
#######################################################
#                                                     #
#                        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 T0350TS168_1
# Molecule2: number of CA atoms  109 ( 1798),  selected  109 , name T0350.pdb
# PARAMETERS: T0350TS168_1.T0350.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           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    I       3      Q      10           #
LGA    E       4      P      11           -
LGA    R       5      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    L       6      D      17          4.161
LGA    T       7      T      18          2.078
LGA    T       8      Q      19          2.687
LGA    L       9      I      20          4.173
LGA    -       -      H      21           -
LGA    -       -      N      22           -
LGA    Q      10      Q      23          2.522
LGA    P      11      K      24          4.464
LGA    V      12      -       -           -
LGA    W      13      -       -           -
LGA    D      14      D      25          4.394
LGA    R      15      N      26          1.280
LGA    Y      16      D      27          3.124
LGA    D      17      N      28          3.632
LGA    T      18      -       -           -
LGA    Q      19      -       -           -
LGA    I      20      E      29          4.882
LGA    H      21      V      30           -
LGA    N      22      P      31           -
LGA    Q      23      -       -           -
LGA    K      24      -       -           -
LGA    D      25      -       -           -
LGA    N      26      -       -           -
LGA    D      27      -       -           -
LGA    N      28      -       -           -
LGA    E      29      -       -           -
LGA    V      30      -       -           -
LGA    P      31      -       -           -
LGA    V      32      -       -           -
LGA    H      33      -       -           -
LGA    Q      34      -       -           -
LGA    V      35      -       -           -
LGA    S      36      -       -           -
LGA    Y      37      -       -           -
LGA    T      38      -       -           -
LGA    N      39      -       -           -
LGA    L      40      V      32           #
LGA    A      41      H      33          4.346
LGA    E      42      Q      34           #
LGA    M      43      -       -           -
LGA    V      44      V      35          4.176
LGA    G      45      S      36          2.090
LGA    E      46      Y      37          4.968
LGA    M      47      T      38          4.178
LGA    N      48      N      39          3.690
LGA    K      49      L      40          4.748
LGA    L      50      -       -           -
LGA    L      51      A      41          4.129
LGA    E      52      E      42           -
LGA    P      53      M      43           -
LGA    S      54      -       -           -
LGA    Q      55      -       -           -
LGA    V      56      -       -           -
LGA    H      57      -       -           -
LGA    L      58      -       -           -
LGA    K      59      -       -           -
LGA    F      60      V      44          4.468
LGA    E      61      G      45          2.575
LGA    L      62      -       -           -
LGA    H      63      E      46          1.937
LGA    D      64      M      47           #
LGA    K      65      N      48           -
LGA    L      66      K      49           -
LGA    N      67      L      50           -
LGA    E      68      L      51           -
LGA    Y      69      E      52           -
LGA    Y      70      P      53           -
LGA    -       -      S      54           -
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    -       -      H      57           -
LGA    -       -      L      58           -
LGA    -       -      K      59           -
LGA    -       -      F      60           -
LGA    -       -      E      61           -
LGA    -       -      L      62           -
LGA    -       -      H      63           -
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    V      71      Y      69           #
