
#######################################################
#                                                     #
#                        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  128 (  128),  selected  128 , name T0322TS168_2-D1
# Molecule2: number of CA atoms  128 (  980),  selected  128 , name T0322_D1.pdb
# PARAMETERS: T0322TS168_2-D1.T0322_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      16      G      16           -
LGA    F      17      F      17           -
LGA    S      18      S      18           -
LGA    Q      19      Q      19           -
LGA    L      20      L      20           -
LGA    N      21      N      21           -
LGA    W      22      -       -           -
LGA    S      23      W      22           #
LGA    R      24      S      23          3.634
LGA    -       -      R      24           -
LGA    G      25      G      25          0.620
LGA    F      26      F      26          1.666
LGA    G      27      G      27          1.740
LGA    R      28      R      28          2.641
LGA    Q      29      Q      29          2.284
LGA    I      30      I      30          1.433
LGA    G      31      G      31          1.363
LGA    P      32      P      32          3.665
LGA    L      33      L      33          3.089
LGA    F      34      F      34          1.161
LGA    E      35      E      35          2.943
LGA    H      36      H      36          2.474
LGA    -       -      R      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    R      37      P      40           #
LGA    E      38      G      41          1.986
LGA    G      39      -       -           -
LGA    P      40      Q      42          3.774
LGA    G      41      -       -           -
LGA    Q      42      -       -           -
LGA    A      43      A      43          1.884
LGA    R      44      R      44          3.309
LGA    L      45      L      45          1.346
LGA    A      46      A      46          1.361
LGA    F      47      F      47          2.959
LGA    R      48      R      48          2.412
LGA    V      49      V      49          0.714
LGA    E      50      E      50          0.469
LGA    E      51      E      51          1.220
LGA    H      52      H      52          1.811
LGA    H      53      H      53          1.534
LGA    T      54      T      54          0.168
LGA    N      55      N      55          1.820
LGA    G      56      G      56          4.060
LGA    L      57      L      57          4.331
LGA    G      58      G      58           #
LGA    N      59      N      59          3.605
LGA    C      60      C      60          1.665
LGA    H      61      H      61          0.930
LGA    G      62      G      62          0.477
LGA    G      63      G      63          0.149
LGA    M      64      M      64          0.162
LGA    L      65      L      65          0.163
LGA    M      66      M      66          0.246
LGA    S      67      S      67          0.439
LGA    F      68      F      68          0.433
LGA    A      69      A      69          0.684
LGA    D      70      D      70          0.873
LGA    M      71      M      71          1.196
LGA    A      72      A      72          1.321
LGA    W      73      W      73          2.684
LGA    G      74      G      74          3.135
LGA    R      75      R      75          2.176
LGA    I      76      I      76          1.881
LGA    I      77      I      77          1.531
LGA    S      78      S      78          1.161
LGA    L      79      L      79          1.028
LGA    Q      80      Q      80          3.276
