
#######################################################
#                                                     #
#                        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_2-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS599_2-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      L      79           -
LGA    E      80      E      80           -
LGA    D      81      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    F      82      A      91           #
LGA    E      83      W      92          3.874
LGA    A      84      -       -           -
LGA    E      85      W      93           #
LGA    L      86      S      94          3.698
LGA    E      87      R      95          3.106
LGA    N      88      D      96          1.712
LGA    L      89      L      97           -
LGA    P      90      A      98          5.934
LGA    A      91      R      99          3.793
LGA    -       -      K     100           -
LGA    W      92      D     101           #
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      F     102          3.177
LGA    L     103      L     103          1.690
LGA    F     104      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    -       -      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    Y     105      L     128          3.648
LGA    T     106      Y     129          1.607
LGA    E     107      -       -           -
LGA    G     108      -       -           -
LGA    L     109      F     130           #
LGA    D     110      G     131           -
LGA    V     111      -       -           -
LGA    D     112      -       -           -
LGA    Q     113      -       -           -
LGA    V     114      -       -           -
LGA    I     115      -       -           -
LGA    A     116      -       -           -
LGA    T     117      -       -           -
LGA    V     118      K     132          4.492
LGA    E     119      -       -           -
LGA    S     120      -       -           -
LGA    L     121      -       -           -
LGA    E     122      -       -           -
LGA    L     123      -       -           -
LGA    K     124      -       -           -
LGA    D     125      -       -           -
LGA    E     126      L     133          0.911
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      G     134          2.843
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      I     135           #
LGA    Y     153      F     136           -
LGA    L     154      W     137           -
LGA    L     155      G     138           -
LGA    K     156      K     139           -
LGA    V     157      F     140           -
LGA    P     158      S     141           -
LGA    F     159      E     142           -
LGA    Y     160      E     143           -
LGA    -       -      S     144           -
LGA    -       -      Y     145           -
LGA    -       -      S     146           -
LGA    -       -      K     147           -
LGA    -       -      T     148           -
LGA    R     161      A     149          2.678
LGA    H     162      Y     150          3.841
LGA    I     163      -       -           -
LGA    T     164      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    I     165      R     166           #
LGA    R     166      N     167           #
LGA    N     167      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     15    3.37    20.00     11.348     0.432

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.998681 * X  +   0.039135 * Y  +   0.033246 * Z  +  14.087368
  Y_new =  -0.004113 * X  +  -0.584382 * Y  +   0.811468 * Z  +  54.214336
  Z_new =   0.051185 * X  +  -0.810534 * Y  +  -0.583450 * Z  +   1.140893 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.194710    0.946883  [ DEG:  -125.7476     54.2524 ]
  Theta =  -0.051207   -3.090386  [ DEG:    -2.9339   -177.0661 ]
  Phi   =  -0.004119    3.137474  [ DEG:    -0.2360    179.7640 ]
 
# 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_2-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS599_2-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   15   3.37   20.00  11.348
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS599_2-D2
PFRMAT TS                                                                       
TARGET T0299                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM     79  CA  LEU    79      13.805  67.930  -9.337  1.00  0.00              
ATOM     80  CA  GLU    80      16.501  67.030 -11.762  1.00  0.00              
ATOM     81  CA  ASP    81      15.955  63.356 -11.361  1.00  0.00              
ATOM     82  CA  PHE    82      12.220  63.648 -11.685  1.00  0.00              
ATOM     83  CA  GLU    83      12.481  65.499 -14.943  1.00  0.00              
ATOM     84  CA  ALA    84      14.835  62.842 -16.324  1.00  0.00              
ATOM     85  CA  GLU    85      12.453  60.070 -15.193  1.00  0.00              
ATOM     86  CA  LEU    86       9.359  61.535 -16.750  1.00  0.00              
ATOM     87  CA  GLU    87      11.092  62.101 -20.027  1.00  0.00              
ATOM     88  CA  ASN    88      12.258  58.533 -20.211  1.00  0.00              
ATOM     89  CA  LEU    89       9.090  56.724 -18.982  1.00  0.00              
ATOM     90  CA  PRO    90      10.070  53.069 -18.744  1.00  0.00              
ATOM     91  CA  ALA    91      10.012  52.200 -15.065  1.00  0.00              
ATOM     92  CA  TRP    92       6.760  50.907 -13.776  1.00  0.00              
ATOM     93  CA  TRP    93       6.784  47.768 -11.876  1.00  0.00              
ATOM     94  CA  SER    94       8.741  45.180 -13.769  1.00  0.00              
ATOM     95  CA  ARG    95       6.960  42.044 -12.758  1.00  0.00              
ATOM     96  CA  ASP    96       6.686  41.338  -9.013  1.00  0.00              