LGA    K      72      Y      70          3.802
LGA    -       -      V      71           -
LGA    V      73      K      72          1.151
LGA    I      74      V      73          4.439
LGA    E      75      I      74          1.799
LGA    D      76      E      75          2.104
LGA    S      77      D      76          2.891
LGA    T      78      S      77           #
LGA    -       -      T      78           -
LGA    N      79      N      79           #
LGA    E      80      E      80           -
LGA    V      81      -       -           -
LGA    I      82      V      81           #
LGA    R      83      I      82           -
LGA    E      84      R      83          4.555
LGA    -       -      E      84           -
LGA    I      85      I      85          1.477
LGA    P      86      P      86          1.312
LGA    P      87      P      87          1.862
LGA    K      88      K      88          1.841
LGA    R      89      R      89          0.636
LGA    W      90      W      90          1.419
LGA    L      91      L      91          1.665
LGA    D      92      D      92          1.160
LGA    F      93      F      93          0.758
LGA    Y      94      Y      94          1.266
LGA    A      95      A      95          1.658
LGA    A      96      A      96          1.225
LGA    M      97      M      97          1.602
LGA    T      98      T      98          1.464
LGA    E      99      E      99          1.464
LGA    F     100      F     100          1.222
LGA    L     101      L     101          1.599
LGA    G     102      G     102          1.532
LGA    L     103      L     103          1.644
LGA    F     104      F     104          1.691
LGA    V     105      V     105           #
LGA    D     106      D     106           -
LGA    E     107      E     107           -
LGA    K     108      K     108           -
LGA    K     109      K     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  109    5.0     49    2.93    51.02     28.161     1.616

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.481792 * X  +  -0.114594 * Y  +   0.868760 * Z  +  -0.683843
  Y_new =  -0.195805 * X  +  -0.952267 * Y  +  -0.234197 * Z  +  -0.039113
  Z_new =   0.854129 * X  +  -0.282942 * Y  +   0.436357 * Z  + -19.365047 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.575263    2.566329  [ DEG:   -32.9601    147.0399 ]
  Theta =  -1.023874   -2.117718  [ DEG:   -58.6637   -121.3363 ]
  Phi   =  -2.755573    0.386020  [ DEG:  -157.8827     22.1173 ]
 
# 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_1                                  
REMARK     2: T0350.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS168_1.T0350.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117  109   5.0   49   2.93   51.02  28.161
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS168_1
PFRMAT TS
TARGET T0350
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      16.930 -14.956 -12.190  1.00 25.00           C
ATOM      2  CA  ASN     2      13.949 -14.367 -14.399  1.00 25.00           C
ATOM      3  CA  ILE     3      10.579 -14.925 -12.808  1.00 25.00           C
ATOM      4  CA  GLU     4       9.787 -18.016 -14.898  1.00 25.00           C
ATOM      5  CA  ARG     5       8.242 -18.497 -18.332  1.00 25.00           C
ATOM      6  CA  LEU     6       8.140 -14.690 -18.702  1.00 25.00           C
ATOM      7  CA  THR     7       5.116 -12.584 -18.061  1.00 25.00           C
ATOM      8  CA  THR     8       2.786 -12.907 -20.985  1.00 25.00           C
ATOM      9  CA  LEU     9      -0.569 -11.380 -21.859  1.00 25.00           C
ATOM     10  CA  GLN    10      -2.578 -14.453 -22.842  1.00 25.00           C
ATOM     11  CA  PRO    11      -5.135 -14.206 -20.021  1.00 25.00           C
ATOM     12  CA  VAL    12      -7.863 -12.282 -18.232  1.00 25.00           C
ATOM     13  CA  TRP    13      -6.235  -9.273 -19.892  1.00 25.00           C
ATOM     14  CA  ASP    14      -6.965  -9.654 -23.632  1.00 25.00           C