LGA    K      81      K      81          3.523
LGA    S      82      S      82          5.490
LGA    Y      83      Y      83          3.235
LGA    S      84      S      84          3.355
LGA    W      85      W      85          1.515
LGA    V      86      V      86          1.613
LGA    T      87      T      87          2.087
LGA    V      88      V      88          2.271
LGA    R      89      R      89          1.385
LGA    L      90      L      90          0.917
LGA    M      91      M      91          1.793
LGA    C      92      C      92          2.021
LGA    D      93      D      93          2.098
LGA    F      94      F      94          0.943
LGA    L      95      L      95          1.981
LGA    S      96      S      96          1.088
LGA    G      97      G      97          1.219
LGA    A      98      A      98          2.253
LGA    K      99      K      99          2.443
LGA    L     100      L     100          2.829
LGA    G     101      G     101          2.131
LGA    D     102      D     102          1.653
LGA    W     103      W     103          3.483
LGA    V     104      V     104          1.002
LGA    E     105      E     105          1.814
LGA    G     106      G     106          1.841
LGA    E     107      E     107          1.609
LGA    G     108      G     108          2.256
LGA    E     109      E     109          3.032
LGA    L     110      -       -           -
LGA    I     111      L     110          1.903
LGA    S     112      I     111          1.223
LGA    E     113      S     112          0.785
LGA    E     114      E     113          5.611
LGA    D     115      E     114          3.451
LGA    -       -      D     115           -
LGA    -       -      M     116           -
LGA    M     116      L     117          3.274
LGA    L     117      F     118          1.592
LGA    F     118      T     119          4.028
LGA    T     119      V     120          1.309
LGA    V     120      R     121          2.594
LGA    R     121      G     122          2.813
LGA    G     122      R     123          1.087
LGA    R     123      I     124          4.192
LGA    I     124      W     125          1.471
LGA    W     125      A     126          3.578
LGA    A     126      G     127          2.631
LGA    G     127      -       -           -
LGA    E     128      E     128          1.856
LGA    R     129      R     129          1.712
LGA    T     130      T     130          1.240
LGA    L     131      L     131          1.455
LGA    I     132      I     132          2.594
LGA    T     133      T     133          3.175
LGA    G     134      G     134          3.219
LGA    T     135      T     135          1.999
LGA    G     136      G     136          2.060
LGA    V     137      V     137          2.721
LGA    F     138      F     138          2.357
LGA    K     139      K     139          1.024
LGA    A     140      A     140          2.798
LGA    L     141      L     141          3.708
LGA    S     142      -       -           -
LGA    A     143      S     142           #
LGA    -       -      A     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  128  128    5.0    111    2.35    83.78     58.927     4.524

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.641876 * X  +  -0.379257 * Y  +   0.666452 * Z  +   9.865437
  Y_new =  -0.236383 * X  +  -0.924663 * Y  +  -0.298531 * Z  +  -5.338507
  Z_new =   0.729464 * X  +   0.034082 * Y  +  -0.683169 * Z  + -15.149520 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.091745   -0.049847  [ DEG:   177.1440     -2.8560 ]
