
#######################################################
#                                                     #
#                        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 T0299TS599_5-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS599_5-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      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      E      80           #
LGA    G     108      D      81          3.231
LGA    L     109      F      82          3.740
LGA    -       -      E      83           -
LGA    D     110      A      84          5.132
LGA    V     111      E      85           #
LGA    D     112      -       -           -
LGA    Q     113      L      86          1.867
LGA    V     114      E      87           #
LGA    I     115      N      88           -
LGA    A     116      -       -           -
LGA    T     117      L      89          2.075
LGA    V     118      P      90          5.564
LGA    E     119      A      91           #
LGA    S     120      W      92          5.090
LGA    L     121      W      93          3.612
LGA    E     122      S      94           #
LGA    L     123      R      95          4.147
LGA    -       -      D      96           -
LGA    K     124      L      97          2.746
LGA    -       -      A      98           -
LGA    D     125      R      99          3.945
LGA    E     126      K     100          1.753
LGA    V     127      D     101          2.406
LGA    L     128      F     102          2.714
LGA    Y     129      L     103          3.169
LGA    F     130      F     104          4.315
LGA    G     131      Y     105          2.034
LGA    K     132      T     106          2.504
LGA    L     133      E     107           #
LGA    -       -      G     108           -
LGA    -       -      L     109           -
LGA    -       -      D     110           -
LGA    -       -      V     111           -
LGA    -       -      D     112           -
LGA    -       -      Q     113           -
LGA    -       -      V     114           -
LGA    -       -      I     115           -
LGA    -       -      A     116           -
LGA    -       -      T     117           -
LGA    -       -      V     118           -
LGA    -       -      E     119           -
LGA    -       -      S     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      L     123           -
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      G     134           #
LGA    I     135      I     135           -
LGA    -       -      F     136           -
LGA    F     136      W     137           #
LGA    W     137      -       -           -
LGA    G     138      G     138           #
LGA    K     139      -       -           -
LGA    F     140      -       -           -
LGA    S     141      K     139           #
LGA    -       -      F     140           -
LGA    -       -      S     141           -
LGA    E     142      E     142          1.740
LGA    E     143      E     143          1.928
LGA    -       -      S     144           -
LGA    S     144      Y     145          0.793
LGA    Y     145      S     146          1.168
LGA    S     146      K     147          2.783
LGA    K     147      T     148          1.897
LGA    -       -      A     149           -
LGA    T     148      Y     150          3.006
LGA    A     149      H     151          1.956
LGA    Y     150      K     152          2.043
LGA    H     151      Y     153          3.175
LGA    K     152      L     154          2.424
LGA    Y     153      L     155          1.702
LGA    L     154      K     156          3.155
LGA    L     155      V     157          4.149
LGA    K     156      -       -           -
LGA    V     157      P     158          3.848
LGA    P     158      F     159          1.747
LGA    F     159      Y     160          4.412
LGA    -       -      R     161           -
LGA    Y     160      H     162          1.637
LGA    R     161      I     163          3.185
LGA    H     162      T     164          3.170
LGA    I     163      I     165          3.786
LGA    T     164      R     166          4.071
LGA    I     165      N     167           #
LGA    R     166      -       -           -
