
#######################################################
#                                                     #
#                        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 T0350TS168_5-D1
# Molecule2: number of CA atoms   91 ( 1511),  selected   91 , name T0350_D1.pdb
# PARAMETERS: T0350TS168_5-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           -
LGA    L       6      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       7      T      18          4.946
LGA    -       -      Q      19           -
LGA    T       8      I      20          2.534
LGA    L       9      H      21           #
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      S      36          3.620
LGA    T      38      Y      37          4.796
LGA    N      39      T      38          4.146
LGA    L      40      N      39          2.049
LGA    A      41      L      40          2.546
LGA    E      42      A      41          2.385
LGA    M      43      E      42          0.757
LGA    V      44      M      43          2.472
LGA    G      45      V      44          2.817
LGA    E      46      G      45          0.986
LGA    M      47      E      46          3.676
LGA    N      48      M      47          4.623
LGA    K      49      N      48          3.298
LGA    L      50      K      49          3.198
LGA    L      51      L      50           #
LGA    E      52      L      51           #
LGA    P      53      E      52          3.268
LGA    S      54      P      53          5.046
LGA    Q      55      S      54          2.990
LGA    V      56      Q      55          3.072
LGA    H      57      V      56          4.012
LGA    L      58      H      57           #
LGA    K      59      L      58          3.212
LGA    -       -      K      59           -
LGA    F      60      F      60          2.872
LGA    E      61      E      61          2.156
LGA    L      62      L      62          2.677
LGA    H      63      H      63          1.876
LGA    D      64      D      64          2.304
LGA    K      65      K      65          3.145
LGA    L      66      L      66           #
LGA    N      67      N      67           -
LGA    E      68      E      68           -
LGA    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    Y      69      V      71          4.973
LGA    Y      70      K      72          1.378
LGA    V      71      V      73          2.938
LGA    K      72      I      74          3.096
LGA    V      73      E      75           #
LGA    I      74      D      76          4.055
LGA    E      75      -       -           -
LGA    D      76      -       -           -
LGA    S      77      S      77          2.902
LGA    T      78      -       -           -
LGA    N      79      T      78           #
LGA    E      80      N      79          1.838
LGA    V      81      E      80           #
LGA    I      82      V      81           #
LGA    R      83      I      82          1.587
LGA    E      84      R      83          1.652
LGA    I      85      E      84          3.289
LGA    P      86      I      85          2.025
LGA    P      87      P      86          2.621
LGA    K      88      P      87          4.114
LGA    R      89      K      88           #
LGA    W      90      R      89           #
LGA    L      91      W      90          2.707
LGA    -       -      L      91           -
LGA    D      92      D      92          3.051
LGA    F      93      F      93          2.984
LGA    Y      94      Y      94          3.424
LGA    A      95      A      95          2.582
LGA    A      96      A      96          2.141
LGA    M      97      M      97          2.285
LGA    T      98      T      98          1.955
LGA    E      99      E      99          2.126
LGA    F     100      F     100          2.601
LGA    L     101      L     101          3.293
LGA    G     102      G     102          2.989
LGA    L     103      L     103          3.460
LGA    F     104      F     104          3.898
LGA    V     105      V     105          5.629