  Theta =  -0.817539   -2.324054  [ DEG:   -46.8415   -133.1585 ]
  Phi   =  -0.352856    2.788737  [ DEG:   -20.2172    159.7828 ]
 
# 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: T0322TS168_2-D1                               
REMARK     2: T0322_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0322TS168_2-D1.T0322_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  128  128   5.0  111   2.35   83.78  58.927
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS168_2-D1
PFRMAT TS
TARGET T0322
MODEL 2
PARENT N/A
ATOM     16  CA  GLY    16      20.593   1.384  12.048  1.00 25.00           C
ATOM     17  CA  PHE    17      18.546   2.977   9.290  1.00 25.00           C
ATOM     18  CA  SER    18      15.321   0.913   9.426  1.00 25.00           C
ATOM     19  CA  GLN    19      12.457  -0.786   7.550  1.00 25.00           C
ATOM     20  CA  LEU    20      10.902   2.461   6.152  1.00 25.00           C
ATOM     21  CA  ASN    21       8.019   4.083   4.258  1.00 25.00           C
ATOM     22  CA  TRP    22       9.650   5.017   0.949  1.00 25.00           C
ATOM     23  CA  SER    23      11.961   2.102   0.264  1.00 25.00           C
ATOM     24  CA  ARG    24      10.630   0.703  -3.031  1.00 25.00           C
ATOM     25  CA  GLY    25       8.041   2.952  -4.643  1.00 25.00           C
ATOM     26  CA  PHE    26       7.376   0.672  -7.635  1.00 25.00           C
ATOM     27  CA  GLY    27       8.221  -2.855  -8.867  1.00 25.00           C
ATOM     28  CA  ARG    28       7.886  -4.209  -5.300  1.00 25.00           C
ATOM     29  CA  GLN    29       4.488  -2.480  -4.937  1.00 25.00           C
ATOM     30  CA  ILE    30       2.168  -4.873  -6.867  1.00 25.00           C
ATOM     31  CA  GLY    31       4.072  -7.483  -4.793  1.00 25.00           C
ATOM     32  CA  PRO    32       5.502  -8.762  -8.089  1.00 25.00           C
ATOM     33  CA  LEU    33       9.315  -8.888  -7.625  1.00 25.00           C
ATOM     34  CA  PHE    34       9.710 -12.472  -8.837  1.00 25.00           C
ATOM     35  CA  GLU    35       9.939 -15.670 -10.897  1.00 25.00           C
ATOM     36  CA  HIS    36      11.220 -17.376 -14.012  1.00 25.00           C
ATOM     37  CA  ARG    37      11.328 -16.971 -17.751  1.00 25.00           C
ATOM     38  CA  GLU    38      13.155 -19.397 -20.017  1.00 25.00           C
ATOM     39  CA  GLY    39      16.605 -20.413 -21.153  1.00 25.00           C
ATOM     40  CA  PRO    40      17.924 -17.764 -18.699  1.00 25.00           C
ATOM     41  CA  GLY    41      18.085 -15.036 -21.394  1.00 25.00           C
ATOM     42  CA  GLN    42      15.627 -12.306 -20.406  1.00 25.00           C
ATOM     43  CA  ALA    43      14.055 -12.446 -16.915  1.00 25.00           C
ATOM     44  CA  ARG    44      10.932 -11.640 -14.886  1.00 25.00           C
ATOM     45  CA  LEU    45       7.477 -12.068 -13.423  1.00 25.00           C
ATOM     46  CA  ALA    46       4.411 -13.302 -11.443  1.00 25.00           C
ATOM     47  CA  PHE    47       2.145 -10.257 -11.569  1.00 25.00           C
ATOM     48  CA  ARG    48       0.566 -11.647  -8.395  1.00 25.00           C
ATOM     49  CA  VAL    49      -3.263 -11.253  -8.174  1.00 25.00           C
ATOM     50  CA  GLU    50      -4.506 -10.645  -4.624  1.00 25.00           C
ATOM     51  CA  GLU    51      -7.910  -9.082  -4.073  1.00 25.00           C
ATOM     52  CA  HIS    52      -6.401  -5.680  -3.173  1.00 25.00           C
ATOM     53  CA  HIS    53      -5.081  -5.292  -6.747  1.00 25.00           C
