
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350TS599_4-D1.T0350_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    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      N       2          4.070
LGA    G      45      -       -           -
LGA    E      46      I       3           #
LGA    M      47      E       4          2.689
LGA    N      48      R       5          3.917
LGA    K      49      L       6           #
LGA    L      50      T       7          3.215
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           -
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    L      51      P      53          5.201
LGA    E      52      S      54          4.067
LGA    P      53      Q      55          2.757
LGA    S      54      V      56          0.889
LGA    Q      55      H      57          0.409
LGA    V      56      L      58           #
LGA    H      57      K      59           -
LGA    L      58      F      60           -
LGA    K      59      E      61           -
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      Y      70           -
LGA    Y      69      V      71           -
LGA    Y      70      -       -           -
LGA    V      71      -       -           -
LGA    K      72      -       -           -
LGA    V      73      -       -           -
LGA    I      74      K      72           #
LGA    E      75      V      73          3.613
LGA    D      76      I      74          2.628
LGA    -       -      E      75           -
LGA    -       -      D      76           -
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    S      77      N      79          3.649
LGA    T      78      E      80          1.544
LGA    N      79      V      81          0.924
LGA    E      80      I      82          4.540
LGA    V      81      R      83          4.154
LGA    I      82      E      84          1.970
LGA    R      83      -       -           -
LGA    E      84      -       -           -
LGA    I      85      -       -           -
LGA    P      86      -       -           -
LGA    P      87      -       -           -
LGA    K      88      -       -           -
LGA    R      89      I      85           #
LGA    W      90      P      86          1.689
LGA    L      91      P      87          1.531
LGA    D      92      K      88          2.486
LGA    F      93      R      89          2.904
LGA    Y      94      W      90          2.097
LGA    A      95      L      91          1.488
LGA    A      96      D      92          1.043
LGA    M      97      F      93          1.283
LGA    T      98      Y      94          1.413
LGA    E      99      A      95          2.927
LGA    F     100      A      96          3.589
LGA    L     101      M      97          4.426
LGA    G     102      T      98          4.960
LGA    L     103      -       -           -
LGA    F     104      -       -           -
LGA    V     105      E      99          4.135
LGA    -       -      F     100           -
LGA    -       -      L     101           -
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   91   91    5.0     31    3.08     0.00     21.503     0.975

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.835358 * X  +  -0.538706 * Y  +   0.109421 * Z  +   0.118244
  Y_new =  -0.207745 * X  +   0.493674 * Y  +   0.844469 * Z  +   3.231670
  Z_new =  -0.508939 * X  +   0.682702 * Y  +  -0.524308 * Z  +  -9.827004 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.225711   -0.915881  [ DEG:   127.5239    -52.4761 ]
  Theta =   0.533951    2.607641  [ DEG:    30.5932    149.4068 ]
  Phi   =  -2.897847    0.243746  [ DEG:  -166.0344     13.9656 ]
 
# 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_4-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS599_4-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   31   3.08    0.00  21.503
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS599_4-D1
