
#######################################################
#                                                     #
#                        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  122 (  122),  selected  122 , name T0342TS168_1-D1
# Molecule2: number of CA atoms  122 (  967),  selected  122 , name T0342_D1.pdb
# PARAMETERS: T0342TS168_1-D1.T0342_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E      14      E      14           -
LGA    E      15      E      15           -
LGA    S      16      S      16           -
LGA    F      17      F      17           -
LGA    L      18      L      18           -
LGA    Y      19      Y      19           -
LGA    F      20      F      20           -
LGA    A      21      A      21           #
LGA    Y      22      Y      22           -
LGA    -       -      G      23           -
LGA    -       -      S      24           -
LGA    G      23      N      25          3.491
LGA    S      24      L      26          3.107
LGA    N      25      L      27          1.305
LGA    -       -      T      28           -
LGA    -       -      E      29           -
LGA    L      26      R      30          2.082
LGA    L      27      I      31          4.383
LGA    T      28      H      32          2.291
LGA    E      29      L      33          4.049
LGA    R      30      R      34           #
LGA    I      31      N      35           #
LGA    H      32      P      36          2.703
LGA    L      33      S      37          1.244
LGA    R      34      A      38          2.517
LGA    N      35      A      39          2.467
LGA    P      36      -       -           -
LGA    S      37      -       -           -
LGA    A      38      -       -           -
LGA    A      39      F      40          2.754
LGA    F      40      F      41           #
LGA    F      41      C      42           -
LGA    C      42      V      43           -
LGA    V      43      A      44           #
LGA    A      44      R      45           -
LGA    R      45      L      46           -
LGA    -       -      Q      47           -
LGA    -       -      D      48           -
LGA    -       -      F      49           -
LGA    -       -      K      50           -
LGA    L      46      L      51          5.137
LGA    Q      47      D      52          1.283
LGA    D      48      F      53          2.450
LGA    F      49      G      54          2.879
LGA    K      50      N      55          3.833
LGA    -       -      S      56           -
LGA    -       -      Q      57           -
LGA    -       -      G      58           -
LGA    -       -      K      59           -
LGA    -       -      T      60           -
LGA    -       -      S      61           -
LGA    -       -      Q      62           -
LGA    -       -      T      63           -
LGA    -       -      W      64           -
LGA    -       -      H      65           -
LGA    -       -      G      66           -
LGA    -       -      G      67           -
LGA    L      51      I      68          1.511
LGA    D      52      A      69          4.516
LGA    F      53      -       -           -
LGA    G      54      -       -           -
LGA    N      55      -       -           -
LGA    S      56      -       -           -
LGA    Q      57      -       -           -
LGA    G      58      -       -           -
LGA    K      59      -       -           -
LGA    T      60      -       -           -
LGA    S      61      -       -           -
LGA    Q      62      -       -           -
LGA    T      63      -       -           -
LGA    W      64      -       -           -
LGA    H      65      -       -           -
LGA    G      66      -       -           -
LGA    G      67      -       -           -
LGA    I      68      -       -           -
LGA    A      69      -       -           -
LGA    T      70      -       -           -
LGA    I      71      T      70           #
LGA    F      72      I      71          3.534
LGA    Q      73      F      72          3.725
LGA    S      74      Q      73          3.525
LGA    P      75      S      74          4.068
LGA    G      76      P      75          2.478
LGA    D      77      G      76          3.034
LGA    -       -      D      77           -
LGA    E      78      E      78          0.931
LGA    V      79      V      79          2.982
LGA    W      80      W      80          1.986
LGA    G      81      G      81          1.929
LGA    V      82      V      82          3.068
LGA    V      83      V      83          0.743