ATOM     15  CA  ARG    15     -10.149 -11.627 -22.834  1.00 25.00           C
ATOM     16  CA  TYR    16     -11.252  -8.903 -20.378  1.00 25.00           C
ATOM     17  CA  ASP    17     -10.623  -6.218 -23.036  1.00 25.00           C
ATOM     18  CA  THR    18     -12.678  -8.217 -25.576  1.00 25.00           C
ATOM     19  CA  GLN    19     -15.531  -8.549 -23.043  1.00 25.00           C
ATOM     20  CA  ILE    20     -15.424  -4.777 -22.390  1.00 25.00           C
ATOM     21  CA  HIS    21     -15.546  -4.097 -26.157  1.00 25.00           C
ATOM     22  CA  ASN    22     -18.549  -6.448 -26.508  1.00 25.00           C
ATOM     23  CA  GLN    23     -22.293  -6.762 -26.803  1.00 25.00           C
ATOM     24  CA  LYS    24     -22.901  -8.410 -23.447  1.00 25.00           C
ATOM     25  CA  ASP    25     -24.579 -11.103 -21.403  1.00 25.00           C
ATOM     26  CA  ASN    26     -24.667  -8.323 -18.756  1.00 25.00           C
ATOM     27  CA  ASP    27     -23.957  -8.349 -14.963  1.00 25.00           C
ATOM     28  CA  ASN    28     -26.168  -5.647 -13.354  1.00 25.00           C
ATOM     29  CA  GLU    29     -24.499  -2.280 -12.601  1.00 25.00           C
ATOM     30  CA  VAL    30     -21.101  -1.036 -11.497  1.00 25.00           C
ATOM     31  CA  PRO    31     -18.533   0.156 -14.047  1.00 25.00           C
ATOM     32  CA  VAL    32     -16.141   0.922 -16.934  1.00 25.00           C
ATOM     33  CA  HIS    33     -16.967   4.324 -18.408  1.00 25.00           C
ATOM     34  CA  GLN    34     -17.261   6.708 -21.406  1.00 25.00           C
ATOM     35  CA  VAL    35     -15.815   6.640 -24.939  1.00 25.00           C
ATOM     36  CA  SER    36     -16.373   6.245 -28.678  1.00 25.00           C
ATOM     37  CA  TYR    37     -13.519   4.997 -30.780  1.00 25.00           C
ATOM     38  CA  THR    38     -12.034   7.306 -33.450  1.00 25.00           C
ATOM     39  CA  ASN    39     -11.136   9.880 -30.760  1.00 25.00           C
ATOM     40  CA  LEU    40      -9.463   7.146 -28.667  1.00 25.00           C
ATOM     41  CA  ALA    41      -7.470   5.990 -31.726  1.00 25.00           C
ATOM     42  CA  GLU    42      -6.365   9.594 -32.399  1.00 25.00           C
ATOM     43  CA  MET    43      -5.270   9.966 -28.748  1.00 25.00           C
ATOM     44  CA  VAL    44      -3.283   6.701 -28.986  1.00 25.00           C
ATOM     45  CA  GLY    45      -1.597   7.930 -32.196  1.00 25.00           C
ATOM     46  CA  GLU    46      -0.698  11.237 -30.486  1.00 25.00           C
ATOM     47  CA  MET    47       0.775   9.327 -27.512  1.00 25.00           C
ATOM     48  CA  ASN    48       2.835   7.152 -29.898  1.00 25.00           C
ATOM     49  CA  LYS    49       4.118  10.286 -31.686  1.00 25.00           C
ATOM     50  CA  LEU    50       5.084  11.840 -28.322  1.00 25.00           C
ATOM     51  CA  LEU    51       6.936   8.634 -27.344  1.00 25.00           C
ATOM     52  CA  GLU    52       8.799   8.662 -30.690  1.00 25.00           C
ATOM     53  CA  PRO    53       9.770  12.326 -30.148  1.00 25.00           C
ATOM     54  CA  SER    54      11.083  11.983 -26.634  1.00 25.00           C
ATOM     55  CA  GLN    55      14.865  11.562 -26.664  1.00 25.00           C
ATOM     56  CA  VAL    56      14.080   8.214 -28.294  1.00 25.00           C
ATOM     57  CA  HIS    57      16.151   6.688 -25.557  1.00 25.00           C
ATOM     58  CA  LEU    58      15.255   6.654 -21.817  1.00 25.00           C
ATOM     59  CA  LYS    59      12.614   9.373 -22.360  1.00 25.00           C
ATOM     60  CA  PHE    60       9.226   9.745 -20.575  1.00 25.00           C
ATOM     61  CA  GLU    61       6.391  11.454 -18.760  1.00 25.00           C
ATOM     62  CA  LEU    62       4.536   8.242 -17.693  1.00 25.00           C
ATOM     63  CA  HIS    63       1.374   9.820 -16.203  1.00 25.00           C
ATOM     64  CA  ASP    64      -0.380  12.957 -17.264  1.00 25.00           C
ATOM     65  CA  LYS    65      -3.808  11.693 -16.060  1.00 25.00           C
ATOM     66  CA  LEU    66      -3.242   8.159 -17.347  1.00 25.00           C
