
#######################################################
#                                                     #
#                        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 T0350TS393_3
# Molecule2: number of CA atoms  109 ( 1798),  selected  109 , name T0350.pdb
# PARAMETERS: T0350TS393_3.T0350.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    N      22      -       -           -
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      M       1           #
LGA    V      32      N       2          2.162
LGA    H      33      I       3          4.758
LGA    Q      34      E       4           -
LGA    V      35      R       5           #
LGA    S      36      L       6          4.149
LGA    Y      37      T       7          0.812
LGA    T      38      T       8          2.578
LGA    N      39      -       -           -
LGA    L      40      -       -           -
LGA    A      41      L       9          1.289
LGA    E      42      Q      10          1.143
LGA    M      43      P      11          1.273
LGA    V      44      V      12          1.418
LGA    G      45      W      13          1.218
LGA    E      46      D      14          1.291
LGA    M      47      R      15          1.683
LGA    N      48      Y      16          1.285
LGA    K      49      D      17          0.514
LGA    L      50      T      18          1.700
LGA    L      51      Q      19          1.916
LGA    E      52      I      20          0.136
LGA    P      53      H      21          2.253
LGA    S      54      N      22          3.085
LGA    Q      55      Q      23           #
LGA    V      56      K      24           -
LGA    H      57      D      25           -
LGA    L      58      N      26           -
LGA    K      59      D      27           -
LGA    F      60      -       -           -
LGA    E      61      N      28          4.141
LGA    L      62      E      29          2.783
LGA    H      63      V      30          3.386
LGA    D      64      P      31           #
LGA    K      65      V      32          2.886
LGA    L      66      H      33          1.854
LGA    N      67      Q      34          3.203
LGA    -       -      V      35           -
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    -       -      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    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    -       -      V      71           -
LGA    -       -      K      72           -
LGA    -       -      V      73           -
LGA    -       -      I      74           -
LGA    -       -      E      75           -
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           -
LGA    -       -      I      85           -
LGA    -       -      P      86           -
LGA    E      68      P      87           #
LGA    Y      69      -       -           -
LGA    Y      70      -       -           -
LGA    V      71      -       -           -
LGA    K      72      -       -           -
LGA    V      73      -       -           -
LGA    I      74      -       -           -
LGA    E      75      -       -           -
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      -       -           -
LGA    I      85      -       -           -
LGA    P      86      K      88          4.672
LGA    P      87      R      89          3.188
LGA    K      88      -       -           -
LGA    R      89      W      90          0.561
LGA    W      90      L      91          2.992
LGA    -       -      D      92           -
LGA    L      91      F      93          0.897
LGA    D      92      Y      94          1.204
LGA    F      93      A      95          3.130
LGA    Y      94      A      96          3.435