ATOM     54  CA  THR    54      -8.215  -6.526  -8.485  1.00 25.00           C
ATOM     55  CA  ASN    55     -11.639  -6.294 -10.097  1.00 25.00           C
ATOM     56  CA  GLY    56     -14.624  -8.136  -8.687  1.00 25.00           C
ATOM     57  CA  LEU    57     -16.245  -7.514 -12.083  1.00 25.00           C
ATOM     58  CA  GLY    58     -14.381 -10.475 -13.504  1.00 25.00           C
ATOM     59  CA  ASN    59     -10.889  -9.602 -14.879  1.00 25.00           C
ATOM     60  CA  CYS    60      -7.580  -8.271 -13.598  1.00 25.00           C
ATOM     61  CA  HIS    61      -7.697  -4.435 -13.779  1.00 25.00           C
ATOM     62  CA  GLY    62      -5.935  -4.543 -17.194  1.00 25.00           C
ATOM     63  CA  GLY    63      -3.961  -1.653 -15.639  1.00 25.00           C
ATOM     64  CA  MET    64      -2.250  -4.087 -13.227  1.00 25.00           C
ATOM     65  CA  LEU    65      -1.348  -6.389 -16.151  1.00 25.00           C
ATOM     66  CA  MET    66       0.100  -3.413 -18.080  1.00 25.00           C
ATOM     67  CA  SER    67       2.166  -2.402 -15.018  1.00 25.00           C
ATOM     68  CA  PHE    68       3.472  -5.987 -14.684  1.00 25.00           C
ATOM     69  CA  ALA    69       4.424  -6.011 -18.394  1.00 25.00           C
ATOM     70  CA  ASP    70       6.258  -2.676 -17.971  1.00 25.00           C
ATOM     71  CA  MET    71       8.141  -4.067 -14.940  1.00 25.00           C
ATOM     72  CA  ALA    72       9.123  -7.177 -16.948  1.00 25.00           C
ATOM     73  CA  TRP    73      10.370  -4.962 -19.813  1.00 25.00           C
ATOM     74  CA  GLY    74      12.426  -2.880 -17.342  1.00 25.00           C
ATOM     75  CA  ARG    75      13.935  -6.075 -15.867  1.00 25.00           C
ATOM     76  CA  ILE    76      14.827  -7.306 -19.383  1.00 25.00           C
ATOM     77  CA  ILE    77      16.478  -3.941 -20.168  1.00 25.00           C
ATOM     78  CA  SER    78      18.484  -4.137 -16.911  1.00 25.00           C
ATOM     79  CA  LEU    79      19.607  -7.691 -17.789  1.00 25.00           C
ATOM     80  CA  GLN    80      22.888  -6.283 -19.003  1.00 25.00           C
ATOM     81  CA  LYS    81      24.066  -2.993 -17.429  1.00 25.00           C
ATOM     82  CA  SER    82      25.529  -1.668 -20.642  1.00 25.00           C
ATOM     83  CA  TYR    83      22.222   0.112 -21.122  1.00 25.00           C
ATOM     84  CA  SER    84      20.527   3.016 -19.308  1.00 25.00           C
ATOM     85  CA  TRP    85      17.120   1.256 -19.241  1.00 25.00           C
ATOM     86  CA  VAL    86      14.326   3.765 -19.992  1.00 25.00           C
ATOM     87  CA  THR    87      10.913   2.128 -20.414  1.00 25.00           C
ATOM     88  CA  VAL    88       9.286   4.512 -22.918  1.00 25.00           C
ATOM     89  CA  ARG    89       6.461   3.438 -25.320  1.00 25.00           C
ATOM     90  CA  LEU    90       3.774   0.818 -24.607  1.00 25.00           C
ATOM     91  CA  MET    91       0.445  -0.699 -25.713  1.00 25.00           C
ATOM     92  CA  CYS    92      -1.259  -3.400 -23.646  1.00 25.00           C
ATOM     93  CA  ASP    93      -4.229  -4.670 -25.655  1.00 25.00           C
ATOM     94  CA  PHE    94      -6.406  -7.531 -24.510  1.00 25.00           C
ATOM     95  CA  LEU    95      -8.697 -10.500 -24.235  1.00 25.00           C
ATOM     96  CA  SER    96      -9.127 -13.602 -21.992  1.00 25.00           C
ATOM     97  CA  GLY    97      -8.663 -13.169 -18.285  1.00 25.00           C
ATOM     98  CA  ALA    98      -8.244 -15.039 -15.004  1.00 25.00           C