ATOM     67  CA  ASN    67      -1.397   9.262 -20.487  1.00 25.00           C
ATOM     68  CA  GLU    68       1.615   7.783 -22.154  1.00 25.00           C
ATOM     69  CA  TYR    69       1.505   5.668 -25.291  1.00 25.00           C
ATOM     70  CA  TYR    70       4.987   4.443 -24.264  1.00 25.00           C
ATOM     71  CA  VAL    71       8.614   4.079 -25.409  1.00 25.00           C
ATOM     72  CA  LYS    72      11.890   3.139 -27.224  1.00 25.00           C
ATOM     73  CA  VAL    73      14.313   2.143 -24.454  1.00 25.00           C
ATOM     74  CA  ILE    74      17.710   1.961 -22.748  1.00 25.00           C
ATOM     75  CA  GLU    75      16.090   2.323 -19.349  1.00 25.00           C
ATOM     76  CA  ASP    76      17.948   4.976 -17.328  1.00 25.00           C
ATOM     77  CA  SER    77      17.276   4.953 -13.599  1.00 25.00           C
ATOM     78  CA  THR    78      16.250   8.316 -12.104  1.00 25.00           C
ATOM     79  CA  ASN    79      17.589  10.107 -15.240  1.00 25.00           C
ATOM     80  CA  GLU    80      14.405   8.789 -16.931  1.00 25.00           C
ATOM     81  CA  VAL    81      11.191   6.736 -16.923  1.00 25.00           C
ATOM     82  CA  ILE    82      10.235   4.460 -19.868  1.00 25.00           C
ATOM     83  CA  ARG    83       8.024   1.590 -21.026  1.00 25.00           C
ATOM     84  CA  GLU    84      10.155  -0.635 -23.270  1.00 25.00           C
ATOM     85  CA  ILE    85       9.166  -0.910 -26.902  1.00 25.00           C
ATOM     86  CA  PRO    86       6.884  -0.379 -29.848  1.00 25.00           C
ATOM     87  CA  PRO    87       3.223   0.001 -30.753  1.00 25.00           C
ATOM     88  CA  LYS    88       0.594  -2.346 -29.255  1.00 25.00           C
ATOM     89  CA  ARG    89       3.229  -3.841 -26.910  1.00 25.00           C
ATOM     90  CA  TRP    90       4.292  -0.325 -25.824  1.00 25.00           C
ATOM     91  CA  LEU    91       0.636   0.597 -25.147  1.00 25.00           C
ATOM     92  CA  ASP    92       0.191  -2.589 -23.069  1.00 25.00           C
ATOM     93  CA  PHE    93       3.349  -1.756 -21.070  1.00 25.00           C
ATOM     94  CA  TYR    94       2.047   1.790 -20.442  1.00 25.00           C
ATOM     95  CA  ALA    95      -1.310   0.374 -19.262  1.00 25.00           C
ATOM     96  CA  ALA    96       0.507  -2.031 -16.900  1.00 25.00           C
ATOM     97  CA  MET    97       2.582   0.869 -15.502  1.00 25.00           C
ATOM     98  CA  THR    98      -0.608   2.916 -14.951  1.00 25.00           C
ATOM     99  CA  GLU    99      -2.226  -0.046 -13.141  1.00 25.00           C
ATOM    100  CA  PHE   100       0.875  -0.415 -10.922  1.00 25.00           C
ATOM    101  CA  LEU   101       0.765   3.324 -10.104  1.00 25.00           C
ATOM    102  CA  GLY   102      -2.948   3.045  -9.207  1.00 25.00           C
ATOM    103  CA  LEU   103      -2.200   0.051  -6.938  1.00 25.00           C
ATOM    104  CA  PHE   104       0.601   2.020  -5.224  1.00 25.00           C
ATOM    105  CA  VAL   105       4.136   2.757  -6.314  1.00 25.00           C
ATOM    106  CA  ASP   106       4.886  -0.418  -4.281  1.00 25.00           C
ATOM    107  CA  GLU   107       2.155  -2.471  -2.533  1.00 25.00           C
ATOM    108  CA  LYS   108       3.802  -1.841   0.866  1.00 25.00           C
ATOM    109  CA  LYS   109       0.434  -0.744   2.323  1.00 25.00           C
ATOM    110  CA  LEU   110      -1.306  -4.089   1.812  1.00 25.00           C
ATOM    111  CA  GLU   111      -4.955  -4.353   0.672  1.00 25.00           C
ATOM    112  CA  HIS   112      -7.362  -7.175  -0.199  1.00 25.00           C
ATOM    113  CA  HIS   113      -6.615 -10.522   1.382  1.00 25.00           C
ATOM    114  CA  HIS   114      -3.575 -12.889   1.458  1.00 25.00           C
ATOM    115  CA  HIS   115      -1.908 -16.301   1.419  1.00 25.00           C
ATOM    116  CA  HIS   116      -3.388 -17.460  -1.892  1.00 25.00           C
ATOM    117  CA  HIS   117      -6.231 -16.826  -4.287  1.00 25.00           C
TER
END
