
#######################################################
#                                                     #
#                        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   21 (  161),  selected   21 , name T0298TS268_1_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS268_1_2-D1.T0298_D1.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    V     316      Q       3           -
LGA    -       -      P       4           -
LGA    -       -      L       5           -
LGA    -       -      N       6           -
LGA    -       -      V       7           -
LGA    -       -      A       8           -
LGA    -       -      V       9           -
LGA    -       -      V      10           -
LGA    -       -      G      11           -
LGA    -       -      A      12           -
LGA    -       -      T      13           -
LGA    -       -      G      14           -
LGA    R     317      S      15           #
LGA    K     318      V      16          2.905
LGA    -       -      G      17           -
LGA    -       -      E      18           -
LGA    -       -      A      19           -
LGA    G     319      L      20          4.323
LGA    -       -      V      21           -
LGA    -       -      G      22           -
LGA    -       -      L      23           -
LGA    -       -      L      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      R      27           -
LGA    -       -      D      28           -
LGA    -       -      F      29           -
LGA    -       -      P      30           -
LGA    -       -      L      31           -
LGA    -       -      H      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      H      35           -
LGA    -       -      L      36           -
LGA    -       -      L      37           -
LGA    -       -      A      38           -
LGA    -       -      S      39           -
LGA    -       -      A      40           -
LGA    -       -      E      41           -
LGA    -       -      S      42           -
LGA    -       -      A      43           -
LGA    -       -      G      44           -
LGA    -       -      Q      45           -
LGA    -       -      R      46           -
LGA    -       -      M      47           -
LGA    -       -      G      48           -
LGA    -       -      F      49           -
LGA    -       -      A      50           -
LGA    -       -      E      51           -
LGA    -       -      S      52           -
LGA    -       -      S      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
LGA    -       -      V      56           -
LGA    -       -      G      57           -
LGA    -       -      D      58           -
LGA    -       -      V      59           -
LGA    -       -      D      60           -
LGA    -       -      S      61           -
LGA    -       -      F      62           -
LGA    -       -      D      63           -
LGA    -       -      F      64           -
LGA    -       -      S      65           -
LGA    -       -      S      66           -
LGA    -       -      V      67           -
LGA    -       -      G      68           -
LGA    -       -      L      69           -
LGA    -       -      A      70           -
LGA    A     320      F      71          3.927
LGA    A     321      F      72          3.929
LGA    L     322      A      73          4.697
LGA    N     323      A      74          4.529
LGA    A     324      A      75          2.102
LGA    V     325      A      76          1.510
LGA    L     326      E      77          2.011
LGA    L     327      V      78          2.240
LGA    -       -      S      79           -
LGA    -       -      R      80           -
LGA    G     328      A      81          2.084
