
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms  122 (  967),  selected  122 , name T0342_D1.pdb
# PARAMETERS: T0342TS168_5-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           -
LGA    E      15      S      16           #
LGA    S      16      F      17          3.858
LGA    -       -      L      18           -
LGA    F      17      Y      19          1.700
LGA    L      18      F      20          3.499
LGA    Y      19      A      21          5.213
LGA    F      20      Y      22           #
LGA    A      21      G      23           -
LGA    Y      22      S      24           -
LGA    G      23      N      25           -
LGA    S      24      L      26           -
LGA    N      25      L      27           -
LGA    -       -      T      28           -
LGA    -       -      E      29           -
LGA    -       -      R      30           -
LGA    -       -      I      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      S      37           -
LGA    -       -      A      38           -
LGA    -       -      A      39           -
LGA    -       -      F      40           -
LGA    -       -      F      41           -
LGA    -       -      C      42           -
LGA    -       -      V      43           -
LGA    -       -      A      44           -
LGA    -       -      R      45           -
LGA    -       -      L      46           -
LGA    -       -      Q      47           -
LGA    -       -      D      48           -
LGA    L      26      F      49          3.472
LGA    L      27      K      50           #
LGA    T      28      -       -           -
LGA    E      29      -       -           -
LGA    R      30      -       -           -
LGA    I      31      -       -           -
LGA    H      32      -       -           -
LGA    L      33      -       -           -
LGA    R      34      -       -           -
LGA    N      35      -       -           -
LGA    P      36      -       -           -
LGA    S      37      -       -           -
LGA    A      38      -       -           -
LGA    A      39      -       -           -
LGA    F      40      -       -           -
LGA    F      41      -       -           -
LGA    C      42      -       -           -
LGA    V      43      -       -           -
LGA    A      44      -       -           -
LGA    R      45      -       -           -
LGA    L      46      -       -           -
LGA    Q      47      L      51           #
LGA    D      48      D      52          3.495
LGA    F      49      F      53          4.141
LGA    K      50      G      54          4.790
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    L      51      T      70          2.412
LGA    D      52      I      71          1.927
LGA    F      53      F      72           #
LGA    -       -      Q      73           -
LGA    -       -      S      74           -
LGA    -       -      P      75           -
LGA    -       -      G      76           -
LGA    G      54      D      77           #
LGA    N      55      E      78          4.452
LGA    S      56      V      79          4.882
LGA    Q      57      -       -           -
LGA    G      58      -       -           -
LGA    K      59      W      80          3.613
LGA    T      60      -       -           -
LGA    S      61      -       -           -
LGA    Q      62      G      81          4.602
LGA    T      63      V      82          3.149
LGA    W      64      V      83          2.554
LGA    H      65      -       -           -
LGA    G      66      -       -           -
LGA    G      67      W      84           #
LGA    I      68      K      85           #
LGA    -       -      M      86           -
LGA    -       -      N      87           -
LGA    -       -      K      88           -
LGA    -       -      S      89           -
LGA    -       -      N      90           -
LGA    A      69      L      91           #
LGA    T      70      N      92           #
LGA    -       -      S      93           -
LGA    -       -      L      94           -
LGA    I      71      D      95          4.918
LGA    F      72      E      96           -
LGA    Q      73      Q      97           -
LGA    S      74      E      98           -
LGA    P      75      G      99           -
LGA    -       -      V     100           -
LGA    G      76      K     101          4.590
LGA    D      77      S     102          3.977
LGA    E      78      G     103          3.529