LGA    W      84      W      84          4.129
LGA    K      85      K      85          3.324
LGA    M      86      M      86           #
LGA    N      87      -       -           -
LGA    K      88      N      87          3.629
LGA    S      89      K      88          1.986
LGA    N      90      S      89          3.463
LGA    L      91      N      90          2.814
LGA    N      92      L      91          1.392
LGA    S      93      N      92          2.980
LGA    L      94      S      93          0.584
LGA    D      95      L      94          3.752
LGA    E      96      D      95           #
LGA    Q      97      -       -           -
LGA    E      98      -       -           -
LGA    G      99      E      96          4.279
LGA    V     100      Q      97           -
LGA    K     101      E      98           -
LGA    S     102      G      99           -
LGA    G     103      -       -           -
LGA    M     104      V     100          3.150
LGA    Y     105      K     101           -
LGA    V     106      S     102           -
LGA    -       -      G     103           -
LGA    -       -      M     104           -
LGA    -       -      Y     105           -
LGA    -       -      V     106           -
LGA    V     107      V     107          2.917
LGA    I     108      I     108           #
LGA    E     109      E     109          5.129
LGA    V     110      V     110           #
LGA    K     111      K     111          3.496
LGA    V     112      V     112          4.327
LGA    A     113      -       -           -
LGA    T     114      -       -           -
LGA    Q     115      -       -           -
LGA    E     116      -       -           -
LGA    G     117      -       -           -
LGA    K     118      A     113          3.869
LGA    E     119      T     114          4.129
LGA    I     120      Q     115          5.498
LGA    T     121      E     116           -
LGA    -       -      G     117           -
LGA    -       -      K     118           -
LGA    -       -      E     119           -
LGA    -       -      I     120           -
LGA    -       -      T     121           -
LGA    C     122      C     122           #
LGA    R     123      R     123           -
LGA    S     124      -       -           -
LGA    Y     125      -       -           -
LGA    L     126      S     124          5.111
LGA    M     127      Y     125          2.978
LGA    T     128      L     126           #
LGA    N     129      M     127           -
LGA    Y     130      T     128           -
LGA    E     131      N     129           -
LGA    S     132      Y     130           -
LGA    A     133      E     131           -
LGA    P     134      S     132           -
LGA    P     135      A     133           -
LGA    -       -      P     134           -
LGA    -       -      P     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  122  122    5.0     52    3.27    25.00     23.469     1.542

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.405834 * X  +   0.160947 * Y  +  -0.899663 * Z  +  -3.465626
  Y_new =   0.648228 * X  +   0.744617 * Y  +  -0.159203 * Z  +  93.152489
  Z_new =   0.644281 * X  +  -0.647797 * Y  +  -0.406522 * Z  +   3.587704 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.131224    1.010369  [ DEG:  -122.1101     57.8899 ]
  Theta =  -0.700083   -2.441509  [ DEG:   -40.1118   -139.8882 ]
  Phi   =   2.130163   -1.011430  [ DEG:   122.0493    -57.9507 ]
 
# 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: T0342TS168_1-D1                               
REMARK     2: T0342_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0342TS168_1-D1.T0342_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  122  122   5.0   52   3.27   25.00  23.469
REMARK  ---------------------------------------------------------- 
MOLECULE T0342TS168_1-D1
PFRMAT TS
TARGET T0342
MODEL 1
PARENT N/A
ATOM     14  CA  GLU    14      -6.031 106.266  -6.432  1.00 25.00           C
ATOM     15  CA  GLU    15      -5.474 104.505  -3.062  1.00 25.00           C
ATOM     16  CA  SER    16      -4.943 101.832  -0.367  1.00 25.00           C
ATOM     17  CA  PHE    17      -4.238  99.085   2.137  1.00 25.00           C
ATOM     18  CA  LEU    18      -2.747  97.874   5.427  1.00 25.00           C
ATOM     19  CA  TYR    19      -0.747  94.712   6.239  1.00 25.00           C
ATOM     20  CA  PHE    20       0.942  91.795   4.489  1.00 25.00           C
ATOM     21  CA  ALA    21      -1.233  88.756   3.604  1.00 25.00           C
