
#######################################################
#                                                     #
#                        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_2_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS268_2_2-D1.T0298_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      -       -           -
LGA    R     317      -       -           -
LGA    K     318      Q       3          3.096
LGA    G     319      P       4          1.957
LGA    A     320      L       5          0.891
LGA    A     321      N       6          1.450
LGA    L     322      V       7          1.777
LGA    N     323      A       8          2.248
LGA    A     324      V       9          1.648
LGA    V     325      V      10          2.213
LGA    -       -      G      11           -
LGA    L     326      A      12          2.028
LGA    L     327      T      13          1.827
LGA    G     328      G      14          1.529
LGA    E     329      S      15          3.361
LGA    -       -      V      16           -
LGA    L     330      G      17          2.042
LGA    -       -      E      18           -
LGA    -       -      A      19           -
LGA    L     331      L      20          3.952
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    -       -      F      71           -
LGA    -       -      F      72           -
LGA    I     332      A      73          2.530
LGA    -       -      A      74           -
LGA    -       -      A      75           -
LGA    -       -      A      76           -
LGA    -       -      E      77           -
LGA    -       -      V      78           -
LGA    -       -      S      79           -
LGA    -       -      R      80           -
LGA    -       -      A      81           -
LGA    -       -      H      82           -
LGA    -       -      A      83           -
LGA    -       -      E      84           -
LGA    -       -      R      85           -
LGA    -       -      A      86           -
LGA    -       -      R      87           -
LGA    -       -      A      88           -
LGA    -       -      A      89           -
LGA    -       -      G      90           -
LGA    -       -      C      91           -
LGA    -       -      S      92           -
LGA    -       -      V      93           -
LGA    K     333      I      94          3.859
LGA    H     334      D      95          1.374
LGA    -       -      L      96           -
LGA    -       -      S      97           -
LGA    -       -      G      98           -
LGA    Y     335      A      99           #
LGA    L     336      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    -       -      L     126           -
LGA    -       -      S     127           -
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     17    2.38    17.65      8.646     0.686

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.361007 * X  +   0.118867 * Y  +  -0.924957 * Z  + -11.296286
  Y_new =   0.173312 * X  +  -0.966013 * Y  +  -0.191787 * Z  +  62.058609
  Z_new =  -0.916317 * X  +  -0.229543 * Y  +   0.328136 * Z  +  44.660507 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.610414    2.531179  [ DEG:   -34.9741    145.0259 ]
  Theta =   1.158785    1.982808  [ DEG:    66.3935    113.6065 ]
  Phi   =   2.694007   -0.447585  [ DEG:   154.3553    -25.6447 ]
 
# 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_2_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_2_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   17   2.38   17.65   8.646
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1t4d_B
ATOM   2298  N   VAL   316     -34.222  63.848 -16.976  1.00  0.00
ATOM   2299  CA  VAL   316     -33.532  64.907 -17.661  1.00  0.00
