  ASN    39      -1.130 -11.391  -4.479  1.00  0.00              
ATOM     40  CA  LEU    40      -2.094  -7.709  -4.297  1.00  0.00              
ATOM     41  CA  ALA    41       0.731  -6.912  -1.973  1.00  0.00              
ATOM     42  CA  GLU    42       3.136  -8.709  -4.354  1.00  0.00              
ATOM     43  CA  MET    43       1.695  -6.716  -7.290  1.00  0.00              
ATOM     44  CA  VAL    44       2.303  -3.409  -5.401  1.00  0.00              
ATOM     45  CA  GLY    45       5.924  -4.386  -4.603  1.00  0.00              
ATOM     46  CA  GLU    46       6.464  -5.254  -8.311  1.00  0.00              
ATOM     47  CA  MET    47       4.939  -1.892  -9.243  1.00  0.00              
ATOM     48  CA  ASN    48       7.225  -0.040  -6.863  1.00  0.00              
ATOM     49  CA  LYS    49      10.141  -1.797  -8.604  1.00  0.00              
ATOM     50  CA  LEU    50       8.793  -0.782 -12.012  1.00  0.00              
ATOM     51  CA  LEU    51       8.491   2.868 -10.891  1.00  0.00              
ATOM     52  CA  GLU    52      12.062   2.866  -9.618  1.00  0.00              
ATOM     53  CA  PRO    53      13.213   1.486 -12.989  1.00  0.00              
ATOM     54  CA  SER    54      11.188   4.181 -14.835  1.00  0.00              
ATOM     55  CA  GLN    55      12.651   6.907 -12.671  1.00  0.00              
ATOM     56  CA  VAL    56      16.117   5.780 -13.949  1.00  0.00              
ATOM     57  CA  HIS    57      15.406   6.911 -17.477  1.00  0.00              
ATOM     58  CA  LEU    58      11.745   7.438 -18.358  1.00  0.00              
ATOM     59  CA  LYS    59      10.604   9.091 -21.521  1.00  0.00              
ATOM     60  CA  PHE    60       6.984  10.277 -21.757  1.00  0.00              
ATOM     61  CA  GLU    61       5.215  10.686 -25.050  1.00  0.00              
ATOM     62  CA  LEU    62       1.795  12.237 -25.157  1.00  0.00              
ATOM     63  CA  HIS    63      -0.318  11.878 -28.182  1.00  0.00              
ATOM     64  CA  ASP    64      -2.592  14.818 -28.608  1.00  0.00              
ATOM     65  CA  LYS    65      -4.961  13.286 -31.069  1.00  0.00              
ATOM     66  CA  LEU    66      -5.662  10.112 -29.223  1.00  0.00              
ATOM     67  CA  ASN    67      -5.336  11.568 -25.741  1.00  0.00              
ATOM     68  CA  GLU    68      -2.997   8.680 -25.066  1.00  0.00              
ATOM     69  CA  TYR    69       0.084   8.534 -22.966  1.00  0.00              
ATOM     70  CA  TYR    70       3.065   6.603 -24.225  1.00  0.00              
ATOM     71  CA  VAL    71       5.844   5.726 -21.881  1.00  0.00              
ATOM     72  CA  LYS    72       9.226   4.898 -23.247  1.00  0.00              
ATOM     73  CA  VAL    73      11.733   3.194 -21.055  1.00  0.00              
ATOM     74  CA  ILE    74      15.340   3.704 -21.829  1.00  0.00              
ATOM     75  CA  GLU    75      18.142   1.989 -19.756  1.00  0.00              
ATOM     76  CA  ASP    76      20.561   4.876 -19.544  1.00  0.00              
ATOM     77  CA  SER    77      23.813   3.211 -19.603  1.00  0.00              
ATOM     78  CA  THR    78      23.293   0.565 -22.227  1.00  0.00              
ATOM     79  CA  ASN    79      20.059   1.562 -24.017  1.00  0.00              
ATOM     80  CA  GLU    80      18.741  -1.924 -23.595  1.00  0.00              
ATOM     81  CA  VAL    81      15.172  -1.936 -22.417  1.00  0.00              
ATOM     82  CA  ILE    82      13.992   0.548 -25.022  1.00  0.00              
ATOM     83  CA  ARG    83      15.652  -1.441 -27.827  1.00  0.00              
ATOM     84  CA  GLU    84      14.094  -4.720 -26.743  1.00  0.00              
ATOM     85  CA  ILE    85      10.619  -3.630 -26.465  1.00  0.00              
ATOM     86  CA  PRO    86       7.954  -4.258 -29.135  1.00  0.00              
ATOM     87  CA  PRO    87       5.680  -1.215 -28.995  1.00  0.00              
ATOM     88  CA  LYS    88       2.673  -3.249 -27.804  1.00  0.00              
ATOM     89  CA  ARG    89       4.487  -4.660 -24.830  1.00  0.00              
ATOM     90  CA  TRP    90       5.713  -1.234 -23.693  1.00  0.00              
ATOM     91  CA  LEU    91       2.143   0.163 -23.819  1.00  0.00              
ATOM     92  CA  ASP    92       0.863  -2.826 -21.797  1.00  0.00              
ATOM     93  CA  PHE    93       3.542  -2.423 -19.145  1.00  0.00              
ATOM     94  CA  TYR    94       2.783   1.334 -18.907  1.00  0.00              
ATOM     95  CA  ALA    95      -0.944   0.599 -18.512  1.00  0.00              
ATOM     96  CA  ALA    96      -0.151  -1.928 -15.776  1.00  0.00              
ATOM     97  CA  MET    97       2.049   0.534 -13.968  1.00  0.00              
ATOM     98  CA  THR    98      -0.503   3.291 -14.001  1.00  0.00              
ATOM     99  CA  GLU    99      -3.180   1.100 -12.574  1.00  0.00              
ATOM    100  CA  PHE   100      -0.963  -0.143  -9.787  1.00  0.00              
ATOM    101  CA  LEU   101       0.961   2.823  -8.366  1.00  0.00              
ATOM    102  CA  GLY   102      -2.117   4.942  -8.555  1.00  0.00              
ATOM    103  CA  LEU   103      -4.325   2.363  -6.967  1.00  0.00              
ATOM    104  CA  PHE   104      -1.975   1.603  -4.067  1.00  0.00              
ATOM    105  CA  VAL   105      -0.801   5.104  -3.367  1.00  0.00              
TER                                                                             
END