ATOM     97  CA  LEU    97       2.922  41.801  -8.538  1.00  0.00              
ATOM     98  CA  ALA    98       2.500  39.946  -5.256  1.00  0.00              
ATOM     99  CA  ARG    99       5.381  41.716  -3.461  1.00  0.00              
ATOM    100  CA  LYS   100       4.986  45.280  -4.628  1.00  0.00              
ATOM    101  CA  ASP   101       4.926  48.264  -2.362  1.00  0.00              
ATOM    102  CA  PHE   102       5.798  51.600  -3.874  1.00  0.00              
ATOM    103  CA  LEU   103       7.031  54.457  -1.740  1.00  0.00              
ATOM    104  CA  PHE   104       7.522  57.912  -3.178  1.00  0.00              
ATOM    105  CA  TYR   105       9.718  60.310  -1.439  1.00  0.00              
ATOM    106  CA  THR   106       9.914  63.870  -2.286  1.00  0.00              
ATOM    107  CA  GLU   107      13.069  65.361  -1.248  1.00  0.00              
ATOM    108  CA  GLY   108      12.244  68.504   0.635  1.00  0.00              
ATOM    109  CA  LEU   109       9.190  67.232   2.517  1.00  0.00              
ATOM    110  CA  ASP   110       9.135  68.498   6.144  1.00  0.00              
ATOM    111  CA  VAL   111       7.965  66.037   8.819  1.00  0.00              
ATOM    112  CA  ASP   112       4.834  68.136   9.464  1.00  0.00              
ATOM    113  CA  GLN   113       4.079  68.171   5.721  1.00  0.00              
ATOM    114  CA  VAL   114       4.511  64.388   5.515  1.00  0.00              
ATOM    115  CA  ILE   115       2.170  63.861   8.491  1.00  0.00              
ATOM    116  CA  ALA   116      -0.402  66.184   6.829  1.00  0.00              
ATOM    117  CA  THR   117      -0.158  64.302   3.522  1.00  0.00              
ATOM    118  CA  VAL   118      -0.590  60.963   5.300  1.00  0.00              
ATOM    119  CA  GLU   119      -3.694  62.238   7.116  1.00  0.00              
ATOM    120  CA  SER   120      -5.429  63.580   3.969  1.00  0.00              
ATOM    121  CA  LEU   121      -4.774  60.473   1.882  1.00  0.00              
ATOM    122  CA  GLU   122      -5.454  57.741   4.531  1.00  0.00              
ATOM    123  CA  LEU   123      -8.378  56.353   2.618  1.00  0.00              
ATOM    124  CA  LYS   124      -6.577  55.926  -0.711  1.00  0.00              
ATOM    125  CA  ASP   125      -3.242  54.578   0.651  1.00  0.00              
ATOM    126  CA  GLU   126      -1.195  57.613  -0.171  1.00  0.00              
ATOM    127  CA  VAL   127      -0.575  58.393  -3.784  1.00  0.00              
ATOM    128  CA  LEU   128       2.499  60.465  -4.789  1.00  0.00              
ATOM    129  CA  TYR   129       2.713  62.003  -8.192  1.00  0.00              
ATOM    130  CA  PHE   130       6.004  62.692  -9.752  1.00  0.00              
ATOM    131  CA  GLY   131       6.170  64.207 -13.188  1.00  0.00              
ATOM    132  CA  LYS   132       3.579  63.276 -15.840  1.00  0.00              
ATOM    133  CA  LEU   133       4.564  59.658 -16.528  1.00  0.00              
ATOM    134  CA  GLY   134       5.487  58.679 -12.924  1.00  0.00              
ATOM    135  CA  ILE   135       3.073  57.497 -10.271  1.00  0.00              
ATOM    136  CA  PHE   136       4.305  56.497  -6.846  1.00  0.00              
ATOM    137  CA  TRP   137       2.121  54.377  -4.539  1.00  0.00              
ATOM    138  CA  GLY   138       2.589  54.334  -0.843  1.00  0.00              
ATOM    139  CA  LYS   139       1.604  51.264   1.122  1.00  0.00              
ATOM    140  CA  PHE   140       0.933  51.759   4.799  1.00  0.00              
ATOM    141  CA  SER   141      -1.240  49.279   6.577  1.00  0.00              
ATOM    142  CA  GLU   142      -3.562  51.478   8.662  1.00  0.00              
ATOM    143  CA  GLU   143      -2.078  50.921  12.064  1.00  0.00              
ATOM    144  CA  SER   144       1.464  51.589  11.116  1.00  0.00              
ATOM    145  CA  TYR   145       1.370  54.927   9.389  1.00  0.00              
ATOM    146  CA  SER   146       3.298  56.739  12.128  1.00  0.00              
ATOM    147  CA  LYS   147       6.033  54.249  13.118  1.00  0.00              
ATOM    148  CA  THR   148       7.152  53.479   9.612  1.00  0.00              
ATOM    149  CA  ALA   149       7.235  56.989   8.257  1.00  0.00              
ATOM    150  CA  TYR   150       9.612  58.146  11.048  1.00  0.00              
ATOM    151  CA  HIS   151      12.157  55.412  10.756  1.00  0.00              
ATOM    152  CA  LYS   152      12.264  55.661   6.986  1.00  0.00              
ATOM    153  CA  TYR   153      12.692  59.400   6.975  1.00  0.00              
ATOM    154  CA  LEU   154      15.612  59.327   9.486  1.00  0.00              
ATOM    155  CA  LEU   155      17.366  56.622   7.568  1.00  0.00              
ATOM    156  CA  LYS   156      17.069  58.353   4.240  1.00  0.00              
ATOM    157  CA  VAL   157      18.396  61.613   5.577  1.00  0.00              
ATOM    158  CA  PRO   158      21.243  60.293   7.697  1.00  0.00              
ATOM    159  CA  PHE   159      22.405  57.858   5.001  1.00  0.00              
ATOM    160  CA  TYR   160      21.529  59.733   1.790  1.00  0.00              
ATOM    161  CA  ARG   161      20.062  56.880  -0.138  1.00  0.00              
ATOM    162  CA  HIS   162      17.475  56.968  -2.842  1.00  0.00              
ATOM    163  CA  ILE   163      16.265  53.628  -4.147  1.00  0.00              
ATOM    164  CA  THR   164      14.581  53.349  -7.492  1.00  0.00              
ATOM    165  CA  ILE   165      13.036  50.064  -8.472  1.00  0.00              
ATOM    166  CA  ARG   166      12.287  49.703 -12.130  1.00  0.00              
ATOM    167  CA  ASN   167      15.334  51.782 -13.169  1.00  0.00              
TER                                                                             
END