PFRMAT TS                                                                       
TARGET T0350                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1     -12.717  -0.882 -15.224  1.00  0.00              
ATOM      2  CA  ASN     2      -9.945   0.687 -12.486  1.00  0.00              
ATOM      3  CA  ILE     3     -13.535   1.198 -14.614  1.00  0.00              
ATOM      4  CA  GLU     4     -13.784   1.875 -11.084  1.00  0.00              
ATOM      5  CA  ARG     5     -12.218   5.358 -11.185  1.00  0.00              
ATOM      6  CA  LEU     6     -14.488   6.659 -13.955  1.00  0.00              
ATOM      7  CA  THR     7     -17.725   5.512 -12.289  1.00  0.00              
ATOM      8  CA  THR     8     -16.748   7.093  -8.968  1.00  0.00              
ATOM      9  CA  LEU     9     -15.864  10.452 -10.564  1.00  0.00              
ATOM     10  CA  GLN    10     -19.206  10.490 -12.465  1.00  0.00              
ATOM     11  CA  PRO    11     -21.161   9.932  -9.206  1.00  0.00              
ATOM     12  CA  VAL    12     -19.161  12.743  -7.668  1.00  0.00              
ATOM     13  CA  TRP    13     -19.944  14.959 -10.703  1.00  0.00              
ATOM     14  CA  ASP    14     -23.615  14.381 -10.011  1.00  0.00              
ATOM     15  CA  ARG    15     -23.252  15.225  -6.280  1.00  0.00              
ATOM     16  CA  TYR    16     -21.917  18.634  -6.338  1.00  0.00              
ATOM     17  CA  ASP    17     -18.260  19.206  -6.798  1.00  0.00              
ATOM     18  CA  THR    18     -17.726  20.469  -3.209  1.00  0.00              
ATOM     19  CA  GLN    19     -19.428  17.327  -1.876  1.00  0.00              
ATOM     20  CA  ILE    20     -17.240  15.026  -3.995  1.00  0.00              
ATOM     21  CA  HIS    21     -14.020  16.786  -2.968  1.00  0.00              
ATOM     36  CA  SER    36      -1.214   5.189  11.991  1.00  0.00              
ATOM     37  CA  TYR    37       0.382   8.547  11.101  1.00  0.00              
ATOM     38  CA  THR    38       3.864   7.391  11.918  1.00  0.00              
ATOM     39  CA  ASN    39       3.418   4.266   9.809  1.00  0.00              
ATOM     40  CA  LEU    40       2.084   6.309   6.865  1.00  0.00              
ATOM     41  CA  ALA    41       5.024   8.674   7.056  1.00  0.00              
ATOM     42  CA  GLU    42       7.391   5.649   7.092  1.00  0.00              
ATOM     43  CA  MET    43       5.562   4.199   4.042  1.00  0.00              
ATOM     44  CA  VAL    44       5.932   7.556   2.209  1.00  0.00              
ATOM     45  CA  GLY    45       9.680   7.662   2.878  1.00  0.00              
ATOM     46  CA  GLU    46       9.976   4.062   1.626  1.00  0.00              
ATOM     47  CA  MET    47       7.985   4.997  -1.541  1.00  0.00              
ATOM     48  CA  ASN    48      10.216   8.000  -2.132  1.00  0.00              
ATOM     49  CA  LYS    49      13.296   5.707  -1.868  1.00  0.00              
ATOM     50  CA  LEU    50      11.661   3.282  -4.310  1.00  0.00              
ATOM     51  CA  LEU    51      10.935   6.134  -6.786  1.00  0.00              
ATOM     52  CA  GLU    52      14.563   7.299  -6.615  1.00  0.00              
ATOM     53  CA  PRO    53      15.639   3.722  -7.448  1.00  0.00              
ATOM     54  CA  SER    54      13.145   3.544 -10.334  1.00  0.00              
ATOM     55  CA  GLN    55      14.202   6.831 -11.796  1.00  0.00              
ATOM     56  CA  VAL    56      17.914   5.791 -11.814  1.00  0.00              
ATOM     57  CA  HIS    57      17.266   2.776 -14.033  1.00  0.00              
ATOM     58  CA  LEU    58      13.989   1.145 -13.547  1.00  0.00              
ATOM     59  CA  LYS    59      13.006  -2.178 -15.038  1.00  0.00              