LGA    E     329      H      82          2.707
LGA    -       -      A      83           -
LGA    -       -      E      84           -
LGA    L     330      R      85          1.610
LGA    -       -      A      86           -
LGA    L     331      R      87          3.100
LGA    I     332      A      88           -
LGA    -       -      A      89           -
LGA    -       -      G      90           -
LGA    -       -      C      91           -
LGA    K     333      S      92          1.829
LGA    H     334      V      93          2.879
LGA    -       -      I      94           -
LGA    -       -      D      95           -
LGA    -       -      L      96           -
LGA    -       -      S      97           -
LGA    -       -      G      98           -
LGA    -       -      A      99           -
LGA    -       -      L     100           -
LGA    -       -      E     101           -
LGA    -       -      P     102           -
LGA    -       -      S     103           -
LGA    -       -      V     104           -
LGA    -       -      A     105           -
LGA    -       -      P     106           -
LGA    -       -      P     107           -
LGA    -       -      V     108           -
LGA    -       -      M     109           -
LGA    -       -      V     110           -
LGA    -       -      S     111           -
LGA    -       -      V     112           -
LGA    -       -      N     113           -
LGA    -       -      A     114           -
LGA    -       -      E     115           -
LGA    -       -      R     116           -
LGA    -       -      L     117           -
LGA    -       -      A     118           -
LGA    -       -      S     119           -
LGA    -       -      Q     120           -
LGA    -       -      A     121           -
LGA    -       -      A     122           -
LGA    -       -      P     123           -
LGA    -       -      F     124           -
LGA    -       -      L     125           -
LGA    Y     335      L     126          2.159
LGA    L     336      S     127          3.168
LGA    -       -      S     128           -
LGA    -       -      P     129           -
LGA    -       -      V     316           -
LGA    -       -      R     317           -
LGA    -       -      K     318           -
LGA    -       -      G     319           -
LGA    -       -      A     320           -
LGA    -       -      A     321           -
LGA    -       -      L     322           -
LGA    -       -      N     323           -
LGA    -       -      A     324           -
LGA    -       -      V     325           -
LGA    -       -      L     326           -
LGA    -       -      L     327           -
LGA    -       -      G     328           -
LGA    -       -      E     329           -
LGA    -       -      L     330           -
LGA    -       -      L     331           -
LGA    -       -      I     332           -
LGA    -       -      K     333           -
LGA    -       -      H     334           -
LGA    -       -      Y     335           -
LGA    -       -      L     336           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21  148    5.0     18    3.04     5.56      8.324     0.573

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.869779 * X  +   0.113394 * Y  +  -0.480236 * Z  + -30.046076
  Y_new =  -0.478954 * X  +  -0.040096 * Y  +  -0.876924 * Z  +  33.448196
  Z_new =  -0.118694 * X  +   0.992741 * Y  +   0.019436 * Z  + -67.216248 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.551221   -1.590372  [ DEG:    88.8784    -91.1216 ]
  Theta =   0.118974    3.022618  [ DEG:     6.8167    173.1833 ]
  Phi   =  -0.503351    2.638242  [ DEG:   -28.8399    151.1601 ]
 
