
#######################################################
#                                                     #
#                        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 T0350TS393_3-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350TS393_3-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      N       2           -
LGA    I       3      I       3           -
LGA    E       4      E       4           #
LGA    R       5      R       5          4.039
LGA    L       6      L       6          4.277
LGA    -       -      T       7           -
LGA    T       7      T       8          2.348
LGA    T       8      L       9          2.962
LGA    L       9      Q      10          1.982
LGA    Q      10      P      11           #
LGA    P      11      V      12           #
LGA    -       -      W      13           -
LGA    V      12      D      14          3.754
LGA    W      13      R      15          0.892
LGA    D      14      Y      16           -
LGA    R      15      D      17           #
LGA    Y      16      T      18          1.600
LGA    D      17      -       -           -
LGA    T      18      -       -           -
LGA    Q      19      Q      19           #
LGA    I      20      I      20           -
LGA    H      21      -       -           -
LGA    S      36      -       -           -
LGA    Y      37      H      21           #
LGA    T      38      S      36           -
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    S      54      -       -           -
LGA    Q      55      -       -           -
LGA    V      56      -       -           -
LGA    H      57      -       -           -
LGA    L      58      Y      37          4.531
LGA    -       -      T      38           -
LGA    K      59      N      39          4.278
LGA    F      60      L      40          2.661
LGA    E      61      A      41          3.379
LGA    -       -      E      42           -
LGA    -       -      M      43           -
LGA    L      62      V      44          1.669
LGA    H      63      G      45          1.973
LGA    D      64      E      46           #
LGA    -       -      M      47           -
LGA    -       -      N      48           -
LGA    K      65      K      49          1.684
LGA    -       -      L      50           -
LGA    L      66      L      51          2.857
LGA    N      67      E      52          3.604
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    -       -      H      57           -
LGA    E      68      L      58          4.632
LGA    Y      69      K      59          2.458
LGA    Y      70      F      60          2.908
LGA    V      71      E      61          4.357
LGA    K      72      L      62          1.611
LGA    V      73      H      63           #
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    I      74      Y      69           #
LGA    E      75      Y      70           -
LGA    D      76      -       -           -
LGA    S      77      -       -           -
LGA    T      78      -       -           -
LGA    N      79      -       -           -
LGA    E      80      -       -           -
LGA    V      81      -       -           -
LGA    I      82      -       -           -
LGA    R      83      -       -           -
LGA    E      84      V      71           #
LGA    I      85      K      72          5.038
LGA    P      86      V      73          3.716
LGA    P      87      I      74          3.657
LGA    -       -      E      75           -
LGA    -       -      D      76           -
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    -       -      N      79           -
LGA    -       -      E      80           -
LGA    -       -      V      81           -
LGA    K      88      I      82          2.889
LGA    R      89      R      83          4.964
LGA    W      90      E      84           #
LGA    L      91      I      85          3.348
LGA    D      92      P      86           -
LGA    F      93      P      87           -
LGA    -       -      K      88           -
LGA    -       -      R      89           -
LGA    Y      94      W      90          3.666
LGA    A      95      L      91           #
LGA    A      96      D      92          4.803
LGA    M      97      F      93          4.891