ATOM     22  CA  TYR    22      -2.938  85.602   2.292  1.00 25.00           C
ATOM     23  CA  GLY    23      -1.069  83.373   4.739  1.00 25.00           C
ATOM     24  CA  SER    24       2.407  83.513   6.157  1.00 25.00           C
ATOM     25  CA  ASN    25       2.459  81.102   9.050  1.00 25.00           C
ATOM     26  CA  LEU    26      -1.155  82.015   9.818  1.00 25.00           C
ATOM     27  CA  LEU    27      -1.870  78.304   9.383  1.00 25.00           C
ATOM     28  CA  THR    28      -4.425  77.974   6.651  1.00 25.00           C
ATOM     29  CA  GLU    29      -5.599  77.497   3.037  1.00 25.00           C
ATOM     30  CA  ARG    30      -2.648  79.589   1.777  1.00 25.00           C
ATOM     31  CA  ILE    31      -0.230  77.487   3.875  1.00 25.00           C
ATOM     32  CA  HIS    32      -1.751  74.273   2.452  1.00 25.00           C
ATOM     33  CA  LEU    33      -1.371  75.640  -1.106  1.00 25.00           C
ATOM     34  CA  ARG    34       2.287  76.527  -0.401  1.00 25.00           C
ATOM     35  CA  ASN    35       4.246  75.503  -3.548  1.00 25.00           C
ATOM     36  CA  PRO    36       4.467  72.142  -1.723  1.00 25.00           C
ATOM     37  CA  SER    37       7.745  73.667  -0.407  1.00 25.00           C
ATOM     38  CA  ALA    38       5.893  74.537   2.766  1.00 25.00           C
ATOM     39  CA  ALA    39       8.002  77.765   2.954  1.00 25.00           C
ATOM     40  CA  PHE    40       4.963  79.991   3.673  1.00 25.00           C
ATOM     41  CA  PHE    41       3.070  82.229   1.337  1.00 25.00           C
ATOM     42  CA  CYS    42       1.489  85.660   0.609  1.00 25.00           C
ATOM     43  CA  VAL    43       4.327  87.767   2.013  1.00 25.00           C
ATOM     44  CA  ALA    44       4.286  89.014   5.607  1.00 25.00           C
ATOM     45  CA  ARG    45       3.998  91.437   8.450  1.00 25.00           C
ATOM     46  CA  LEU    46       3.102  94.975   9.458  1.00 25.00           C
ATOM     47  CA  GLN    47       5.289  97.374  11.493  1.00 25.00           C
ATOM     48  CA  ASP    48       3.358  99.477  14.034  1.00 25.00           C
ATOM     49  CA  PHE    49       0.615  99.208  11.329  1.00 25.00           C
ATOM     50  CA  LYS    50      -2.686  97.373  11.847  1.00 25.00           C
ATOM     51  CA  LEU    51      -1.591  93.796  11.153  1.00 25.00           C
ATOM     52  CA  ASP    52      -0.840  90.403   9.657  1.00 25.00           C
ATOM     53  CA  PHE    53      -0.418  86.872   8.266  1.00 25.00           C
ATOM     54  CA  GLY    54       2.775  86.745  10.301  1.00 25.00           C
ATOM     55  CA  ASN    55       0.717  86.185  13.472  1.00 25.00           C
ATOM     56  CA  SER    56       3.430  88.145  15.378  1.00 25.00           C
ATOM     57  CA  GLN    57       5.423  88.665  18.616  1.00 25.00           C
ATOM     58  CA  GLY    58       8.290  87.423  16.428  1.00 25.00           C
ATOM     59  CA  LYS    59      10.420  87.991  19.576  1.00 25.00           C
ATOM     60  CA  THR    60      10.028  84.222  19.907  1.00 25.00           C
ATOM     61  CA  SER    61      10.616  82.190  16.736  1.00 25.00           C
ATOM     62  CA  GLN    62       9.566  78.892  18.244  1.00 25.00           C
ATOM     63  CA  THR    63       5.977  79.986  18.525  1.00 25.00           C
ATOM     64  CA  TRP    64       3.096  80.940  16.255  1.00 25.00           C
ATOM     65  CA  HIS    65       4.656  83.010  13.516  1.00 25.00           C
ATOM     66  CA  GLY    66       6.445  79.975  11.980  1.00 25.00           C
ATOM     67  CA  GLY    67       7.602  82.459   9.293  1.00 25.00           C
ATOM     68  CA  ILE    68       7.383  84.963   6.437  1.00 25.00           C
ATOM     69  CA  ALA    69       7.988  87.917   8.802  1.00 25.00           C
ATOM     70  CA  THR    70       8.679  91.285  10.445  1.00 25.00           C
ATOM     71  CA  ILE    71       8.244  94.266   8.168  1.00 25.00           C
ATOM     72  CA  PHE    72       8.789  97.206   5.737  1.00 25.00           C
ATOM     73  CA  GLN    73       9.504  99.997   3.263  1.00 25.00           C
ATOM     74  CA  SER    74      12.277 101.524   1.147  1.00 25.00           C
ATOM     75  CA  PRO    75      14.458 104.647   1.738  1.00 25.00           C
ATOM     76  CA  GLY    76      14.151 103.662   5.407  1.00 25.00           C
ATOM     77  CA  ASP    77      15.809 100.452   6.542  1.00 25.00           C
ATOM     78  CA  GLU    78      15.279  96.700   6.602  1.00 25.00           C