# 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: T0298TS268_1_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_1_2-D1.T0298_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21  148   5.0   18   3.04    5.56   8.324
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1t4b_A
ATOM   2298  N   VAL   316     -19.209  68.723  -2.238  1.00  0.00
ATOM   2299  CA  VAL   316     -17.982  69.284  -2.716  1.00  0.00
ATOM   2300  C   VAL   316     -16.930  68.245  -2.962  1.00  0.00
ATOM   2301  O   VAL   316     -16.329  68.210  -4.035  1.00  0.00
ATOM   2302  CB  VAL   316     -17.389  70.286  -1.709  1.00  0.00
ATOM   2303  CG1 VAL   316     -16.000  70.725  -2.149  1.00  0.00
ATOM   2304  CG2 VAL   316     -18.271  71.520  -1.603  1.00  0.00
ATOM   2305  N   ARG   317     -16.686  67.358  -1.977  1.00  0.00
ATOM   2306  CA  ARG   317     -15.548  66.488  -2.103  1.00  0.00
ATOM   2307  C   ARG   317     -15.650  65.572  -3.286  1.00  0.00
ATOM   2308  O   ARG   317     -14.918  65.724  -4.263  1.00  0.00
ATOM   2309  CB  ARG   317     -15.406  65.609  -0.858  1.00  0.00
ATOM   2310  CG  ARG   317     -14.218  64.661  -0.901  1.00  0.00
ATOM   2311  CD  ARG   317     -12.903  65.420  -0.824  1.00  0.00
ATOM   2312  NE  ARG   317     -12.730  66.087   0.463  1.00  0.00
ATOM   2313  CZ  ARG   317     -11.716  66.896   0.755  1.00  0.00
ATOM   2314  NH1 ARG   317     -11.641  67.459   1.954  1.00  0.00
ATOM   2315  NH2 ARG   317     -10.781  67.142  -0.152  1.00  0.00
ATOM   2316  N   LYS   318     -16.586  64.605  -3.231  1.00  0.00
ATOM   2317  CA  LYS   318     -16.798  63.644  -4.279  1.00  0.00
ATOM   2318  C   LYS   318     -17.505  64.285  -5.425  1.00  0.00
ATOM   2319  O   LYS   318     -17.184  64.058  -6.590  1.00  0.00
ATOM   2320  CB  LYS   318     -17.648  62.477  -3.771  1.00  0.00
ATOM   2321  CG  LYS   318     -17.860  61.373  -4.794  1.00  0.00
ATOM   2322  CD  LYS   318     -18.559  60.173  -4.175  1.00  0.00
ATOM   2323  CE  LYS   318     -18.768  59.068  -5.197  1.00  0.00
ATOM   2324  NZ  LYS   318     -19.407  57.867  -4.593  1.00  0.00
ATOM   2325  N   GLY   319     -18.487  65.134  -5.083  1.00  0.00
ATOM   2326  CA  GLY   319     -19.396  65.727  -6.016  1.00  0.00
ATOM   2327  C   GLY   319     -18.693  66.596  -6.996  1.00  0.00
ATOM   2328  O   GLY   319     -19.118  66.681  -8.146  1.00  0.00
ATOM   2329  N   ALA   320     -17.645  67.324  -6.573  1.00  0.00
ATOM   2330  CA  ALA   320     -16.987  68.138  -7.548  1.00  0.00
ATOM   2331  C   ALA   320     -16.436  67.207  -8.577  1.00  0.00
ATOM   2332  O   ALA   320     -16.586  67.425  -9.779  1.00  0.00
ATOM   2333  CB  ALA   320     -15.867  68.938  -6.901  1.00  0.00
ATOM   2334  N   ALA   321     -15.800  66.115  -8.115  1.00  0.00
ATOM   2335  CA  ALA   321     -15.245  65.162  -9.025  1.00  0.00
ATOM   2336  C   ALA   321     -14.333  64.297  -8.227  1.00  0.00
ATOM   2337  O   ALA   321     -14.314  64.360  -6.999  1.00  0.00
ATOM   2338  CB  ALA   321     -14.478  65.869 -10.131  1.00  0.00
ATOM   2339  N   LEU   322     -13.551  63.445  -8.915  1.00  0.00
ATOM   2340  CA  LEU   322     -12.615  62.633  -8.201  1.00  0.00
ATOM   2341  C   LEU   322     -11.684  63.603  -7.559  1.00  0.00
ATOM   2342  O   LEU   322     -11.525  64.718  -8.047  1.00  0.00
ATOM   2343  CB  LEU   322     -11.873  61.701  -9.161  1.00  0.00
ATOM   2344  CG  LEU   322     -12.716  60.628  -9.851  1.00  0.00
ATOM   2345  CD1 LEU   322     -11.884  59.862 -10.869  1.00  0.00
ATOM   2346  CD2 LEU   322     -13.258  59.633  -8.835  1.00  0.00
ATOM   2347  N   ASN   323     -11.070  63.220  -6.426  1.00  0.00
ATOM   2348  CA  ASN   323     -10.229  64.157  -5.751  1.00  0.00
