
#######################################################
#                                                     #
#                        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  116 (  116),  selected  116 , name T0323TS393_5-D2
# Molecule2: number of CA atoms  116 (  868),  selected  116 , name T0323_D2.pdb
# PARAMETERS: T0323TS393_5-D2.T0323_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    P      34      P      34           -
LGA    T      35      T      35           -
LGA    K      36      K      36           -
LGA    P      37      P      37           -
LGA    N      38      N      38           -
LGA    P      39      P      39          4.282
LGA    F      40      F      40          5.455
LGA    Q      41      Q      41          4.699
LGA    S      42      S      42          2.266
LGA    L      43      L      43          2.632
LGA    V      44      V      44          2.911
LGA    S      45      S      45          1.801
LGA    S      46      S      46          1.320
LGA    I      47      I      47          1.783
LGA    V      48      V      48          1.163
LGA    E      49      E      49          2.150
LGA    Q      50      Q      50          2.388
LGA    Q      51      Q      51          4.837
LGA    -       -      L      52           -
LGA    -       -      S      53           -
LGA    -       -      I      54           -
LGA    -       -      K      55           -
LGA    L      52      A      56          4.512
LGA    S      53      A      57          3.885
LGA    I      54      S      58          2.226
LGA    K      55      A      59          0.871
LGA    A      56      I      60          0.991
LGA    A      57      Y      61          1.574
LGA    S      58      G      62          1.470
LGA    A      59      R      63          1.256
LGA    I      60      V      64          1.361
LGA    Y      61      E      65          2.413
LGA    G      62      Q      66          2.902
LGA    R      63      L      67          2.515
LGA    V      64      V      68          2.896
LGA    E      65      G      69          3.621
LGA    Q      66      G      70          4.017
LGA    L      67      -       -           -
LGA    V      68      -       -           -
LGA    G      69      A      71           #
LGA    G      70      L      72           -
LGA    A      71      -       -           -
LGA    L      72      -       -           -
LGA    E      73      -       -           -
LGA    K      74      -       -           -
LGA    P      75      -       -           -
LGA    E      76      -       -           -
LGA    Q      77      -       -           -
LGA    L      78      E      73          4.996
LGA    -       -      K      74           -
LGA    Y      79      P      75          3.425
LGA    R      80      E      76          1.613
LGA    -       -      Q      77           -
LGA    V      81      L      78          3.797
LGA    S      82      Y      79          1.992
LGA    D      83      R      80           #
LGA    E      84      V      81          4.798
LGA    A      85      S      82          2.676
LGA    L      86      D      83          2.948
LGA    R      87      E      84          3.380
LGA    Q      88      A      85          2.661
LGA    -       -      L      86           -
LGA    A      89      R      87          2.158
LGA    -       -      Q      88           -
LGA    -       -      A      89           -
LGA    G      90      G      90          2.077
LGA    V      91      V      91          1.339
LGA    S      92      S      92          1.499
LGA    K      93      K      93          3.128
LGA    R      94      R      94          2.061
LGA    K      95      K      95          2.521
LGA    I      96      I      96          2.462
LGA    E      97      E      97          1.637
LGA    Y      98      Y      98          1.411
LGA    I      99      I      99          1.232
LGA    R     100      R     100          1.742
LGA    H     101      H     101          2.449
LGA    V     102      V     102          2.300
LGA    C     103      C     103          2.037
LGA    E     104      E     104          3.640
LGA    H     105      H     105          4.174
LGA    V     106      V     106          3.836
LGA    E     107      E     107          4.205