LGA    N     167      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     40    3.16    10.00     27.848     1.229

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.375664 * X  +  -0.535721 * Y  +  -0.756227 * Z  +   8.209743
  Y_new =  -0.877567 * X  +   0.467940 * Y  +   0.104446 * Z  +  61.447582
  Z_new =   0.297915 * X  +   0.702876 * Y  +  -0.645919 * Z  +   1.043262 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.313992   -0.827601  [ DEG:   132.5819    -47.4181 ]
  Theta =  -0.302508   -2.839084  [ DEG:   -17.3324   -162.6676 ]
  Phi   =  -1.975268    1.166324  [ DEG:  -113.1745     66.8255 ]
 
# 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: T0299TS599_5-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS599_5-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   40   3.16   10.00  27.848
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS599_5-D2
PFRMAT TS                                                                       
TARGET T0299                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM     79  CA  LEU    79      -7.735  63.178   7.170  1.00  0.00              
ATOM     80  CA  GLU    80      -8.660  60.908  10.008  1.00  0.00              
ATOM     81  CA  ASP    81      -5.626  58.781   9.378  1.00  0.00              
ATOM     82  CA  PHE    82      -3.279  61.825   9.165  1.00  0.00              
ATOM     83  CA  GLU    83      -4.430  63.093  12.485  1.00  0.00              
ATOM     84  CA  ALA    84      -3.872  59.733  14.041  1.00  0.00              
ATOM     85  CA  GLU    85      -0.387  59.423  12.590  1.00  0.00              
ATOM     86  CA  LEU    86       0.833  62.825  13.689  1.00  0.00              
ATOM     87  CA  GLU    87      -0.521  62.402  17.163  1.00  0.00              
ATOM     88  CA  ASN    88       1.059  59.013  17.636  1.00  0.00              
ATOM     89  CA  LEU    89       4.523  59.735  16.136  1.00  0.00              
ATOM     90  CA  PRO    90       6.299  56.550  15.289  1.00  0.00              
ATOM     91  CA  ALA    91       6.911  57.028  11.548  1.00  0.00              
ATOM     92  CA  TRP    92      10.456  58.271  11.296  1.00  0.00              
ATOM     93  CA  TRP    93      12.122  55.376   9.370  1.00  0.00              
ATOM     94  CA  SER    94      15.250  54.958  11.489  1.00  0.00              
ATOM     95  CA  ARG    95      17.883  54.655   8.872  1.00  0.00              
ATOM     96  CA  ASP    96      18.623  57.609   6.547  1.00  0.00              
ATOM     97  CA  LEU    97      21.417  56.048   4.498  1.00  0.00              
ATOM     98  CA  ALA    98      20.047  56.921   1.024  1.00  0.00              
ATOM     99  CA  ARG    99      18.819  60.397   1.694  1.00  0.00              
ATOM    100  CA  LYS   100      15.067  60.326   0.875  1.00  0.00              
ATOM    101  CA  ASP   101      12.610  63.010   1.822  1.00  0.00              
ATOM    102  CA  PHE   102       9.019  61.998   2.713  1.00  0.00              
ATOM    103  CA  LEU   103       6.102  64.273   1.888  1.00  0.00              
ATOM    104  CA  PHE   104       2.825  63.706   3.500  1.00  0.00              
ATOM    105  CA  TYR   105      -0.225  65.054   1.844  1.00  0.00              
ATOM    106  CA  THR   106      -3.366  65.342   3.631  1.00  0.00              
ATOM    107  CA  GLU   107      -6.299  65.201   1.407  1.00  0.00              
ATOM    108  CA  GLY   108      -7.505  61.942   0.046  1.00  0.00              
ATOM    109  CA  LEU   109      -5.452  61.408  -3.035  1.00  0.00              
ATOM    110  CA  ASP   110      -6.663  58.531  -5.149  1.00  0.00              
ATOM    111  CA  VAL   111      -4.190  55.988  -6.481  1.00  0.00              
ATOM    112  CA  ASP   112      -4.773  57.271 -10.027  1.00  0.00              
ATOM    113  CA  GLN   113      -3.825  60.772  -8.838  1.00  0.00              
ATOM    114  CA  VAL   114      -0.563  59.379  -7.399  1.00  0.00              
ATOM    115  CA  ILE   115       0.232  57.590 -10.688  1.00  0.00              
ATOM    116  CA  ALA   116      -0.374  60.801 -12.674  1.00  0.00              