ATOM     79  CA  VAL    79      13.779  93.936   8.720  1.00 25.00           C
ATOM     80  CA  TRP    80      12.940  90.341   7.897  1.00 25.00           C
ATOM     81  CA  GLY    81      11.369  88.351   5.048  1.00 25.00           C
ATOM     82  CA  VAL    82       9.182  87.132   2.222  1.00 25.00           C
ATOM     83  CA  VAL    83       7.629  84.186   0.286  1.00 25.00           C
ATOM     84  CA  TRP    84       5.555  85.591  -2.559  1.00 25.00           C
ATOM     85  CA  LYS    85       2.633  83.396  -3.742  1.00 25.00           C
ATOM     86  CA  MET    86       1.195  86.912  -4.333  1.00 25.00           C
ATOM     87  CA  ASN    87      -1.565  86.985  -6.903  1.00 25.00           C
ATOM     88  CA  LYS    88      -1.743  83.329  -8.036  1.00 25.00           C
ATOM     89  CA  SER    89      -5.262  82.654  -9.387  1.00 25.00           C
ATOM     90  CA  ASN    90      -6.303  81.182  -6.009  1.00 25.00           C
ATOM     91  CA  LEU    91      -4.909  84.261  -4.208  1.00 25.00           C
ATOM     92  CA  ASN    92      -6.838  86.557  -6.590  1.00 25.00           C
ATOM     93  CA  SER    93     -10.049  84.574  -5.941  1.00 25.00           C
ATOM     94  CA  LEU    94      -9.491  84.859  -2.163  1.00 25.00           C
ATOM     95  CA  ASP    95      -8.959  88.637  -2.502  1.00 25.00           C
ATOM     96  CA  GLU    96     -12.189  88.933  -4.540  1.00 25.00           C
ATOM     97  CA  GLN    97     -14.085  86.945  -1.871  1.00 25.00           C
ATOM     98  CA  GLU    98     -14.083  90.298  -0.144  1.00 25.00           C
ATOM     99  CA  GLY    99     -12.009  92.832  -2.045  1.00 25.00           C
ATOM    100  CA  VAL   100     -10.135  93.666  -5.268  1.00 25.00           C
ATOM    101  CA  LYS   101      -6.328  93.548  -5.714  1.00 25.00           C
ATOM    102  CA  SER   102      -6.307  96.833  -3.746  1.00 25.00           C
ATOM    103  CA  GLY   103      -8.123  96.334  -0.436  1.00 25.00           C
ATOM    104  CA  MET   104      -7.080  92.680  -0.831  1.00 25.00           C
ATOM    105  CA  TYR   105      -4.733  89.781   0.164  1.00 25.00           C
ATOM    106  CA  VAL   106      -2.295  90.473  -2.694  1.00 25.00           C
ATOM    107  CA  VAL   107      -0.018  93.515  -3.114  1.00 25.00           C
ATOM    108  CA  ILE   108       2.340  91.702  -0.744  1.00 25.00           C
ATOM    109  CA  GLU   109       5.651  93.508  -1.232  1.00 25.00           C
ATOM    110  CA  VAL   110       7.282  90.105  -1.275  1.00 25.00           C
ATOM    111  CA  LYS   111      10.380  90.530  -3.361  1.00 25.00           C
ATOM    112  CA  VAL   112      11.619  87.068  -2.214  1.00 25.00           C
ATOM    113  CA  ALA   113      14.885  85.254  -1.778  1.00 25.00           C
ATOM    114  CA  THR   114      18.348  83.872  -1.043  1.00 25.00           C
ATOM    115  CA  GLN   115      21.283  86.308  -1.226  1.00 25.00           C
ATOM    116  CA  GLU   116      22.483  85.464  -4.663  1.00 25.00           C
ATOM    117  CA  GLY   117      21.416  87.570  -7.614  1.00 25.00           C
ATOM    118  CA  LYS   118      18.438  88.821  -5.648  1.00 25.00           C
ATOM    119  CA  GLU   119      16.930  89.861  -2.279  1.00 25.00           C
ATOM    120  CA  ILE   120      16.204  89.004   1.343  1.00 25.00           C
ATOM    121  CA  THR   121      12.965  90.965   0.978  1.00 25.00           C
ATOM    122  CA  CYS   122      10.389  93.687   1.104  1.00 25.00           C
ATOM    123  CA  ARG   123       8.410  91.912   3.758  1.00 25.00           C
ATOM    124  CA  SER   124       5.321  94.128   3.791  1.00 25.00           C
ATOM    125  CA  TYR   125       2.961  97.107   3.816  1.00 25.00           C
ATOM    126  CA  LEU   126       0.336  95.931   1.310  1.00 25.00           C
ATOM    127  CA  MET   127      -2.723  93.783   1.589  1.00 25.00           C
ATOM    128  CA  THR   128      -5.792  94.200   3.782  1.00 25.00           C
ATOM    129  CA  ASN   129      -9.324  95.421   4.668  1.00 25.00           C
ATOM    130  CA  TYR   130     -12.227  95.489   7.191  1.00 25.00           C
ATOM    131  CA  GLU   131     -14.388  96.265  10.222  1.00 25.00           C
ATOM    132  CA  SER   132     -16.036  96.775  13.608  1.00 25.00           C
ATOM    133  CA  ALA   133     -18.620  94.747  15.468  1.00 25.00           C
ATOM    134  CA  PRO   134     -16.229  91.857  14.882  1.00 25.00           C
ATOM    135  CA  PRO   135     -13.653  89.383  16.185  1.00 25.00           C
TER
END