LGA    S     108      S     108           -
LGA    G     109      -       -           -
LGA    R     110      -       -           -
LGA    L     111      -       -           -
LGA    D     112      -       -           -
LGA    F     113      -       -           -
LGA    T     114      -       -           -
LGA    E     115      G     109           #
LGA    -       -      R     110           -
LGA    -       -      L     111           -
LGA    L     116      D     112           #
LGA    E     117      F     113           #
LGA    G     118      T     114           #
LGA    A     119      E     115           -
LGA    E     120      L     116           #
LGA    -       -      E     117           -
LGA    -       -      G     118           -
LGA    -       -      A     119           -
LGA    -       -      E     120           -
LGA    -       -      A     121           -
LGA    -       -      T     122           -
LGA    -       -      T     123           -
LGA    -       -      V     124           -
LGA    A     121      I     125          3.837
LGA    T     122      E     126          2.618
LGA    T     123      K     127          1.325
LGA    V     124      L     128          1.798
LGA    I     125      T     129          2.905
LGA    E     126      A     130          2.719
LGA    K     127      I     131          2.013
LGA    -       -      K     132           -
LGA    L     128      G     133          4.172
LGA    T     129      I     134          3.170
LGA    A     130      -       -           -
LGA    I     131      -       -           -
LGA    K     132      -       -           -
LGA    G     133      -       -           -
LGA    I     134      -       -           -
LGA    G     135      G     135           #
LGA    Q     136      Q     136           -
LGA    W     137      -       -           -
LGA    T     138      -       -           -
LGA    A     139      -       -           -
LGA    E     140      W     137          4.770
LGA    M     141      -       -           -
LGA    F     142      T     138          4.561
LGA    M     143      A     139          3.278
LGA    M     144      E     140          2.601
LGA    F     145      M     141          1.868
LGA    S     146      F     142          1.665
LGA    L     147      M     143          2.047
LGA    G     148      M     144          5.459
LGA    -       -      F     145           -
LGA    -       -      S     146           -
LGA    -       -      L     147           -
LGA    -       -      G     148           -
LGA    R     149      R     149           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  116  116    5.0     74    2.99    43.24     38.097     2.398

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.647563 * X  +  -0.738940 * Y  +   0.186089 * Z  +  13.246499
  Y_new =   0.692989 * X  +  -0.672638 * Y  +  -0.259469 * Z  +  41.286949
  Z_new =   0.316902 * X  +  -0.039065 * Y  +   0.947653 * Z  +  -0.465361 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.041200    3.100393  [ DEG:    -2.3606    177.6394 ]
  Theta =  -0.322462   -2.819131  [ DEG:   -18.4757   -161.5243 ]
  Phi   =   2.322321   -0.819271  [ DEG:   133.0592    -46.9408 ]
 
# 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: T0323TS393_5-D2                               
REMARK     2: T0323_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0323TS393_5-D2.T0323_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  116  116   5.0   74   2.99   43.24  38.097
REMARK  ---------------------------------------------------------- 
MOLECULE T0323TS393_5-D2
PFRMAT TS
TARGET T0323
MODEL 5
PARENT N/A
ATOM     34  CA  PRO    34      32.980  42.392  -1.804  1.00 25.00           C
ATOM     35  CA  THR    35      30.348  42.247  -4.582  1.00 25.00           C
ATOM     36  CA  LYS    36      26.668  41.730  -5.580  1.00 25.00           C
ATOM     37  CA  PRO    37      23.552  43.630  -6.544  1.00 25.00           C
ATOM     38  CA  ASN    38      19.777  43.482  -5.758  1.00 25.00           C
ATOM     39  CA  PRO    39      16.737  41.187  -5.301  1.00 25.00           C
ATOM     40  CA  PHE    40      13.835  43.396  -6.469  1.00 25.00           C
ATOM     41  CA  GLN    41      12.112  40.350  -8.026  1.00 25.00           C