ATOM   2349  C   ASN   323      -9.115  64.527  -6.670  1.00  0.00
ATOM   2350  O   ASN   323      -8.164  63.769  -6.856  1.00  0.00
ATOM   2351  CB  ASN   323      -9.657  63.541  -4.472  1.00  0.00
ATOM   2352  CG  ASN   323      -8.856  64.534  -3.654  1.00  0.00
ATOM   2353  OD1 ASN   323      -8.971  65.745  -3.844  1.00  0.00
ATOM   2354  ND2 ASN   323      -8.039  64.023  -2.740  1.00  0.00
ATOM   2355  N   ALA   324      -9.237  65.724  -7.277  1.00  0.00
ATOM   2356  CA  ALA   324      -8.256  66.277  -8.161  1.00  0.00
ATOM   2357  C   ALA   324      -8.994  67.235  -9.031  1.00  0.00
ATOM   2358  O   ALA   324     -10.204  67.108  -9.212  1.00  0.00
ATOM   2359  CB  ALA   324      -7.610  65.178  -8.989  1.00  0.00
ATOM   2360  N   VAL   325      -8.293  68.235  -9.595  1.00  0.00
ATOM   2361  CA  VAL   325      -9.004  69.105 -10.475  1.00  0.00
ATOM   2362  C   VAL   325      -8.405  68.986 -11.837  1.00  0.00
ATOM   2363  O   VAL   325      -7.316  69.489 -12.112  1.00  0.00
ATOM   2364  CB  VAL   325      -8.914  70.572 -10.013  1.00  0.00
ATOM   2365  CG1 VAL   325      -9.670  71.480 -10.971  1.00  0.00
ATOM   2366  CG2 VAL   325      -9.514  70.730  -8.624  1.00  0.00
ATOM   2367  N   LEU   326      -9.113  68.270 -12.729  1.00  0.00
ATOM   2368  CA  LEU   326      -8.665  68.163 -14.081  1.00  0.00
ATOM   2369  C   LEU   326      -9.879  67.792 -14.861  1.00  0.00
ATOM   2370  O   LEU   326     -10.383  66.676 -14.736  1.00  0.00
ATOM   2371  CB  LEU   326      -7.580  67.091 -14.203  1.00  0.00
ATOM   2372  CG  LEU   326      -7.020  66.850 -15.606  1.00  0.00
ATOM   2373  CD1 LEU   326      -6.354  68.109 -16.142  1.00  0.00
ATOM   2374  CD2 LEU   326      -5.984  65.736 -15.587  1.00  0.00
ATOM   2375  N   LEU   327     -10.403  68.719 -15.679  1.00  0.00
ATOM   2376  CA  LEU   327     -11.563  68.351 -16.428  1.00  0.00
ATOM   2377  C   LEU   327     -11.644  69.228 -17.630  1.00  0.00
ATOM   2378  O   LEU   327     -11.232  70.388 -17.599  1.00  0.00
ATOM   2379  CB  LEU   327     -12.825  68.526 -15.581  1.00  0.00
ATOM   2380  CG  LEU   327     -14.153  68.197 -16.266  1.00  0.00
ATOM   2381  CD1 LEU   327     -14.251  66.708 -16.560  1.00  0.00
ATOM   2382  CD2 LEU   327     -15.327  68.585 -15.380  1.00  0.00
ATOM   2383  N   GLY   328     -12.161  68.671 -18.741  1.00  0.00
ATOM   2384  CA  GLY   328     -12.327  69.452 -19.928  1.00  0.00
ATOM   2385  C   GLY   328     -13.697  69.155 -20.440  1.00  0.00
ATOM   2386  O   GLY   328     -14.058  67.998 -20.649  1.00  0.00
ATOM   2387  N   GLU   329     -14.498  70.213 -20.657  1.00  0.00
ATOM   2388  CA  GLU   329     -15.834  70.038 -21.141  1.00  0.00
ATOM   2389  C   GLU   329     -16.392  71.400 -21.343  1.00  0.00
ATOM   2390  O   GLU   329     -15.661  72.389 -21.361  1.00  0.00
ATOM   2391  CB  GLU   329     -16.674  69.260 -20.126  1.00  0.00
ATOM   2392  CG  GLU   329     -16.749  69.911 -18.754  1.00  0.00
ATOM   2393  CD  GLU   329     -17.507  69.067 -17.750  1.00  0.00
ATOM   2394  OE1 GLU   329     -17.918  67.943 -18.108  1.00  0.00
ATOM   2395  OE2 GLU   329     -17.691  69.528 -16.604  1.00  0.00
ATOM   2396  N   LEU   330     -17.720  71.478 -21.525  1.00  0.00
ATOM   2397  CA  LEU   330     -18.350  72.751 -21.662  1.00  0.00
ATOM   2398  C   LEU   330     -18.090  73.394 -20.335  1.00  0.00
ATOM   2399  O   LEU   330     -17.916  72.697 -19.337  1.00  0.00
ATOM   2400  CB  LEU   330     -19.844  72.582 -21.942  1.00  0.00
ATOM   2401  CG  LEU   330     -20.214  71.934 -23.278  1.00  0.00
ATOM   2402  CD1 LEU   330     -21.717  71.711 -23.368  1.00  0.00
ATOM   2403  CD2 LEU   330     -19.795  72.821 -24.440  1.00  0.00