ATOM   2300  C   VAL   316     -34.496  65.690 -18.489  1.00  0.00
ATOM   2301  O   VAL   316     -34.456  65.685 -19.720  1.00  0.00
ATOM   2302  CB  VAL   316     -32.435  64.356 -18.591  1.00  0.00
ATOM   2303  CG1 VAL   316     -31.700  65.495 -19.281  1.00  0.00
ATOM   2304  CG2 VAL   316     -31.424  63.542 -17.798  1.00  0.00
ATOM   2305  N   ARG   317     -35.356  66.441 -17.783  1.00  0.00
ATOM   2306  CA  ARG   317     -36.360  67.290 -18.343  1.00  0.00
ATOM   2307  C   ARG   317     -36.700  68.220 -17.229  1.00  0.00
ATOM   2308  O   ARG   317     -35.951  69.141 -16.911  1.00  0.00
ATOM   2309  CB  ARG   317     -37.571  66.467 -18.787  1.00  0.00
ATOM   2310  CG  ARG   317     -38.698  67.294 -19.384  1.00  0.00
ATOM   2311  CD  ARG   317     -38.274  67.942 -20.691  1.00  0.00
ATOM   2312  NE  ARG   317     -38.007  66.952 -21.732  1.00  0.00
ATOM   2313  CZ  ARG   317     -37.458  67.234 -22.908  1.00  0.00
ATOM   2314  NH1 ARG   317     -37.252  66.267 -23.793  1.00  0.00
ATOM   2315  NH2 ARG   317     -37.116  68.481 -23.199  1.00  0.00
ATOM   2316  N   LYS   318     -37.860  67.985 -16.599  1.00  0.00
ATOM   2317  CA  LYS   318     -38.255  68.798 -15.493  1.00  0.00
ATOM   2318  C   LYS   318     -37.195  68.655 -14.446  1.00  0.00
ATOM   2319  O   LYS   318     -36.810  69.633 -13.807  1.00  0.00
ATOM   2320  CB  LYS   318     -39.607  68.336 -14.944  1.00  0.00
ATOM   2321  CG  LYS   318     -40.128  69.175 -13.790  1.00  0.00
ATOM   2322  CD  LYS   318     -41.506  68.710 -13.347  1.00  0.00
ATOM   2323  CE  LYS   318     -42.015  69.532 -12.174  1.00  0.00
ATOM   2324  NZ  LYS   318     -43.359  69.078 -11.719  1.00  0.00
ATOM   2325  N   GLY   319     -36.675  67.424 -14.261  1.00  0.00
ATOM   2326  CA  GLY   319     -35.686  67.199 -13.249  1.00  0.00
ATOM   2327  C   GLY   319     -34.369  67.718 -13.722  1.00  0.00
ATOM   2328  O   GLY   319     -34.138  67.895 -14.916  1.00  0.00
ATOM   2329  N   ALA   320     -33.451  67.956 -12.767  1.00  0.00
ATOM   2330  CA  ALA   320     -32.170  68.479 -13.123  1.00  0.00
ATOM   2331  C   ALA   320     -31.156  67.437 -12.800  1.00  0.00
ATOM   2332  O   ALA   320     -31.318  66.662 -11.859  1.00  0.00
ATOM   2333  CB  ALA   320     -31.880  69.749 -12.338  1.00  0.00
ATOM   2334  N   ALA   321     -30.081  67.385 -13.608  1.00  0.00
ATOM   2335  CA  ALA   321     -29.042  66.431 -13.374  1.00  0.00
ATOM   2336  C   ALA   321     -27.854  67.201 -12.917  1.00  0.00
ATOM   2337  O   ALA   321     -27.609  68.316 -13.369  1.00  0.00
ATOM   2338  CB  ALA   321     -28.723  65.670 -14.652  1.00  0.00
ATOM   2339  N   LEU   322     -27.088  66.614 -11.982  1.00  0.00
ATOM   2340  CA  LEU   322     -25.928  67.271 -11.462  1.00  0.00
ATOM   2341  C   LEU   322     -24.733  66.620 -12.077  1.00  0.00
ATOM   2342  O   LEU   322     -24.711  65.408 -12.279  1.00  0.00
ATOM   2343  CB  LEU   322     -25.873  67.135  -9.939  1.00  0.00
ATOM   2344  CG  LEU   322     -27.041  67.744  -9.162  1.00  0.00
ATOM   2345  CD1 LEU   322     -26.901  67.465  -7.674  1.00  0.00
ATOM   2346  CD2 LEU   322     -27.092  69.251  -9.360  1.00  0.00
ATOM   2347  N   ASN   323     -23.702  67.418 -12.413  1.00  0.00
ATOM   2348  CA  ASN   323     -22.537  66.823 -12.995  1.00  0.00
ATOM   2349  C   ASN   323     -21.485  66.795 -11.941  1.00  0.00
ATOM   2350  O   ASN   323     -21.017  67.832 -11.477  1.00  0.00
ATOM   2351  CB  ASN   323     -22.058  67.642 -14.195  1.00  0.00
ATOM   2352  CG  ASN   323     -20.877  67.007 -14.900  1.00  0.00
ATOM   2353  OD1 ASN   323     -20.177  66.170 -14.329  1.00  0.00
ATOM   2354  ND2 ASN   323     -20.653  67.402 -16.148  1.00  0.00
