
#######################################################
#                                                     #
#                        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   89 (   89),  selected   89 , name T0299TS393_4-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS393_4-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      F      82           -
LGA    -       -      E      83           -
LGA    -       -      A      84           -
LGA    -       -      E      85           -
LGA    -       -      L      86           -
LGA    -       -      E      87           -
LGA    -       -      N      88           -
LGA    -       -      L      89           -
LGA    -       -      P      90           -
LGA    -       -      A      91           -
LGA    -       -      W      92           -
LGA    -       -      W      93           -
LGA    -       -      S      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    -       -      L      97           -
LGA    -       -      A      98           -
LGA    -       -      R      99           -
LGA    -       -      K     100           -
LGA    -       -      D     101           -
LGA    -       -      F     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      Y     105           -
LGA    -       -      T     106           -
LGA    -       -      E     107           -
LGA    -       -      G     108           -
LGA    -       -      L     109           -
LGA    -       -      D     110           -
LGA    -       -      V     111           -
LGA    -       -      D     112           -
LGA    L      79      Q     113           #
LGA    E      80      V     114           #
LGA    -       -      I     115           -
LGA    D      81      A     116           #
LGA    F      82      T     117          4.502
LGA    E      83      V     118          1.007
LGA    A      84      E     119          2.094
LGA    -       -      S     120           -
LGA    E      85      L     121          2.964
LGA    L      86      E     122           -
LGA    E      87      -       -           -
LGA    N      88      L     123          4.762
LGA    L      89      K     124          3.831
LGA    P      90      D     125          2.918
LGA    A      91      E     126          4.314
LGA    W      92      V     127          1.096
LGA    W      93      L     128          3.977
LGA    -       -      Y     129           -
LGA    -       -      F     130           -
LGA    -       -      G     131           -
LGA    -       -      K     132           -
LGA    -       -      L     133           -
LGA    -       -      G     134           -
LGA    -       -      I     135           -
LGA    -       -      F     136           -
LGA    -       -      W     137           -
LGA    S      94      G     138          3.050
LGA    R      95      K     139          3.031
LGA    D      96      F     140          3.711
LGA    -       -      S     141           -
LGA    L      97      E     142          4.621
LGA    A      98      E     143           -
LGA    R      99      S     144          3.486
LGA    K     100      Y     145          3.238
LGA    D     101      S     146          3.626
LGA    -       -      K     147           -
LGA    -       -      T     148           -
LGA    -       -      A     149           -
LGA    -       -      Y     150           -
LGA    F     102      H     151          4.002
LGA    L     103      K     152          1.397
LGA    F     104      Y     153          2.076
LGA    -       -      L     154           -
LGA    -       -      L     155           -
LGA    Y     105      K     156          2.041
LGA    T     106      V     157          2.927
LGA    E     107      P     158          2.671
LGA    G     108      F     159          1.411
LGA    L     109      Y     160          2.608
LGA    D     110      R     161          4.537
LGA    V     111      H     162          2.237
LGA    D     112      I     163           #
LGA    Q     113      T     164          4.245
LGA    V     114      -       -           -
LGA    I     115      -       -           -
LGA    A     116      -       -           -
LGA    T     117      -       -           -
LGA    V     118      -       -           -
LGA    E     119      -       -           -
LGA    S     120      -       -           -
LGA    L     121      I     165          2.644
LGA    E     122      R     166          1.989
LGA    L     123      N     167           #
LGA    K     124      -       -           -
LGA    D     125      -       -           -
LGA    E     126      -       -           -
LGA    V     127      -       -           -
LGA    L     128      -       -           -
LGA    Y     129      -       -           -
LGA    F     130      -       -           -
LGA    G     131      -       -           -