LGA    V      79      M     104           #
LGA    W      80      Y     105          1.292
LGA    G      81      V     106          4.505
LGA    V      82      V     107          2.598
LGA    V      83      I     108          2.351
LGA    W      84      E     109          0.931
LGA    K      85      V     110          1.950
LGA    M      86      K     111          2.506
LGA    N      87      V     112          1.530
LGA    K      88      A     113          1.460
LGA    -       -      T     114           -
LGA    -       -      Q     115           -
LGA    -       -      E     116           -
LGA    S      89      G     117          3.630
LGA    N      90      K     118          4.228
LGA    L      91      E     119          2.779
LGA    N      92      I     120           #
LGA    S      93      -       -           -
LGA    L      94      -       -           -
LGA    D      95      -       -           -
LGA    E      96      -       -           -
LGA    Q      97      -       -           -
LGA    E      98      -       -           -
LGA    G      99      -       -           -
LGA    V     100      -       -           -
LGA    K     101      -       -           -
LGA    S     102      T     121          1.787
LGA    G     103      C     122           #
LGA    -       -      R     123           -
LGA    M     104      S     124           #
LGA    Y     105      -       -           -
LGA    V     106      -       -           -
LGA    V     107      Y     125           #
LGA    I     108      -       -           -
LGA    E     109      -       -           -
LGA    V     110      -       -           -
LGA    K     111      -       -           -
LGA    V     112      -       -           -
LGA    A     113      -       -           -
LGA    T     114      -       -           -
LGA    Q     115      -       -           -
LGA    E     116      -       -           -
LGA    G     117      -       -           -
LGA    K     118      -       -           -
LGA    E     119      -       -           -
LGA    I     120      -       -           -
LGA    T     121      -       -           -
LGA    C     122      L     126          4.375
LGA    R     123      M     127          1.991
LGA    S     124      T     128          4.368
LGA    Y     125      N     129           -
LGA    L     126      Y     130           -
LGA    M     127      E     131           -
LGA    T     128      S     132           -
LGA    N     129      A     133           -
LGA    Y     130      P     134           -
LGA    E     131      P     135           -
LGA    S     132      -       -           -
LGA    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     36    3.47     8.33     16.916     1.009

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.303147 * X  +  -0.254103 * Y  +   0.918441 * Z  +   4.349907
  Y_new =  -0.861022 * X  +   0.339953 * Y  +   0.378249 * Z  +  94.373642
  Z_new =  -0.408341 * X  +  -0.905463 * Y  +  -0.115733 * Z  +  -4.796286 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.697923    1.443670  [ DEG:   -97.2838     82.7162 ]
  Theta =   0.420636    2.720957  [ DEG:    24.1007    155.8994 ]
  Phi   =  -1.232271    1.909322  [ DEG:   -70.6039    109.3961 ]
 
# 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_5-D1                               
REMARK     2: T0342_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0342TS168_5-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   36   3.47    8.33  16.916
REMARK  ---------------------------------------------------------- 
MOLECULE T0342TS168_5-D1
PFRMAT TS
TARGET T0342
MODEL 5
PARENT N/A
ATOM     14  CA  GLU    14      -4.409  79.843  -3.743  1.00 25.00           C
ATOM     15  CA  GLU    15      -1.644  82.310  -4.701  1.00 25.00           C
ATOM     16  CA  SER    16       0.239  85.452  -5.709  1.00 25.00           C
ATOM     17  CA  PHE    17       1.584  86.399  -2.238  1.00 25.00           C
ATOM     18  CA  LEU    18       2.533  89.699  -0.569  1.00 25.00           C
ATOM     19  CA  TYR    19       2.070  92.228   2.231  1.00 25.00           C
ATOM     20  CA  PHE    20       2.368  95.974   2.231  1.00 25.00           C
ATOM     21  CA  ALA    21       3.457  97.926  -0.800  1.00 25.00           C
ATOM     22  CA  TYR    22       3.240 101.664  -0.115  1.00 25.00           C
ATOM     23  CA  GLY    23       5.313 102.901   2.826  1.00 25.00           C