ATOM     99  CA  LYS    99     -10.938 -14.398 -12.374  1.00 25.00           C
ATOM    100  CA  LEU   100      -8.364 -15.481  -9.891  1.00 25.00           C
ATOM    101  CA  GLY   101      -6.374 -17.867  -7.741  1.00 25.00           C
ATOM    102  CA  ASP   102      -3.456 -18.333 -10.101  1.00 25.00           C
ATOM    103  CA  TRP   103      -2.862 -14.995 -11.893  1.00 25.00           C
ATOM    104  CA  VAL   104      -0.020 -13.995 -14.196  1.00 25.00           C
ATOM    105  CA  GLU   105       2.889 -13.438 -16.584  1.00 25.00           C
ATOM    106  CA  GLY   106       4.915 -10.663 -18.084  1.00 25.00           C
ATOM    107  CA  GLU   107       8.119 -12.357 -19.070  1.00 25.00           C
ATOM    108  CA  GLY   108       9.383  -9.772 -21.556  1.00 25.00           C
ATOM    109  CA  GLU   109      11.350 -12.287 -23.618  1.00 25.00           C
ATOM    110  CA  LEU   110      14.437 -10.586 -25.077  1.00 25.00           C
ATOM    111  CA  ILE   111      13.532 -10.535 -28.713  1.00 25.00           C
ATOM    112  CA  SER   112      13.830  -7.535 -31.018  1.00 25.00           C
ATOM    113  CA  GLU   113      16.419  -5.522 -33.017  1.00 25.00           C
ATOM    114  CA  GLU   114      15.800  -3.521 -36.246  1.00 25.00           C
ATOM    115  CA  ASP   115      15.615  -0.280 -34.266  1.00 25.00           C
ATOM    116  CA  MET   116      14.729  -0.684 -30.593  1.00 25.00           C
ATOM    117  CA  LEU   117      15.782  -3.566 -28.394  1.00 25.00           C
ATOM    118  CA  PHE   118      13.564  -5.556 -26.044  1.00 25.00           C
ATOM    119  CA  THR   119      10.133  -7.177 -26.303  1.00 25.00           C
ATOM    120  CA  VAL   120       7.058  -9.368 -25.974  1.00 25.00           C
ATOM    121  CA  ARG   121       3.980 -11.456 -26.722  1.00 25.00           C
ATOM    122  CA  GLY   122       3.765 -11.724 -22.889  1.00 25.00           C
ATOM    123  CA  ARG   123       4.476 -15.228 -21.596  1.00 25.00           C
ATOM    124  CA  ILE   124       0.816 -15.711 -20.632  1.00 25.00           C
ATOM    125  CA  TRP   125       1.500 -18.245 -17.907  1.00 25.00           C
ATOM    126  CA  ALA   126      -0.721 -19.831 -15.218  1.00 25.00           C
ATOM    127  CA  GLY   127      -1.351 -22.970 -17.270  1.00 25.00           C
ATOM    128  CA  GLU   128      -4.120 -22.533 -19.827  1.00 25.00           C
ATOM    129  CA  ARG   129      -3.313 -19.721 -22.158  1.00 25.00           C
ATOM    130  CA  THR   130      -3.829 -15.994 -22.607  1.00 25.00           C
ATOM    131  CA  LEU   131      -3.840 -13.387 -19.886  1.00 25.00           C
ATOM    132  CA  ILE   132      -2.053 -10.048 -20.658  1.00 25.00           C
ATOM    133  CA  THR   133      -0.955  -8.535 -23.935  1.00 25.00           C
ATOM    134  CA  GLY   134       2.482  -7.055 -24.150  1.00 25.00           C
ATOM    135  CA  THR   135       4.905  -4.787 -26.098  1.00 25.00           C
ATOM    136  CA  GLY   136       7.267  -2.749 -23.896  1.00 25.00           C
ATOM    137  CA  VAL   137      10.644  -1.003 -24.478  1.00 25.00           C
ATOM    138  CA  PHE   138      14.356  -0.810 -23.904  1.00 25.00           C
ATOM    139  CA  LYS   139      15.635   2.506 -25.121  1.00 25.00           C
ATOM    140  CA  ALA   140      19.137   0.924 -24.994  1.00 25.00           C
ATOM    141  CA  LEU   141      20.185   4.550 -24.450  1.00 25.00           C
ATOM    142  CA  SER   142      22.331   7.442 -23.226  1.00 25.00           C
ATOM    143  CA  ALA   143      26.022   7.284 -24.063  1.00 25.00           C
TER
END