LGA    K     132      -       -           -
LGA    L     133      -       -           -
LGA    G     134      -       -           -
LGA    I     135      -       -           -
LGA    F     136      -       -           -
LGA    W     137      -       -           -
LGA    G     138      -       -           -
LGA    K     139      -       -           -
LGA    F     140      -       -           -
LGA    S     141      -       -           -
LGA    E     142      -       -           -
LGA    E     143      -       -           -
LGA    S     144      -       -           -
LGA    Y     145      -       -           -
LGA    S     146      -       -           -
LGA    K     147      -       -           -
LGA    T     148      -       -           -
LGA    A     149      -       -           -
LGA    Y     150      -       -           -
LGA    H     151      -       -           -
LGA    K     152      -       -           -
LGA    Y     153      -       -           -
LGA    L     154      -       -           -
LGA    L     155      -       -           -
LGA    K     156      -       -           -
LGA    V     157      -       -           -
LGA    P     158      -       -           -
LGA    F     159      -       -           -
LGA    Y     160      -       -           -
LGA    R     161      -       -           -
LGA    H     162      -       -           -
LGA    I     163      -       -           -
LGA    T     164      -       -           -
LGA    I     165      -       -           -
LGA    R     166      -       -           -
LGA    N     167      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     30    3.22     0.00     19.338     0.904

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.515787 * X  +  -0.258684 * Y  +  -0.816729 * Z  +  20.131935
  Y_new =   0.147465 * X  +   0.912288 * Y  +  -0.382079 * Z  +  45.925404
  Z_new =   0.843930 * X  +  -0.317511 * Y  +  -0.432400 * Z  +   5.897345 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.508216    0.633377  [ DEG:  -143.7102     36.2898 ]
  Theta =  -1.004567   -2.137026  [ DEG:   -57.5575   -122.4425 ]
  Phi   =   2.863118   -0.278475  [ DEG:   164.0446    -15.9554 ]
 
# 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: T0299TS393_4-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS393_4-D2.T0299_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   89   89   5.0   30   3.22    0.00  19.338
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS393_4-D2
PFRMAT TS
TARGET T0299
MODEL 4
PARENT N/A
ATOM     79  CA  LEU    79      16.829  56.941  10.331  1.00 25.00           C
ATOM     80  CA  GLU    80      16.531  60.595   9.223  1.00 25.00           C
ATOM     81  CA  ASP    81      19.524  60.150   6.875  1.00 25.00           C
ATOM     82  CA  PHE    82      17.931  56.996   5.400  1.00 25.00           C
ATOM     83  CA  GLU    83      14.640  58.880   4.861  1.00 25.00           C
ATOM     84  CA  ALA    84      16.526  61.725   3.124  1.00 25.00           C
ATOM     85  CA  GLU    85      18.310  59.198   0.866  1.00 25.00           C
ATOM     86  CA  LEU    86      14.954  57.575  -0.011  1.00 25.00           C
ATOM     87  CA  GLU    87      13.483  61.011  -0.848  1.00 25.00           C
ATOM     88  CA  ASN    88      16.520  62.937  -2.118  1.00 25.00           C
ATOM     89  CA  LEU    89      19.951  61.733  -3.140  1.00 25.00           C
ATOM     90  CA  PRO    90      19.513  61.005  -6.897  1.00 25.00           C
ATOM     91  CA  ALA    91      17.347  64.066  -7.443  1.00 25.00           C
ATOM     92  CA  TRP    92      13.890  62.689  -6.487  1.00 25.00           C
ATOM     93  CA  TRP    93      14.889  59.100  -5.536  1.00 25.00           C
ATOM     94  CA  SER    94      15.298  59.254  -9.282  1.00 25.00           C
ATOM     95  CA  ARG    95      18.245  58.330 -11.549  1.00 25.00           C
ATOM     96  CA  ASP    96      16.200  55.156 -12.188  1.00 25.00           C
ATOM     97  CA  LEU    97      19.156  52.995 -11.067  1.00 25.00           C
ATOM     98  CA  ALA    98      19.514  55.091  -7.883  1.00 25.00           C
ATOM     99  CA  ARG    99      23.206  54.658  -8.511  1.00 25.00           C
ATOM    100  CA  LYS   100      23.133  50.883  -8.798  1.00 25.00           C
ATOM    101  CA  ASP   101      20.822  47.841  -8.880  1.00 25.00           C
ATOM    102  CA  PHE   102      22.261  47.858  -5.325  1.00 25.00           C
ATOM    103  CA  LEU   103      20.778  49.970  -2.496  1.00 25.00           C
ATOM    104  CA  PHE   104      18.588  49.461   0.577  1.00 25.00           C
ATOM    105  CA  TYR   105      19.073  47.459   3.794  1.00 25.00           C
ATOM    106  CA  THR   106      16.264  47.507   6.442  1.00 25.00           C
ATOM    107  CA  GLU   107      14.052  50.494   7.321  1.00 25.00           C