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   91   91    5.0     56    3.15    42.86     37.667     1.722

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.653556 * X  +   0.515816 * Y  +   0.553894 * Z  +   2.821491
  Y_new =  -0.159842 * X  +   0.809371 * Y  +  -0.565128 * Z  +   0.325508
  Z_new =  -0.739808 * X  +   0.280808 * Y  +   0.611418 * Z  + -19.431639 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.430539   -2.711054  [ DEG:    24.6680   -155.3320 ]
  Theta =   0.832784    2.308808  [ DEG:    47.7150    132.2850 ]
  Phi   =  -0.239864    2.901729  [ DEG:   -13.7432    166.2568 ]
 
# 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: T0350TS168_5-D1                               
REMARK     2: T0350_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS168_5-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   56   3.15   42.86  37.667
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS168_5-D1
PFRMAT TS
TARGET T0350
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      13.724 -21.985 -17.677  1.00 25.00           C
ATOM      2  CA  ASN     2      12.452 -18.461 -18.465  1.00 25.00           C
ATOM      3  CA  ILE     3       9.262 -19.225 -20.390  1.00 25.00           C
ATOM      4  CA  GLU     4       6.373 -21.062 -22.049  1.00 25.00           C
ATOM      5  CA  ARG     5       5.354 -19.141 -25.099  1.00 25.00           C
ATOM      6  CA  LEU     6       6.342 -15.610 -24.157  1.00 25.00           C
ATOM      7  CA  THR     7       4.846 -12.405 -22.686  1.00 25.00           C
ATOM      8  CA  THR     8       2.980 -11.416 -25.872  1.00 25.00           C
ATOM      9  CA  LEU     9       0.215 -10.069 -23.536  1.00 25.00           C
ATOM     10  CA  GLN    10      -3.526 -10.705 -23.893  1.00 25.00           C
ATOM     11  CA  PRO    11      -5.435 -10.773 -20.601  1.00 25.00           C
ATOM     12  CA  VAL    12      -8.007  -8.413 -22.057  1.00 25.00           C
ATOM     13  CA  TRP    13      -6.248  -5.731 -19.986  1.00 25.00           C
ATOM     14  CA  ASP    14      -9.279  -3.478 -19.353  1.00 25.00           C
ATOM     15  CA  ARG    15      -7.800  -0.797 -21.653  1.00 25.00           C
ATOM     16  CA  TYR    16      -7.214  -3.424 -24.378  1.00 25.00           C
ATOM     17  CA  ASP    17     -10.830  -4.636 -24.022  1.00 25.00           C
ATOM     18  CA  THR    18     -12.093  -1.031 -24.310  1.00 25.00           C
ATOM     19  CA  GLN    19      -9.971  -0.514 -27.457  1.00 25.00           C
ATOM     20  CA  ILE    20     -11.378  -3.742 -28.965  1.00 25.00           C
ATOM     21  CA  HIS    21     -14.942  -2.581 -28.185  1.00 25.00           C
ATOM     36  CA  SER    36      -5.671  11.857 -33.503  1.00 25.00           C
ATOM     37  CA  TYR    37      -3.114   9.098 -32.933  1.00 25.00           C
ATOM     38  CA  THR    38      -0.731  12.044 -32.377  1.00 25.00           C
ATOM     39  CA  ASN    39      -2.392  12.785 -29.007  1.00 25.00           C
ATOM     40  CA  LEU    40      -2.036   9.108 -27.995  1.00 25.00           C
ATOM     41  CA  ALA    41       1.665   9.171 -28.979  1.00 25.00           C
ATOM     42  CA  GLU    42       2.185  12.353 -26.911  1.00 25.00           C
ATOM     43  CA  MET    43       0.466  10.711 -23.908  1.00 25.00           C
ATOM     44  CA  VAL    44       2.705   7.627 -24.280  1.00 25.00           C
ATOM     45  CA  GLY    45       5.809   9.866 -24.416  1.00 25.00           C
ATOM     46  CA  GLU    46       4.655  11.700 -21.258  1.00 25.00           C
ATOM     47  CA  MET    47       4.114   8.351 -19.482  1.00 25.00           C
ATOM     48  CA  ASN    48       7.619   7.207 -20.518  1.00 25.00           C
ATOM     49  CA  LYS    49       9.105  10.480 -19.197  1.00 25.00           C
ATOM     50  CA  LEU    50       7.246  10.014 -15.880  1.00 25.00           C
ATOM     51  CA  LEU    51       8.568   6.429 -15.615  1.00 25.00           C
ATOM     52  CA  GLU    52      12.130   7.667 -16.286  1.00 25.00           C
ATOM     53  CA  PRO    53      11.733  10.348 -13.580  1.00 25.00           C
ATOM     54  CA  SER    54      10.416   8.003 -10.851  1.00 25.00           C