ATOM     42  CA  SER    42      12.557  38.399  -4.761  1.00 25.00           C
ATOM     43  CA  LEU    43      11.070  41.321  -2.783  1.00 25.00           C
ATOM     44  CA  VAL    44       8.085  41.458  -5.179  1.00 25.00           C
ATOM     45  CA  SER    45       7.553  37.688  -4.770  1.00 25.00           C
ATOM     46  CA  SER    46       7.666  38.061  -0.960  1.00 25.00           C
ATOM     47  CA  ILE    47       5.104  40.901  -1.136  1.00 25.00           C
ATOM     48  CA  VAL    48       2.825  38.741  -3.329  1.00 25.00           C
ATOM     49  CA  GLU    49       3.123  35.850  -0.835  1.00 25.00           C
ATOM     50  CA  GLN    50       2.243  38.214   2.046  1.00 25.00           C
ATOM     51  CA  GLN    51      -0.805  39.484   0.107  1.00 25.00           C
ATOM     52  CA  LEU    52      -1.969  35.942  -0.283  1.00 25.00           C
ATOM     53  CA  SER    53      -2.391  32.266   0.768  1.00 25.00           C
ATOM     54  CA  ILE    54       0.377  30.128  -0.724  1.00 25.00           C
ATOM     55  CA  LYS    55      -1.929  28.841  -3.498  1.00 25.00           C
ATOM     56  CA  ALA    56      -1.841  32.271  -5.198  1.00 25.00           C
ATOM     57  CA  ALA    57       1.983  32.301  -4.995  1.00 25.00           C
ATOM     58  CA  SER    58       2.116  28.794  -6.527  1.00 25.00           C
ATOM     59  CA  ALA    59      -0.205  29.915  -9.358  1.00 25.00           C
ATOM     60  CA  ILE    60       2.017  32.967 -10.004  1.00 25.00           C
ATOM     61  CA  TYR    61       5.116  30.719 -10.109  1.00 25.00           C
ATOM     62  CA  GLY    62       3.366  28.382 -12.588  1.00 25.00           C
ATOM     63  CA  ARG    63       2.425  31.375 -14.784  1.00 25.00           C
ATOM     64  CA  VAL    64       6.050  32.606 -14.703  1.00 25.00           C
ATOM     65  CA  GLU    65       7.282  29.119 -15.697  1.00 25.00           C
ATOM     66  CA  GLN    66       4.778  29.032 -18.593  1.00 25.00           C
ATOM     67  CA  LEU    67       5.965  32.483 -19.755  1.00 25.00           C
ATOM     68  CA  VAL    68       9.606  31.304 -19.617  1.00 25.00           C
ATOM     69  CA  GLY    69       9.895  27.510 -19.678  1.00 25.00           C
ATOM     70  CA  GLY    70      12.772  25.163 -20.171  1.00 25.00           C
ATOM     71  CA  ALA    71      13.825  26.871 -23.381  1.00 25.00           C
ATOM     72  CA  LEU    72      13.051  30.575 -23.978  1.00 25.00           C
ATOM     73  CA  GLU    73      15.018  33.730 -24.863  1.00 25.00           C
ATOM     74  CA  LYS    74      18.729  34.266 -23.943  1.00 25.00           C
ATOM     75  CA  PRO    75      18.141  36.146 -20.679  1.00 25.00           C
ATOM     76  CA  GLU    76      16.255  39.297 -21.769  1.00 25.00           C
ATOM     77  CA  GLN    77      12.926  37.420 -21.516  1.00 25.00           C
ATOM     78  CA  LEU    78      13.852  36.199 -18.006  1.00 25.00           C
ATOM     79  CA  TYR    79      14.744  39.776 -16.970  1.00 25.00           C
ATOM     80  CA  ARG    80      11.391  41.032 -18.331  1.00 25.00           C
ATOM     81  CA  VAL    81       7.850  42.387 -18.657  1.00 25.00           C
ATOM     82  CA  SER    82       4.252  43.012 -19.642  1.00 25.00           C
ATOM     83  CA  ASP    83       0.515  43.785 -19.786  1.00 25.00           C
ATOM     84  CA  GLU    84      -2.692  41.739 -19.346  1.00 25.00           C
ATOM     85  CA  ALA    85      -0.894  39.403 -16.901  1.00 25.00           C
ATOM     86  CA  LEU    86       0.387  42.422 -14.923  1.00 25.00           C
ATOM     87  CA  ARG    87      -3.156  43.869 -14.788  1.00 25.00           C
ATOM     88  CA  GLN    88      -4.507  40.508 -13.545  1.00 25.00           C
ATOM     89  CA  ALA    89      -3.305  40.869  -9.970  1.00 25.00           C
ATOM     90  CA  GLY    90      -4.717  37.642  -8.489  1.00 25.00           C
ATOM     91  CA  VAL    91      -2.440  38.571  -5.525  1.00 25.00           C
ATOM     92  CA  SER    92      -4.110  41.676  -4.007  1.00 25.00           C
ATOM     93  CA  LYS    93      -1.452  44.233  -4.980  1.00 25.00           C
ATOM     94  CA  ARG    94       1.299  46.732  -4.055  1.00 25.00           C
ATOM     95  CA  LYS    95       3.908  43.930  -4.144  1.00 25.00           C