LGA    T      98      Y      94          4.477
LGA    E      99      -       -           -
LGA    F     100      A      95          2.963
LGA    L     101      A      96           -
LGA    G     102      M      97           -
LGA    L     103      T      98           -
LGA    F     104      E      99           -
LGA    V     105      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     33    3.49    18.18     20.614     0.919

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.381523 * X  +   0.672275 * Y  +  -0.634418 * Z  +   4.404284
  Y_new =  -0.303372 * X  +   0.739384 * Y  +   0.601063 * Z  +  -1.625031
  Z_new =   0.873158 * X  +  -0.036855 * Y  +   0.486042 * Z  + -21.223450 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.075682    3.065911  [ DEG:    -4.3362    175.6638 ]
  Theta =  -1.061644   -2.079949  [ DEG:   -60.8277   -119.1723 ]
  Phi   =  -0.671783    2.469810  [ DEG:   -38.4903    141.5097 ]
 
# 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: T0350TS393_3-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS393_3-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   33   3.49   18.18  20.614
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS393_3-D1
PFRMAT TS
TARGET T0350
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      20.999  -2.916  -0.894  1.00 25.00           C
ATOM      2  CA  ASN     2      19.543  -4.765  -3.960  1.00 25.00           C
ATOM      3  CA  ILE     3      15.759  -4.269  -4.003  1.00 25.00           C
ATOM      4  CA  GLU     4      14.413  -1.814  -1.432  1.00 25.00           C
ATOM      5  CA  ARG     5      12.100   0.777  -2.863  1.00 25.00           C
ATOM      6  CA  LEU     6      11.777  -1.218  -6.042  1.00 25.00           C
ATOM      7  CA  THR     7       9.791  -2.286  -9.108  1.00 25.00           C
ATOM      8  CA  THR     8       8.301  -5.479 -10.546  1.00 25.00           C
ATOM      9  CA  LEU     9      11.397  -7.447 -11.348  1.00 25.00           C
ATOM     10  CA  GLN    10      11.184 -11.285 -11.500  1.00 25.00           C
ATOM     11  CA  PRO    11       7.371 -11.000 -11.736  1.00 25.00           C
ATOM     12  CA  VAL    12       3.660 -10.827 -10.736  1.00 25.00           C
ATOM     13  CA  TRP    13       2.917  -9.393 -14.148  1.00 25.00           C
ATOM     14  CA  ASP    14       0.170 -12.030 -14.563  1.00 25.00           C
ATOM     15  CA  ARG    15       0.808 -12.136 -18.337  1.00 25.00           C
ATOM     16  CA  TYR    16       4.562 -12.573 -17.716  1.00 25.00           C
ATOM     17  CA  ASP    17       3.849 -15.424 -15.260  1.00 25.00           C
ATOM     18  CA  THR    18       1.571 -17.106 -17.839  1.00 25.00           C
ATOM     19  CA  GLN    19       4.304 -16.781 -20.502  1.00 25.00           C
ATOM     20  CA  ILE    20       6.860 -18.320 -18.103  1.00 25.00           C
ATOM     21  CA  HIS    21       4.468 -21.222 -17.377  1.00 25.00           C
ATOM     36  CA  SER    36       3.166 -16.191 -32.006  1.00 25.00           C
ATOM     37  CA  TYR    37       5.443 -15.525 -29.015  1.00 25.00           C
ATOM     38  CA  THR    38       8.623 -15.092 -31.104  1.00 25.00           C
ATOM     39  CA  ASN    39       6.894 -12.414 -33.227  1.00 25.00           C
ATOM     40  CA  LEU    40       5.769 -10.589 -30.052  1.00 25.00           C
ATOM     41  CA  ALA    41       9.345 -10.714 -28.685  1.00 25.00           C
ATOM     42  CA  GLU    42      10.682  -9.308 -31.987  1.00 25.00           C
ATOM     43  CA  MET    43       8.098  -6.485 -31.860  1.00 25.00           C
ATOM     44  CA  VAL    44       9.113  -5.684 -28.255  1.00 25.00           C
ATOM     45  CA  GLY    45      12.800  -5.598 -29.287  1.00 25.00           C
ATOM     46  CA  GLU    46      11.961  -3.241 -32.186  1.00 25.00           C
ATOM     47  CA  MET    47      10.021  -0.958 -29.801  1.00 25.00           C
ATOM     48  CA  ASN    48      12.990  -0.920 -27.383  1.00 25.00           C
ATOM     49  CA  LYS    49      15.355  -0.030 -30.261  1.00 25.00           C
ATOM     50  CA  LEU    50      13.020   2.810 -31.332  1.00 25.00           C
ATOM     51  CA  LEU    51      12.922   4.120 -27.735  1.00 25.00           C