ATOM     55  CA  GLN    55      13.006   7.723  -8.071  1.00 25.00           C
ATOM     56  CA  VAL    56      13.655   4.277  -9.472  1.00 25.00           C
ATOM     57  CA  HIS    57      15.002   1.402 -11.656  1.00 25.00           C
ATOM     58  CA  LEU    58      11.897   2.053 -13.741  1.00 25.00           C
ATOM     59  CA  LYS    59      13.519   2.634 -17.136  1.00 25.00           C
ATOM     60  CA  PHE    60      11.707   4.288 -20.109  1.00 25.00           C
ATOM     61  CA  GLU    61      12.652   6.448 -23.102  1.00 25.00           C
ATOM     62  CA  LEU    62      10.622   5.773 -26.228  1.00 25.00           C
ATOM     63  CA  HIS    63      12.886   6.324 -29.216  1.00 25.00           C
ATOM     64  CA  ASP    64      12.968   4.687 -32.635  1.00 25.00           C
ATOM     65  CA  LYS    65      12.265   1.381 -34.330  1.00 25.00           C
ATOM     66  CA  LEU    66      11.693  -1.775 -32.267  1.00 25.00           C
ATOM     67  CA  ASN    67      15.074  -2.657 -30.834  1.00 25.00           C
ATOM     68  CA  GLU    68      17.173  -0.101 -28.859  1.00 25.00           C
ATOM     69  CA  TYR    69      13.679   1.368 -28.899  1.00 25.00           C
ATOM     70  CA  TYR    70      14.566   2.220 -25.260  1.00 25.00           C
ATOM     71  CA  VAL    71      16.307   3.180 -21.969  1.00 25.00           C
ATOM     72  CA  LYS    72      17.188   6.702 -20.946  1.00 25.00           C
ATOM     73  CA  VAL    73      17.076   8.627 -17.635  1.00 25.00           C
ATOM     74  CA  ILE    74      16.563   8.965 -13.914  1.00 25.00           C
ATOM     75  CA  GLU    75      17.656   5.476 -12.926  1.00 25.00           C
ATOM     76  CA  ASP    76      18.280   6.811  -9.401  1.00 25.00           C
ATOM     77  CA  SER    77      21.814   5.381  -9.831  1.00 25.00           C
ATOM     78  CA  THR    78      22.412   8.636 -11.758  1.00 25.00           C
ATOM     79  CA  ASN    79      22.877   8.284 -15.519  1.00 25.00           C
ATOM     80  CA  GLU    80      21.276   5.383 -17.421  1.00 25.00           C
ATOM     81  CA  VAL    81      21.179   2.453 -14.908  1.00 25.00           C
ATOM     82  CA  ILE    82      18.393   1.234 -17.220  1.00 25.00           C
ATOM     83  CA  ARG    83      16.208  -1.310 -19.057  1.00 25.00           C
ATOM     84  CA  GLU    84      13.729  -3.780 -20.545  1.00 25.00           C
ATOM     85  CA  ILE    85      12.019  -0.794 -22.166  1.00 25.00           C
ATOM     86  CA  PRO    86      10.830  -2.049 -25.521  1.00 25.00           C
ATOM     87  CA  PRO    87       8.163   0.019 -27.176  1.00 25.00           C
ATOM     88  CA  LYS    88       4.872  -1.889 -26.727  1.00 25.00           C
ATOM     89  CA  ARG    89       6.315  -3.711 -23.683  1.00 25.00           C
ATOM     90  CA  TRP    90       7.445  -0.371 -22.189  1.00 25.00           C
ATOM     91  CA  LEU    91       3.951   1.091 -22.750  1.00 25.00           C
ATOM     92  CA  ASP    92       2.375  -1.957 -21.049  1.00 25.00           C
ATOM     93  CA  PHE    93       4.758  -1.561 -18.077  1.00 25.00           C
ATOM     94  CA  TYR    94       3.847   2.149 -17.810  1.00 25.00           C
ATOM     95  CA  ALA    95       0.122   1.263 -17.874  1.00 25.00           C
ATOM     96  CA  ALA    96       0.667  -1.340 -15.118  1.00 25.00           C
ATOM     97  CA  MET    97       2.544   1.250 -13.010  1.00 25.00           C
ATOM     98  CA  THR    98      -0.314   3.753 -13.497  1.00 25.00           C
ATOM     99  CA  GLU    99      -2.857   1.094 -12.435  1.00 25.00           C
ATOM    100  CA  PHE   100      -0.776   0.313  -9.317  1.00 25.00           C
ATOM    101  CA  LEU   101      -0.614   4.043  -8.461  1.00 25.00           C
ATOM    102  CA  GLY   102      -4.411   4.328  -8.876  1.00 25.00           C
ATOM    103  CA  LEU   103      -4.913   1.298  -6.587  1.00 25.00           C
ATOM    104  CA  PHE   104      -2.602   2.865  -3.966  1.00 25.00           C
ATOM    105  CA  VAL   105       0.964   1.487  -4.443  1.00 25.00           C
TER
END