ATOM     60  CA  PHE    60       9.116  -2.608 -15.303  1.00  0.00              
ATOM     61  CA  GLU    61       7.362  -6.101 -15.447  1.00  0.00              
ATOM     62  CA  LEU    62       3.709  -6.040 -16.318  1.00  0.00              
ATOM     63  CA  HIS    63       1.452  -8.670 -15.108  1.00  0.00              
ATOM     64  CA  ASP    64      -1.528  -9.472 -17.223  1.00  0.00              
ATOM     65  CA  LYS    65      -1.430 -13.266 -16.835  1.00  0.00              
ATOM     66  CA  LEU    66      -1.158 -13.301 -13.089  1.00  0.00              
ATOM     67  CA  ASN    67      -3.649 -10.444 -12.711  1.00  0.00              
ATOM     68  CA  GLU    68      -1.158  -8.400 -10.709  1.00  0.00              
ATOM     69  CA  TYR    69      -0.169  -5.003 -11.977  1.00  0.00              
ATOM     70  CA  TYR    70       3.443  -4.015 -12.019  1.00  0.00              
ATOM     71  CA  VAL    71       4.417  -0.852 -13.776  1.00  0.00              
ATOM     72  CA  LYS    72       8.102  -0.711 -15.038  1.00  0.00              
ATOM     73  CA  VAL    73       9.680   2.451 -15.968  1.00  0.00              
ATOM     74  CA  ILE    74      12.480   1.954 -18.357  1.00  0.00              
ATOM     75  CA  GLU    75      15.302   4.432 -18.638  1.00  0.00              
ATOM     76  CA  ASP    76      16.576   5.318 -22.064  1.00  0.00              
ATOM     77  CA  SER    77      20.219   5.496 -20.934  1.00  0.00              
ATOM     78  CA  THR    78      20.553   1.935 -19.633  1.00  0.00              
ATOM     79  CA  ASN    79      17.708   0.628 -21.837  1.00  0.00              
ATOM     80  CA  GLU    80      19.675  -1.958 -23.733  1.00  0.00              
ATOM     81  CA  VAL    81      16.740  -4.366 -24.303  1.00  0.00              
ATOM     82  CA  ILE    82      14.520  -1.482 -25.480  1.00  0.00              
ATOM     83  CA  ARG    83      17.217  -0.278 -27.857  1.00  0.00              
ATOM     84  CA  GLU    84      17.290  -3.654 -29.634  1.00  0.00              
ATOM     85  CA  ILE    85      13.590  -3.867 -30.123  1.00  0.00              
ATOM     86  CA  PRO    86      11.920  -2.698 -33.341  1.00  0.00              
ATOM     87  CA  PRO    87      10.085   0.626 -32.770  1.00  0.00              
ATOM     88  CA  LYS    88       6.723  -1.018 -33.308  1.00  0.00              
ATOM     89  CA  ARG    89       7.457  -3.670 -30.724  1.00  0.00              
ATOM     90  CA  TRP    90       8.569  -1.138 -28.064  1.00  0.00              
ATOM     91  CA  LEU    91       5.453   0.910 -28.568  1.00  0.00              
ATOM     92  CA  ASP    92       3.413  -2.253 -28.247  1.00  0.00              
ATOM     93  CA  PHE    93       5.100  -3.344 -25.043  1.00  0.00              
ATOM     94  CA  TYR    94       4.543   0.129 -23.546  1.00  0.00              
ATOM     95  CA  ALA    95       0.857   0.103 -24.542  1.00  0.00              
ATOM     96  CA  ALA    96       0.297  -3.313 -23.103  1.00  0.00              
ATOM     97  CA  MET    97       1.912  -2.258 -19.799  1.00  0.00              
ATOM     98  CA  THR    98      -0.197   0.832 -19.671  1.00  0.00              
ATOM     99  CA  GLU    99      -3.475  -1.005 -20.230  1.00  0.00              
ATOM    100  CA  PHE   100      -2.663  -3.512 -17.475  1.00  0.00              
ATOM    101  CA  LEU   101      -1.684  -0.908 -14.868  1.00  0.00              
ATOM    102  CA  GLY   102      -4.922   0.986 -15.572  1.00  0.00              
ATOM    103  CA  LEU   103      -6.845  -2.254 -15.102  1.00  0.00              
ATOM    104  CA  PHE   104      -5.510  -3.092 -11.616  1.00  0.00              
ATOM    105  CA  VAL   105      -5.553   0.303  -9.993  1.00  0.00              
TER                                                                             
END