ATOM     96  CA  ILE    96       2.643  42.828  -7.587  1.00 25.00           C
ATOM     97  CA  GLU    97       2.865  46.435  -8.852  1.00 25.00           C
ATOM     98  CA  TYR    98       6.445  46.708  -7.518  1.00 25.00           C
ATOM     99  CA  ILE    99       7.371  43.429  -9.266  1.00 25.00           C
ATOM    100  CA  ARG   100       5.862  44.718 -12.541  1.00 25.00           C
ATOM    101  CA  HIS   101       7.851  47.973 -12.205  1.00 25.00           C
ATOM    102  CA  VAL   102      11.062  45.976 -11.596  1.00 25.00           C
ATOM    103  CA  CYS   103      10.349  43.838 -14.692  1.00 25.00           C
ATOM    104  CA  GLU   104       9.778  47.000 -16.774  1.00 25.00           C
ATOM    105  CA  HIS   105      13.081  48.464 -15.504  1.00 25.00           C
ATOM    106  CA  VAL   106      14.897  45.216 -16.411  1.00 25.00           C
ATOM    107  CA  GLU   107      13.355  45.305 -19.915  1.00 25.00           C
ATOM    108  CA  SER   108      11.322  43.055 -22.276  1.00 25.00           C
ATOM    109  CA  GLY   109       9.092  39.977 -22.136  1.00 25.00           C
ATOM    110  CA  ARG   110       8.344  37.452 -19.380  1.00 25.00           C
ATOM    111  CA  LEU   111       9.538  37.594 -15.802  1.00 25.00           C
ATOM    112  CA  ASP   112      12.345  37.292 -13.314  1.00 25.00           C
ATOM    113  CA  PHE   113      15.818  38.116 -12.040  1.00 25.00           C
ATOM    114  CA  THR   114      19.097  38.086 -14.019  1.00 25.00           C
ATOM    115  CA  GLU   115      20.370  41.083 -12.004  1.00 25.00           C
ATOM    116  CA  LEU   116      19.453  39.306  -8.737  1.00 25.00           C
ATOM    117  CA  GLU   117      21.302  36.161  -9.900  1.00 25.00           C
ATOM    118  CA  GLY   118      23.588  37.051  -7.036  1.00 25.00           C
ATOM    119  CA  ALA   119      22.445  39.062  -3.967  1.00 25.00           C
ATOM    120  CA  GLU   120      22.133  42.028  -1.551  1.00 25.00           C
ATOM    121  CA  ALA   121      21.310  45.626  -0.630  1.00 25.00           C
ATOM    122  CA  THR   122      20.334  49.320  -0.372  1.00 25.00           C
ATOM    123  CA  THR   123      18.638  49.136  -3.802  1.00 25.00           C
ATOM    124  CA  VAL   124      16.722  46.004  -2.713  1.00 25.00           C
ATOM    125  CA  ILE   125      15.601  47.773   0.494  1.00 25.00           C
ATOM    126  CA  GLU   126      14.424  50.789  -1.553  1.00 25.00           C
ATOM    127  CA  LYS   127      12.472  48.470  -3.893  1.00 25.00           C
ATOM    128  CA  LEU   128      10.844  46.757  -0.878  1.00 25.00           C
ATOM    129  CA  THR   129       9.880  50.169   0.570  1.00 25.00           C
ATOM    130  CA  ALA   130       8.360  51.194  -2.792  1.00 25.00           C
ATOM    131  CA  ILE   131       5.856  48.360  -2.173  1.00 25.00           C
ATOM    132  CA  LYS   132       3.416  49.665   0.447  1.00 25.00           C
ATOM    133  CA  GLY   133       2.622  46.146   1.563  1.00 25.00           C
ATOM    134  CA  ILE   134       6.135  45.855   3.120  1.00 25.00           C
ATOM    135  CA  GLY   135       4.976  45.558   6.724  1.00 25.00           C
ATOM    136  CA  GLN   136       3.034  42.396   5.869  1.00 25.00           C
ATOM    137  CA  TRP   137       5.207  40.290   8.217  1.00 25.00           C
ATOM    138  CA  THR   138       6.242  38.049   5.289  1.00 25.00           C
ATOM    139  CA  ALA   139       7.144  41.138   3.212  1.00 25.00           C
ATOM    140  CA  GLU   140       9.231  42.511   6.114  1.00 25.00           C
ATOM    141  CA  MET   141      11.039  39.150   6.436  1.00 25.00           C
ATOM    142  CA  PHE   142      11.759  39.149   2.675  1.00 25.00           C
ATOM    143  CA  MET   143      13.136  42.714   2.912  1.00 25.00           C
ATOM    144  CA  MET   144      15.372  41.682   5.845  1.00 25.00           C
ATOM    145  CA  PHE   145      16.653  38.679   3.843  1.00 25.00           C
ATOM    146  CA  SER   146      17.407  40.959   0.859  1.00 25.00           C
ATOM    147  CA  LEU   147      20.339  41.817   3.209  1.00 25.00           C
ATOM    148  CA  GLY   148      22.482  41.873   6.359  1.00 25.00           C
ATOM    149  CA  ARG   149      23.309  39.174   8.883  1.00 25.00           C
TER
END