ATOM    117  CA  THR   117       1.919  62.756 -10.312  1.00  0.00              
ATOM    118  CA  VAL   118       4.662  60.088 -10.622  1.00  0.00              
ATOM    119  CA  GLU   119       4.316  60.266 -14.424  1.00  0.00              
ATOM    120  CA  SER   120       4.520  64.044 -14.744  1.00  0.00              
ATOM    121  CA  LEU   121       7.406  64.945 -12.390  1.00  0.00              
ATOM    122  CA  GLU   122       9.268  61.589 -12.305  1.00  0.00              
ATOM    123  CA  LEU   123      12.162  62.154 -14.664  1.00  0.00              
ATOM    124  CA  LYS   124      14.179  59.068 -13.525  1.00  0.00              
ATOM    125  CA  ASP   125      11.140  56.762 -13.750  1.00  0.00              
ATOM    126  CA  GLU   126      11.124  55.724 -10.167  1.00  0.00              
ATOM    127  CA  VAL   127       7.783  55.569  -8.349  1.00  0.00              
ATOM    128  CA  LEU   128       7.725  55.767  -4.564  1.00  0.00              
ATOM    129  CA  TYR   129       4.516  55.679  -2.567  1.00  0.00              
ATOM    130  CA  PHE   130       4.743  56.021   1.195  1.00  0.00              
ATOM    131  CA  GLY   131       1.760  55.270   3.301  1.00  0.00              
ATOM    132  CA  LYS   132       1.529  52.504   5.813  1.00  0.00              
ATOM    133  CA  LEU   133       2.045  49.383   3.775  1.00  0.00              
ATOM    134  CA  GLY   134       4.828  50.851   1.598  1.00  0.00              
ATOM    135  CA  ILE   135       4.869  50.408  -2.196  1.00  0.00              
ATOM    136  CA  PHE   136       8.128  50.535  -3.985  1.00  0.00              
ATOM    137  CA  TRP   137       8.349  50.446  -7.811  1.00  0.00              
ATOM    138  CA  GLY   138      11.685  49.757  -9.448  1.00  0.00              
ATOM    139  CA  LYS   139      12.500  50.825 -13.048  1.00  0.00              
ATOM    140  CA  PHE   140      16.088  50.165 -13.965  1.00  0.00              
ATOM    141  CA  SER   141      18.358  52.872 -15.218  1.00  0.00              
ATOM    142  CA  GLU   142      21.626  51.003 -15.700  1.00  0.00              
ATOM    143  CA  GLU   143      23.822  53.222 -13.531  1.00  0.00              
ATOM    144  CA  SER   144      21.842  53.112 -10.483  1.00  0.00              
ATOM    145  CA  TYR   145      22.610  49.716  -9.025  1.00  0.00              
ATOM    146  CA  SER   146      24.429  50.763  -5.892  1.00  0.00              
ATOM    147  CA  LYS   147      22.314  53.599  -4.563  1.00  0.00              
ATOM    148  CA  THR   148      19.033  51.889  -5.156  1.00  0.00              
ATOM    149  CA  ALA   149      19.312  48.415  -3.636  1.00  0.00              
ATOM    150  CA  TYR   150      20.242  50.070  -0.304  1.00  0.00              
ATOM    151  CA  HIS   151      17.513  52.739   0.008  1.00  0.00              
ATOM    152  CA  LYS   152      14.827  50.288  -0.935  1.00  0.00              
ATOM    153  CA  TYR   153      15.893  47.654   1.527  1.00  0.00              
ATOM    154  CA  LEU   154      16.048  50.079   4.474  1.00  0.00              
ATOM    155  CA  LEU   155      12.614  51.480   3.660  1.00  0.00              
ATOM    156  CA  LYS   156      11.153  47.953   3.275  1.00  0.00              
ATOM    157  CA  VAL   157      12.356  46.772   6.619  1.00  0.00              
ATOM    158  CA  PRO   158      11.035  49.717   8.683  1.00  0.00              
ATOM    159  CA  PHE   159       7.791  49.838   6.739  1.00  0.00              
ATOM    160  CA  TYR   160       6.628  46.377   5.601  1.00  0.00              
ATOM    161  CA  ARG   161       7.377  46.954   1.877  1.00  0.00              
ATOM    162  CA  HIS   162       5.983  45.726  -1.295  1.00  0.00              
ATOM    163  CA  ILE   163       8.326  45.836  -4.127  1.00  0.00              
ATOM    164  CA  THR   164       7.297  46.012  -7.725  1.00  0.00              
ATOM    165  CA  ILE   165       9.914  45.291 -10.318  1.00  0.00              
ATOM    166  CA  ARG   166       9.555  46.394 -13.893  1.00  0.00              
ATOM    167  CA  ASN   167      13.114  46.053 -15.292  1.00  0.00              
TER                                                                             
END