ATOM     24  CA  SER    24       3.935 102.488   6.294  1.00 25.00           C
ATOM     25  CA  ASN    25       7.157 104.229   7.468  1.00 25.00           C
ATOM     26  CA  LEU    26       9.509 101.784   5.689  1.00 25.00           C
ATOM     27  CA  LEU    27      10.258 102.563   1.997  1.00 25.00           C
ATOM     28  CA  THR    28       9.157 106.148   2.427  1.00 25.00           C
ATOM     29  CA  GLU    29       8.486 109.543   4.069  1.00 25.00           C
ATOM     30  CA  ARG    30       6.279 110.565   1.110  1.00 25.00           C
ATOM     31  CA  ILE    31       4.341 107.274   1.387  1.00 25.00           C
ATOM     32  CA  HIS    32       3.847 107.852   5.140  1.00 25.00           C
ATOM     33  CA  LEU    33       2.580 111.401   4.451  1.00 25.00           C
ATOM     34  CA  ARG    34       0.140 110.047   1.829  1.00 25.00           C
ATOM     35  CA  ASN    35      -2.264 112.417   3.700  1.00 25.00           C
ATOM     36  CA  PRO    36      -1.839 114.929   0.834  1.00 25.00           C
ATOM     37  CA  SER    37      -3.847 112.694  -1.407  1.00 25.00           C
ATOM     38  CA  ALA    38      -0.458 111.626  -2.878  1.00 25.00           C
ATOM     39  CA  ALA    39       2.178 108.884  -2.924  1.00 25.00           C
ATOM     40  CA  PHE    40       4.360 105.930  -3.915  1.00 25.00           C
ATOM     41  CA  PHE    41       7.120 104.303  -1.974  1.00 25.00           C
ATOM     42  CA  CYS    42       8.305 100.800  -2.786  1.00 25.00           C
ATOM     43  CA  VAL    43       7.622  97.065  -2.280  1.00 25.00           C
ATOM     44  CA  ALA    44       6.592  94.441   0.301  1.00 25.00           C
ATOM     45  CA  ARG    45       6.595  92.935   3.856  1.00 25.00           C
ATOM     46  CA  LEU    46       5.209  92.255   7.342  1.00 25.00           C
ATOM     47  CA  GLN    47       5.607  91.966  11.115  1.00 25.00           C
ATOM     48  CA  ASP    48       5.398  95.268  12.948  1.00 25.00           C
ATOM     49  CA  PHE    49       5.581  99.043  12.404  1.00 25.00           C
ATOM     50  CA  LYS    50       2.346  98.808  10.445  1.00 25.00           C
ATOM     51  CA  LEU    51       4.602  97.410   7.696  1.00 25.00           C
ATOM     52  CA  ASP    52       6.336  98.254   4.362  1.00 25.00           C
ATOM     53  CA  PHE    53       9.113  97.638   1.784  1.00 25.00           C
ATOM     54  CA  GLY    54      12.143  96.635   3.872  1.00 25.00           C
ATOM     55  CA  ASN    55      10.629  94.570   6.737  1.00 25.00           C
ATOM     56  CA  SER    56      10.438  96.673   9.902  1.00 25.00           C
ATOM     57  CA  GLN    57      14.167  95.920  10.123  1.00 25.00           C
ATOM     58  CA  GLY    58      15.568  93.211   7.898  1.00 25.00           C
ATOM     59  CA  LYS    59      14.737  89.658   8.817  1.00 25.00           C
ATOM     60  CA  THR    60      12.238  88.362  11.356  1.00 25.00           C
ATOM     61  CA  SER    61      10.055  87.018   8.591  1.00 25.00           C
ATOM     62  CA  GLN    62      11.645  83.874   7.055  1.00 25.00           C
ATOM     63  CA  THR    63      11.195  82.788   3.401  1.00 25.00           C
ATOM     64  CA  TRP    64       8.930  85.213   1.540  1.00 25.00           C
ATOM     65  CA  HIS    65       9.440  88.794   2.804  1.00 25.00           C
ATOM     66  CA  GLY    66       8.184  89.767  -0.660  1.00 25.00           C
ATOM     67  CA  GLY    67       6.406  88.933  -3.884  1.00 25.00           C
ATOM     68  CA  ILE    68       3.083  89.964  -5.542  1.00 25.00           C
ATOM     69  CA  ALA    69      -0.579  90.898  -5.172  1.00 25.00           C
ATOM     70  CA  THR    70      -3.258  93.404  -6.191  1.00 25.00           C
ATOM     71  CA  ILE    71      -5.540  94.662  -3.350  1.00 25.00           C
ATOM     72  CA  PHE    72      -6.111  98.068  -4.962  1.00 25.00           C
ATOM     73  CA  GLN    73      -8.892  97.652  -7.497  1.00 25.00           C
ATOM     74  CA  SER    74     -12.058  99.525  -8.404  1.00 25.00           C
ATOM     75  CA  PRO    75     -15.273  97.542  -8.067  1.00 25.00           C
ATOM     76  CA  GLY    76     -14.746  96.317  -4.528  1.00 25.00           C
ATOM     77  CA  ASP    77     -13.674  97.787  -1.177  1.00 25.00           C
ATOM     78  CA  GLU    78     -10.477  99.787  -0.973  1.00 25.00           C
ATOM     79  CA  VAL    79      -6.802 100.567  -0.121  1.00 25.00           C