LGA    A      95      M      97          3.231
LGA    A      96      T      98          3.865
LGA    M      97      E      99           #
LGA    -       -      F     100           -
LGA    -       -      L     101           -
LGA    T      98      G     102          4.339
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    E      99      V     105           #
LGA    F     100      -       -           -
LGA    L     101      D     106           #
LGA    G     102      E     107          2.595
LGA    L     103      K     108          2.785
LGA    F     104      K     109           #
LGA    V     105      -       -           -
LGA    D     106      -       -           -
LGA    E     107      -       -           -
LGA    K     108      -       -           -
LGA    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     38    2.66     5.26     23.609     1.375

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.400596 * X  +  -0.210913 * Y  +  -0.891649 * Z  +   0.125430
  Y_new =   0.669847 * X  +  -0.596565 * Y  +   0.442058 * Z  +   2.005185
  Z_new =  -0.625162 * X  +  -0.774355 * Y  +  -0.097702 * Z  + -16.103085 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.696306    1.445287  [ DEG:   -97.1912     82.8088 ]
  Theta =   0.675340    2.466253  [ DEG:    38.6941    141.3059 ]
  Phi   =   1.031818   -2.109774  [ DEG:    59.1188   -120.8812 ]
 
# 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                                  
REMARK     2: T0350.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS393_3.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   38   2.66    5.26  23.609
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS393_3
PFRMAT TS
TARGET T0350
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1       9.205  12.131 -38.584  1.00 25.00           C
ATOM      2  CA  ASN     2      10.101  10.931 -35.021  1.00 25.00           C
ATOM      3  CA  ILE     3       7.519  12.320 -32.577  1.00 25.00           C
ATOM      4  CA  GLU     4       4.551  14.077 -34.175  1.00 25.00           C
ATOM      5  CA  ARG     5       1.218  12.905 -32.899  1.00 25.00           C
ATOM      6  CA  LEU     6       2.895  11.186 -29.997  1.00 25.00           C
ATOM      7  CA  THR     7       2.851   9.916 -26.409  1.00 25.00           C
ATOM      8  CA  THR     8       4.698  10.578 -23.149  1.00 25.00           C
ATOM      9  CA  LEU     9       8.145   9.346 -23.984  1.00 25.00           C
ATOM     10  CA  GLN    10      11.155  10.765 -22.055  1.00 25.00           C
ATOM     11  CA  PRO    11       8.743  12.087 -19.390  1.00 25.00           C
ATOM     12  CA  VAL    12       6.386  14.424 -17.444  1.00 25.00           C
ATOM     13  CA  TRP    13       5.049  11.394 -15.632  1.00 25.00           C
ATOM     14  CA  ASP    14       5.642  13.221 -12.319  1.00 25.00           C
ATOM     15  CA  ARG    15       6.382   9.889 -10.584  1.00 25.00           C
ATOM     16  CA  TYR    16       8.855   8.965 -13.359  1.00 25.00           C
ATOM     17  CA  ASP    17      10.577  12.366 -12.990  1.00 25.00           C
ATOM     18  CA  THR    18      10.828  11.854  -9.203  1.00 25.00           C
ATOM     19  CA  GLN    19      12.340   8.379  -9.747  1.00 25.00           C
ATOM     20  CA  ILE    20      14.885   9.844 -12.205  1.00 25.00           C
ATOM     21  CA  HIS    21      15.811  12.558  -9.666  1.00 25.00           C
ATOM     22  CA  ASN    22      16.266   9.897  -6.950  1.00 25.00           C
ATOM     23  CA  GLN    23      18.545  12.570  -5.351  1.00 25.00           C
ATOM     24  CA  LYS    24      17.844  15.423  -2.885  1.00 25.00           C