ATOM     52  CA  GLU    52      16.746   4.012 -27.565  1.00 25.00           C
ATOM     53  CA  PRO    53      16.971   5.927 -30.874  1.00 25.00           C
ATOM     54  CA  SER    54      13.728   7.821 -31.378  1.00 25.00           C
ATOM     55  CA  GLN    55      13.091   7.991 -35.141  1.00 25.00           C
ATOM     56  CA  VAL    56      10.988   4.848 -35.873  1.00 25.00           C
ATOM     57  CA  HIS    57       7.849   6.788 -34.816  1.00 25.00           C
ATOM     58  CA  LEU    58       4.893   5.142 -33.057  1.00 25.00           C
ATOM     59  CA  LYS    59       2.484   5.965 -30.179  1.00 25.00           C
ATOM     60  CA  PHE    60       5.282   6.074 -27.605  1.00 25.00           C
ATOM     61  CA  GLU    61       3.352   8.204 -25.102  1.00 25.00           C
ATOM     62  CA  LEU    62       4.882  10.306 -22.365  1.00 25.00           C
ATOM     63  CA  HIS    63       5.192  11.258 -18.737  1.00 25.00           C
ATOM     64  CA  ASP    64       8.102  13.235 -17.328  1.00 25.00           C
ATOM     65  CA  LYS    65       7.453  11.372 -14.115  1.00 25.00           C
ATOM     66  CA  LEU    66       8.906   7.814 -14.141  1.00 25.00           C
ATOM     67  CA  ASN    67      12.171   9.744 -13.558  1.00 25.00           C
ATOM     68  CA  GLU    68      13.351   9.809 -17.173  1.00 25.00           C
ATOM     69  CA  TYR    69      12.380   6.209 -18.058  1.00 25.00           C
ATOM     70  CA  TYR    70       9.535   7.733 -20.083  1.00 25.00           C
ATOM     71  CA  VAL    71       9.150   8.099 -23.822  1.00 25.00           C
ATOM     72  CA  LYS    72      10.543   8.719 -27.361  1.00 25.00           C
ATOM     73  CA  VAL    73       8.629  10.792 -29.902  1.00 25.00           C
ATOM     74  CA  ILE    74       5.596  10.579 -32.194  1.00 25.00           C
ATOM     75  CA  GLU    75       1.950  10.988 -31.011  1.00 25.00           C
ATOM     76  CA  ASP    76       0.704  10.276 -34.541  1.00 25.00           C
ATOM     77  CA  SER    77       2.945  12.478 -36.658  1.00 25.00           C
ATOM     78  CA  THR    78       2.297  15.418 -34.356  1.00 25.00           C
ATOM     79  CA  ASN    79       5.973  15.696 -33.467  1.00 25.00           C
ATOM     80  CA  GLU    80       5.625  15.528 -29.706  1.00 25.00           C
ATOM     81  CA  VAL    81       6.719  15.928 -26.075  1.00 25.00           C
ATOM     82  CA  ILE    82       9.377  13.375 -25.250  1.00 25.00           C
ATOM     83  CA  ARG    83      12.613  12.019 -23.658  1.00 25.00           C
ATOM     84  CA  GLU    84      15.944  10.421 -22.814  1.00 25.00           C
ATOM     85  CA  ILE    85      14.325   7.017 -23.556  1.00 25.00           C
ATOM     86  CA  PRO    86      16.441   4.804 -21.233  1.00 25.00           C
ATOM     87  CA  PRO    87      16.004   1.264 -22.459  1.00 25.00           C
ATOM     88  CA  LYS    88      14.471  -1.759 -20.679  1.00 25.00           C
ATOM     89  CA  ARG    89      12.721   0.565 -18.187  1.00 25.00           C
ATOM     90  CA  TRP    90      11.351   2.672 -21.078  1.00 25.00           C
ATOM     91  CA  LEU    91      10.065  -0.493 -22.809  1.00 25.00           C
ATOM     92  CA  ASP    92       8.371  -1.611 -19.562  1.00 25.00           C
ATOM     93  CA  PHE    93       6.734   1.833 -19.202  1.00 25.00           C
ATOM     94  CA  TYR    94       5.487   1.646 -22.818  1.00 25.00           C
ATOM     95  CA  ALA    95       4.046  -1.842 -22.166  1.00 25.00           C
ATOM     96  CA  ALA    96       2.283  -0.552 -19.020  1.00 25.00           C
ATOM     97  CA  MET    97       0.825   2.378 -21.009  1.00 25.00           C
ATOM     98  CA  THR    98      -0.416  -0.039 -23.708  1.00 25.00           C
ATOM     99  CA  GLU    99      -2.038  -2.238 -21.025  1.00 25.00           C
ATOM    100  CA  PHE   100      -3.745   0.833 -19.502  1.00 25.00           C
ATOM    101  CA  LEU   101      -5.041   1.857 -22.958  1.00 25.00           C
ATOM    102  CA  GLY   102      -6.395  -1.680 -23.525  1.00 25.00           C
ATOM    103  CA  LEU   103      -8.140  -1.585 -20.117  1.00 25.00           C
ATOM    104  CA  PHE   104      -9.690   1.811 -20.978  1.00 25.00           C
ATOM    105  CA  VAL   105      -8.764   5.203 -22.499  1.00 25.00           C
TER
END