ATOM     80  CA  TRP    80      -5.173  97.732   1.797  1.00 25.00           C
ATOM     81  CA  GLY    81      -2.869  94.664   1.984  1.00 25.00           C
ATOM     82  CA  VAL    82      -0.935  94.265  -1.314  1.00 25.00           C
ATOM     83  CA  VAL    83       2.409  94.262  -3.058  1.00 25.00           C
ATOM     84  CA  TRP    84       5.031  94.189  -5.851  1.00 25.00           C
ATOM     85  CA  LYS    85       8.606  93.088  -5.376  1.00 25.00           C
ATOM     86  CA  MET    86      11.501  93.254  -2.940  1.00 25.00           C
ATOM     87  CA  ASN    87      13.701  90.392  -1.689  1.00 25.00           C
ATOM     88  CA  LYS    88      16.397  88.492  -3.648  1.00 25.00           C
ATOM     89  CA  SER    89      19.036  89.027  -6.372  1.00 25.00           C
ATOM     90  CA  ASN    90      16.317  88.904  -9.065  1.00 25.00           C
ATOM     91  CA  LEU    91      14.238  91.465  -7.118  1.00 25.00           C
ATOM     92  CA  ASN    92      17.296  93.751  -6.813  1.00 25.00           C
ATOM     93  CA  SER    93      17.929  93.448 -10.578  1.00 25.00           C
ATOM     94  CA  LEU    94      14.268  94.321 -11.288  1.00 25.00           C
ATOM     95  CA  ASP    95      14.523  97.373  -8.989  1.00 25.00           C
ATOM     96  CA  GLU    96      17.712  98.493 -10.790  1.00 25.00           C
ATOM     97  CA  GLN    97      15.965  98.105 -14.176  1.00 25.00           C
ATOM     98  CA  GLU    98      12.178  98.657 -14.277  1.00 25.00           C
ATOM     99  CA  GLY    99      11.879  95.862 -16.845  1.00 25.00           C
ATOM    100  CA  VAL   100       9.085  94.479 -14.637  1.00 25.00           C
ATOM    101  CA  LYS   101       9.736  91.052 -12.981  1.00 25.00           C
ATOM    102  CA  SER   102       8.371  90.060  -9.554  1.00 25.00           C
ATOM    103  CA  GLY   103       4.889  91.052 -10.780  1.00 25.00           C
ATOM    104  CA  MET   104       4.378  94.816 -10.979  1.00 25.00           C
ATOM    105  CA  TYR   105       5.607  97.922  -9.160  1.00 25.00           C
ATOM    106  CA  VAL   106       4.615  99.854  -6.073  1.00 25.00           C
ATOM    107  CA  VAL   107       1.597 101.848  -5.044  1.00 25.00           C
ATOM    108  CA  ILE   108      -0.529 104.466  -3.183  1.00 25.00           C
ATOM    109  CA  GLU   109      -1.912 104.099   0.295  1.00 25.00           C
ATOM    110  CA  VAL   110      -0.182 104.616   3.638  1.00 25.00           C
ATOM    111  CA  LYS   111      -3.357 103.059   5.078  1.00 25.00           C
ATOM    112  CA  VAL   112      -5.272 100.224   6.580  1.00 25.00           C
ATOM    113  CA  ALA   113      -8.294  98.716   8.277  1.00 25.00           C
ATOM    114  CA  THR   114      -8.172  98.187  12.019  1.00 25.00           C
ATOM    115  CA  GLN   115      -9.613  95.024  13.639  1.00 25.00           C
ATOM    116  CA  GLU   116     -12.591  92.700  13.972  1.00 25.00           C
ATOM    117  CA  GLY   117     -11.934  89.484  12.050  1.00 25.00           C
ATOM    118  CA  LYS   118      -9.978  90.556   9.036  1.00 25.00           C
ATOM    119  CA  GLU   119      -8.257  93.894   8.938  1.00 25.00           C
ATOM    120  CA  ILE   120      -4.803  94.633   7.532  1.00 25.00           C
ATOM    121  CA  THR   121      -2.684  96.756   9.867  1.00 25.00           C
ATOM    122  CA  CYS   122      -0.162  96.003   7.106  1.00 25.00           C
ATOM    123  CA  ARG   123      -0.292  99.647   6.242  1.00 25.00           C
ATOM    124  CA  SER   124      -0.325  99.625   2.448  1.00 25.00           C
ATOM    125  CA  TYR   125      -1.394  99.805  -1.237  1.00 25.00           C
ATOM    126  CA  LEU   126      -0.942  97.755  -4.462  1.00 25.00           C
ATOM    127  CA  MET   127       0.139  97.997  -8.099  1.00 25.00           C
ATOM    128  CA  THR   128       1.323 100.449 -10.749  1.00 25.00           C
ATOM    129  CA  ASN   129       4.073 101.523 -13.100  1.00 25.00           C
ATOM    130  CA  TYR   130       3.303 103.927 -15.934  1.00 25.00           C
ATOM    131  CA  GLU   131       3.336 106.523 -18.713  1.00 25.00           C
ATOM    132  CA  SER   132       5.810 108.235 -21.020  1.00 25.00           C
ATOM    133  CA  ALA   133       9.560 107.747 -21.325  1.00 25.00           C
ATOM    134  CA  PRO   134      12.691 106.036 -19.884  1.00 25.00           C
ATOM    135  CA  PRO   135      16.095 104.543 -19.082  1.00 25.00           C
TER
END