ATOM     25  CA  ASP    25      15.081  17.375  -1.273  1.00 25.00           C
ATOM     26  CA  ASN    26      11.900  19.295  -0.277  1.00 25.00           C
ATOM     27  CA  ASP    27      10.779  16.175   1.586  1.00 25.00           C
ATOM     28  CA  ASN    28       9.708  16.187   5.236  1.00 25.00           C
ATOM     29  CA  GLU    29       6.464  14.687   4.117  1.00 25.00           C
ATOM     30  CA  VAL    30       4.075  11.808   3.535  1.00 25.00           C
ATOM     31  CA  PRO    31       3.760   9.367   0.600  1.00 25.00           C
ATOM     32  CA  VAL    32       4.534   6.460  -1.758  1.00 25.00           C
ATOM     33  CA  HIS    33       4.732   3.272   0.413  1.00 25.00           C
ATOM     34  CA  GLN    34       6.340  -0.174   0.155  1.00 25.00           C
ATOM     35  CA  VAL    35       8.371  -1.569  -2.747  1.00 25.00           C
ATOM     36  CA  SER    36      12.077  -0.813  -2.717  1.00 25.00           C
ATOM     37  CA  TYR    37      12.621   0.423  -6.288  1.00 25.00           C
ATOM     38  CA  THR    38      14.262  -2.812  -7.516  1.00 25.00           C
ATOM     39  CA  ASN    39      11.247  -4.834  -6.294  1.00 25.00           C
ATOM     40  CA  LEU    40       8.873  -2.437  -8.109  1.00 25.00           C
ATOM     41  CA  ALA    41      10.934  -2.789 -11.319  1.00 25.00           C
ATOM     42  CA  GLU    42      10.811  -6.605 -11.008  1.00 25.00           C
ATOM     43  CA  MET    43       7.015  -6.469 -10.524  1.00 25.00           C
ATOM     44  CA  VAL    44       6.676  -4.242 -13.622  1.00 25.00           C
ATOM     45  CA  GLY    45       8.811  -6.693 -15.647  1.00 25.00           C
ATOM     46  CA  GLU    46       6.629  -9.610 -14.465  1.00 25.00           C
ATOM     47  CA  MET    47       3.472  -7.688 -15.468  1.00 25.00           C
ATOM     48  CA  ASN    48       4.971  -6.980 -18.921  1.00 25.00           C
ATOM     49  CA  LYS    49       5.829 -10.689 -19.337  1.00 25.00           C
ATOM     50  CA  LEU    50       2.253 -11.650 -18.358  1.00 25.00           C
ATOM     51  CA  LEU    51       0.858  -9.149 -20.900  1.00 25.00           C
ATOM     52  CA  GLU    52       3.139 -10.597 -23.614  1.00 25.00           C
ATOM     53  CA  PRO    53       1.962 -14.137 -22.748  1.00 25.00           C
ATOM     54  CA  SER    54      -1.411 -13.886 -21.038  1.00 25.00           C
ATOM     55  CA  GLN    55      -1.631 -16.772 -18.545  1.00 25.00           C
ATOM     56  CA  VAL    56      -0.231 -15.288 -15.277  1.00 25.00           C
ATOM     57  CA  HIS    57      -3.701 -13.817 -14.542  1.00 25.00           C
ATOM     58  CA  LEU    58      -4.200 -10.489 -12.748  1.00 25.00           C
ATOM     59  CA  LYS    59      -6.477  -7.409 -13.058  1.00 25.00           C
ATOM     60  CA  PHE    60      -5.147  -6.528 -16.511  1.00 25.00           C
ATOM     61  CA  GLU    61      -8.182  -4.455 -17.519  1.00 25.00           C
ATOM     62  CA  LEU    62      -9.218  -3.653 -21.060  1.00 25.00           C
ATOM     63  CA  HIS    63     -10.088  -1.165 -23.746  1.00 25.00           C
ATOM     64  CA  ASP    64     -10.125  -1.995 -27.444  1.00 25.00           C
ATOM     65  CA  LYS    65      -9.227   1.627 -27.983  1.00 25.00           C
ATOM     66  CA  LEU    66      -5.493   2.334 -27.410  1.00 25.00           C
ATOM     67  CA  ASN    67      -5.224   0.691 -30.868  1.00 25.00           C
ATOM     68  CA  GLU    68      -4.322  -2.807 -29.677  1.00 25.00           C
ATOM     69  CA  TYR    69      -1.887  -1.757 -26.911  1.00 25.00           C
ATOM     70  CA  TYR    70      -4.614  -2.786 -24.456  1.00 25.00           C
ATOM     71  CA  VAL    71      -4.850  -5.833 -22.238  1.00 25.00           C