ATOM   2404  N   LEU   331     -18.009  74.737 -20.291  1.00  0.00
ATOM   2405  CA  LEU   331     -17.672  75.403 -19.067  1.00  0.00
ATOM   2406  C   LEU   331     -18.644  74.982 -18.018  1.00  0.00
ATOM   2407  O   LEU   331     -19.813  74.725 -18.296  1.00  0.00
ATOM   2408  CB  LEU   331     -17.741  76.922 -19.245  1.00  0.00
ATOM   2409  CG  LEU   331     -16.717  77.538 -20.200  1.00  0.00
ATOM   2410  CD1 LEU   331     -16.980  79.025 -20.383  1.00  0.00
ATOM   2411  CD2 LEU   331     -15.305  77.369 -19.656  1.00  0.00
ATOM   2412  N   ILE   332     -18.147  74.877 -16.771  1.00  0.00
ATOM   2413  CA  ILE   332     -18.941  74.418 -15.673  1.00  0.00
ATOM   2414  C   ILE   332     -20.061  75.383 -15.467  1.00  0.00
ATOM   2415  O   ILE   332     -19.854  76.593 -15.401  1.00  0.00
ATOM   2416  CB  ILE   332     -18.114  74.327 -14.378  1.00  0.00
ATOM   2417  CG1 ILE   332     -17.023  73.261 -14.515  1.00  0.00
ATOM   2418  CG2 ILE   332     -19.003  73.956 -13.201  1.00  0.00
ATOM   2419  CD1 ILE   332     -16.031  73.252 -13.373  1.00  0.00
ATOM   2420  N   LYS   333     -21.295  74.852 -15.377  1.00  0.00
ATOM   2421  CA  LYS   333     -22.433  75.696 -15.185  1.00  0.00
ATOM   2422  C   LYS   333     -22.271  76.373 -13.870  1.00  0.00
ATOM   2423  O   LYS   333     -22.503  77.575 -13.748  1.00  0.00
ATOM   2424  CB  LYS   333     -23.720  74.870 -15.192  1.00  0.00
ATOM   2425  CG  LYS   333     -24.091  74.308 -16.555  1.00  0.00
ATOM   2426  CD  LYS   333     -25.377  73.502 -16.489  1.00  0.00
ATOM   2427  CE  LYS   333     -25.734  72.920 -17.847  1.00  0.00
ATOM   2428  NZ  LYS   333     -26.976  72.099 -17.791  1.00  0.00
ATOM   2429  N   HIS   334     -21.847  75.616 -12.842  1.00  0.00
ATOM   2430  CA  HIS   334     -21.704  76.222 -11.558  1.00  0.00
ATOM   2431  C   HIS   334     -20.577  77.190 -11.648  1.00  0.00
ATOM   2432  O   HIS   334     -19.572  76.934 -12.309  1.00  0.00
ATOM   2433  CB  HIS   334     -21.402  75.162 -10.496  1.00  0.00
ATOM   2434  CG  HIS   334     -22.544  74.234 -10.228  1.00  0.00
ATOM   2435  ND1 HIS   334     -23.654  74.609  -9.503  1.00  0.00
ATOM   2436  CD2 HIS   334     -22.861  72.853 -10.562  1.00  0.00
ATOM   2437  CE1 HIS   334     -24.504  73.569  -9.431  1.00  0.00
ATOM   2438  NE2 HIS   334     -24.034  72.512 -10.064  1.00  0.00
ATOM   2439  N   TYR   335     -20.733  78.349 -10.990  1.00  0.00
ATOM   2440  CA  TYR   335     -19.688  79.318 -11.024  1.00  0.00
ATOM   2441  C   TYR   335     -19.235  79.502  -9.616  1.00  0.00
ATOM   2442  O   TYR   335     -20.042  79.726  -8.715  1.00  0.00
ATOM   2443  CB  TYR   335     -20.201  80.641 -11.597  1.00  0.00
ATOM   2444  CG  TYR   335     -19.164  81.740 -11.625  1.00  0.00
ATOM   2445  CD1 TYR   335     -18.143  81.729 -12.566  1.00  0.00
ATOM   2446  CD2 TYR   335     -19.210  82.786 -10.712  1.00  0.00
ATOM   2447  CE1 TYR   335     -17.190  82.730 -12.601  1.00  0.00
ATOM   2448  CE2 TYR   335     -18.266  83.794 -10.730  1.00  0.00
ATOM   2449  CZ  TYR   335     -17.251  83.759 -11.686  1.00  0.00
ATOM   2450  OH  TYR   335     -16.304  84.757 -11.717  1.00  0.00
ATOM   2451  N   LEU   336     -17.914  79.389  -9.393  1.00  0.00
ATOM   2452  CA  LEU   336     -17.415  79.560  -8.066  1.00  0.00
ATOM   2453  C   LEU   336     -17.533  81.045  -7.793  1.00  0.00
ATOM   2454  O   LEU   336     -18.254  81.421  -6.830  1.00  0.00
ATOM   2455  CB  LEU   336     -15.960  79.094  -7.977  1.00  0.00
ATOM   2456  CG  LEU   336     -15.695  77.630  -8.333  1.00  0.00
ATOM   2457  CD1 LEU   336     -14.203  77.331  -8.302  1.00  0.00
ATOM   2458  CD2 LEU   336     -16.386  76.702  -7.344  1.00  0.00
TER
END