ATOM    108  CA  GLY   108      10.335  51.053   8.017  1.00 25.00           C
ATOM    109  CA  LEU   109       9.195  49.570   4.704  1.00 25.00           C
ATOM    110  CA  ASP   110       5.568  48.500   4.295  1.00 25.00           C
ATOM    111  CA  VAL   111       6.088  45.439   6.438  1.00 25.00           C
ATOM    112  CA  ASP   112       4.524  42.831   4.108  1.00 25.00           C
ATOM    113  CA  GLN   113       5.908  44.690   1.059  1.00 25.00           C
ATOM    114  CA  VAL   114       9.385  44.784   2.664  1.00 25.00           C
ATOM    115  CA  ILE   115       9.187  41.026   3.370  1.00 25.00           C
ATOM    116  CA  ALA   116       8.173  40.370  -0.263  1.00 25.00           C
ATOM    117  CA  THR   117      11.115  42.490  -1.493  1.00 25.00           C
ATOM    118  CA  VAL   118       9.191  45.462  -2.758  1.00 25.00           C
ATOM    119  CA  GLU   119       7.960  43.237  -5.651  1.00 25.00           C
ATOM    120  CA  SER   120       8.921  46.067  -7.935  1.00 25.00           C
ATOM    121  CA  LEU   121       6.142  47.877  -6.079  1.00 25.00           C
ATOM    122  CA  GLU   122       3.013  49.975  -6.701  1.00 25.00           C
ATOM    123  CA  LEU   123       3.786  51.580  -3.417  1.00 25.00           C
ATOM    124  CA  LYS   124       6.801  53.807  -2.939  1.00 25.00           C
ATOM    125  CA  ASP   125       7.172  55.025   0.622  1.00 25.00           C
ATOM    126  CA  GLU   126      10.473  54.125   2.353  1.00 25.00           C
ATOM    127  CA  VAL   127      13.465  51.800   2.508  1.00 25.00           C
ATOM    128  CA  LEU   128      13.941  48.063   1.978  1.00 25.00           C
ATOM    129  CA  TYR   129      15.498  44.908   0.685  1.00 25.00           C
ATOM    130  CA  PHE   130      18.842  45.053  -1.019  1.00 25.00           C
ATOM    131  CA  GLY   131      19.024  43.433  -4.454  1.00 25.00           C
ATOM    132  CA  LYS   132      18.272  39.767  -3.795  1.00 25.00           C
ATOM    133  CA  LEU   133      21.954  39.423  -2.857  1.00 25.00           C
ATOM    134  CA  GLY   134      20.928  40.078   0.687  1.00 25.00           C
ATOM    135  CA  ILE   135      17.372  40.425   1.965  1.00 25.00           C
ATOM    136  CA  PHE   136      17.896  42.727   4.995  1.00 25.00           C
ATOM    137  CA  TRP   137      15.994  42.299   8.312  1.00 25.00           C
ATOM    138  CA  GLY   138      14.247  44.811  10.570  1.00 25.00           C
ATOM    139  CA  LYS   139      11.567  45.870  13.047  1.00 25.00           C
ATOM    140  CA  PHE   140       8.345  47.777  13.529  1.00 25.00           C
ATOM    141  CA  SER   141       5.068  48.634  15.241  1.00 25.00           C
ATOM    142  CA  GLU   142       1.302  48.455  15.734  1.00 25.00           C
ATOM    143  CA  GLU   143      -0.941  45.447  15.190  1.00 25.00           C
ATOM    144  CA  SER   144       0.022  43.090  12.379  1.00 25.00           C
ATOM    145  CA  TYR   145       2.405  43.399   9.395  1.00 25.00           C
ATOM    146  CA  SER   146       5.382  43.754  11.779  1.00 25.00           C
ATOM    147  CA  LYS   147       4.243  40.646  13.705  1.00 25.00           C
ATOM    148  CA  THR   148       3.938  38.694  10.423  1.00 25.00           C
ATOM    149  CA  ALA   149       7.460  39.804   9.408  1.00 25.00           C
ATOM    150  CA  TYR   150       8.818  38.694  12.813  1.00 25.00           C
ATOM    151  CA  HIS   151       7.102  35.294  12.417  1.00 25.00           C
ATOM    152  CA  LYS   152       5.631  35.652  15.954  1.00 25.00           C
ATOM    153  CA  TYR   153       6.178  34.423  19.511  1.00 25.00           C
ATOM    154  CA  LEU   154       9.834  34.436  18.424  1.00 25.00           C
ATOM    155  CA  LEU   155      12.061  32.071  20.366  1.00 25.00           C
ATOM    156  CA  LYS   156      12.762  29.311  22.928  1.00 25.00           C
ATOM    157  CA  VAL   157      15.453  29.321  25.617  1.00 25.00           C
ATOM    158  CA  PRO   158      18.937  30.550  26.476  1.00 25.00           C
ATOM    159  CA  PHE   159      21.157  33.293  25.233  1.00 25.00           C
ATOM    160  CA  TYR   160      24.123  34.958  26.902  1.00 25.00           C
ATOM    161  CA  ARG   161      26.654  37.705  26.411  1.00 25.00           C
ATOM    162  CA  HIS   162      28.106  40.333  23.978  1.00 25.00           C
ATOM    163  CA  ILE   163      26.515  41.292  20.694  1.00 25.00           C
ATOM    164  CA  THR   164      24.279  41.617  17.704  1.00 25.00           C
ATOM    165  CA  ILE   165      22.613  41.392  14.242  1.00 25.00           C
ATOM    166  CA  ARG   166      19.963  42.590  11.768  1.00 25.00           C
ATOM    167  CA  ASN   167      18.000  45.067  13.960  1.00 25.00           C
TER
END