ATOM     72  CA  LYS    72      -4.283  -9.569 -21.484  1.00 25.00           C
ATOM     73  CA  VAL    73      -6.880 -11.627 -19.630  1.00 25.00           C
ATOM     74  CA  ILE    74      -8.282 -12.138 -16.127  1.00 25.00           C
ATOM     75  CA  GLU    75     -10.808  -9.768 -14.434  1.00 25.00           C
ATOM     76  CA  ASP    76     -10.680 -11.868 -11.257  1.00 25.00           C
ATOM     77  CA  SER    77     -11.018 -15.395 -12.596  1.00 25.00           C
ATOM     78  CA  THR    78     -13.957 -14.341 -14.743  1.00 25.00           C
ATOM     79  CA  ASN    79     -12.131 -15.282 -17.931  1.00 25.00           C
ATOM     80  CA  GLU    80     -12.480 -11.979 -19.738  1.00 25.00           C
ATOM     81  CA  VAL    81     -12.450  -9.613 -22.729  1.00 25.00           C
ATOM     82  CA  ILE    82      -8.902  -9.100 -23.920  1.00 25.00           C
ATOM     83  CA  ARG    83      -6.054  -8.657 -26.476  1.00 25.00           C
ATOM     84  CA  GLU    84      -2.897  -8.777 -28.569  1.00 25.00           C
ATOM     85  CA  ILE    85      -1.006  -7.409 -25.517  1.00 25.00           C
ATOM     86  CA  PRO    86       1.839  -5.564 -27.328  1.00 25.00           C
ATOM     87  CA  PRO    87       4.559  -5.045 -24.767  1.00 25.00           C
ATOM     88  CA  LYS    88       5.999  -1.784 -23.369  1.00 25.00           C
ATOM     89  CA  ARG    89       2.910   0.129 -24.583  1.00 25.00           C
ATOM     90  CA  TRP    90       0.626  -2.461 -22.926  1.00 25.00           C
ATOM     91  CA  LEU    91       2.590  -2.138 -19.654  1.00 25.00           C
ATOM     92  CA  ASP    92       2.275   1.676 -19.813  1.00 25.00           C
ATOM     93  CA  PHE    93      -1.497   1.365 -20.396  1.00 25.00           C
ATOM     94  CA  TYR    94      -1.790  -1.005 -17.401  1.00 25.00           C
ATOM     95  CA  ALA    95       0.167   1.466 -15.225  1.00 25.00           C
ATOM     96  CA  ALA    96      -2.138   4.313 -16.343  1.00 25.00           C
ATOM     97  CA  MET    97      -5.211   2.190 -15.497  1.00 25.00           C
ATOM     98  CA  THR    98      -3.757   1.416 -12.040  1.00 25.00           C
ATOM     99  CA  GLU    99      -3.106   5.144 -11.453  1.00 25.00           C
ATOM    100  CA  PHE   100      -6.704   5.960 -12.480  1.00 25.00           C
ATOM    101  CA  LEU   101      -8.022   3.285 -10.077  1.00 25.00           C
ATOM    102  CA  GLY   102      -5.884   4.735  -7.251  1.00 25.00           C
ATOM    103  CA  LEU   103      -7.226   8.242  -8.001  1.00 25.00           C
ATOM    104  CA  PHE   104     -10.816   6.910  -7.934  1.00 25.00           C
ATOM    105  CA  VAL   105     -12.926   3.981  -9.218  1.00 25.00           C
ATOM    106  CA  ASP   106     -14.144   6.503 -11.743  1.00 25.00           C
ATOM    107  CA  GLU   107     -15.758   9.254  -9.701  1.00 25.00           C
ATOM    108  CA  LYS   108     -14.049  11.503 -12.286  1.00 25.00           C
ATOM    109  CA  LYS   109     -17.190  11.413 -14.477  1.00 25.00           C
ATOM    110  CA  LEU   110     -17.929  15.010 -15.530  1.00 25.00           C
ATOM    111  CA  GLU   111     -17.239  13.537 -19.004  1.00 25.00           C
ATOM    112  CA  HIS   112     -15.068  16.643 -19.559  1.00 25.00           C
ATOM    113  CA  HIS   113     -15.810  20.328 -18.946  1.00 25.00           C
ATOM    114  CA  HIS   114     -13.159  20.876 -21.641  1.00 25.00           C
ATOM    115  CA  HIS   115     -11.750  24.230 -20.349  1.00 25.00           C
ATOM    116  CA  HIS   116      -8.414  23.588 -18.603  1.00 25.00           C
ATOM    117  CA  HIS   117      -4.807  22.778 -17.746  1.00 25.00           C
TER
END