ATOM   2355  N   ALA   324     -21.097  65.579 -11.526  1.00  0.00
ATOM   2356  CA  ALA   324     -20.071  65.437 -10.540  1.00  0.00
ATOM   2357  C   ALA   324     -19.489  64.093 -10.779  1.00  0.00
ATOM   2358  O   ALA   324     -20.138  63.240 -11.383  1.00  0.00
ATOM   2359  CB  ALA   324     -20.662  65.542  -9.142  1.00  0.00
ATOM   2360  N   VAL   325     -18.241  63.855 -10.335  1.00  0.00
ATOM   2361  CA  VAL   325     -17.731  62.539 -10.555  1.00  0.00
ATOM   2362  C   VAL   325     -18.237  61.704  -9.430  1.00  0.00
ATOM   2363  O   VAL   325     -17.870  61.884  -8.270  1.00  0.00
ATOM   2364  CB  VAL   325     -16.191  62.527 -10.573  1.00  0.00
ATOM   2365  CG1 VAL   325     -15.671  61.109 -10.755  1.00  0.00
ATOM   2366  CG2 VAL   325     -15.665  63.381 -11.717  1.00  0.00
ATOM   2367  N   LEU   326     -19.137  60.761  -9.759  1.00  0.00
ATOM   2368  CA  LEU   326     -19.718  59.948  -8.739  1.00  0.00
ATOM   2369  C   LEU   326     -18.635  59.107  -8.153  1.00  0.00
ATOM   2370  O   LEU   326     -18.558  58.943  -6.938  1.00  0.00
ATOM   2371  CB  LEU   326     -20.810  59.052  -9.325  1.00  0.00
ATOM   2372  CG  LEU   326     -21.544  58.143  -8.337  1.00  0.00
ATOM   2373  CD1 LEU   326     -22.248  58.965  -7.270  1.00  0.00
ATOM   2374  CD2 LEU   326     -22.588  57.301  -9.055  1.00  0.00
ATOM   2375  N   LEU   327     -17.747  58.563  -9.008  1.00  0.00
ATOM   2376  CA  LEU   327     -16.702  57.729  -8.496  1.00  0.00
ATOM   2377  C   LEU   327     -15.765  58.622  -7.759  1.00  0.00
ATOM   2378  O   LEU   327     -15.626  59.798  -8.090  1.00  0.00
ATOM   2379  CB  LEU   327     -15.974  57.019  -9.639  1.00  0.00
ATOM   2380  CG  LEU   327     -16.803  56.030 -10.460  1.00  0.00
ATOM   2381  CD1 LEU   327     -15.995  55.491 -11.631  1.00  0.00
ATOM   2382  CD2 LEU   327     -17.239  54.852  -9.602  1.00  0.00
ATOM   2383  N   GLY   328     -15.120  58.087  -6.709  1.00  0.00
ATOM   2384  CA  GLY   328     -14.226  58.907  -5.958  1.00  0.00
ATOM   2385  C   GLY   328     -15.074  59.743  -5.063  1.00  0.00
ATOM   2386  O   GLY   328     -16.148  59.322  -4.635  1.00  0.00
ATOM   2387  N   GLU   329     -14.605  60.963  -4.755  1.00  0.00
ATOM   2388  CA  GLU   329     -15.365  61.795  -3.878  1.00  0.00
ATOM   2389  C   GLU   329     -16.629  62.146  -4.575  1.00  0.00
ATOM   2390  O   GLU   329     -16.662  62.306  -5.794  1.00  0.00
ATOM   2391  CB  GLU   329     -14.587  63.067  -3.537  1.00  0.00
ATOM   2392  CG  GLU   329     -15.286  63.972  -2.536  1.00  0.00
ATOM   2393  CD  GLU   329     -14.461  65.194  -2.180  1.00  0.00
ATOM   2394  OE1 GLU   329     -13.349  65.340  -2.729  1.00  0.00
ATOM   2395  OE2 GLU   329     -14.928  66.007  -1.355  1.00  0.00
ATOM   2396  N   LEU   330     -17.717  62.237  -3.790  1.00  0.00
ATOM   2397  CA  LEU   330     -19.003  62.572  -4.312  1.00  0.00
ATOM   2398  C   LEU   330     -19.016  64.060  -4.454  1.00  0.00
ATOM   2399  O   LEU   330     -18.263  64.745  -3.763  1.00  0.00
ATOM   2400  CB  LEU   330     -20.106  62.110  -3.358  1.00  0.00
ATOM   2401  CG  LEU   330     -20.203  60.604  -3.113  1.00  0.00
ATOM   2402  CD1 LEU   330     -21.268  60.295  -2.072  1.00  0.00
ATOM   2403  CD2 LEU   330     -20.568  59.873  -4.396  1.00  0.00
ATOM   2404  N   LEU   331     -19.872  64.568  -5.367  1.00  0.00
ATOM   2405  CA  LEU   331     -20.075  65.950  -5.731  1.00  0.00
ATOM   2406  C   LEU   331     -18.844  66.776  -5.504  1.00  0.00
ATOM   2407  O   LEU   331     -18.533  67.174  -4.384  1.00  0.00
ATOM   2408  CB  LEU   331     -21.204  66.563  -4.900  1.00  0.00
ATOM   2409  CG  LEU   331     -21.549  68.023  -5.198  1.00  0.00
ATOM   2410  CD1 LEU   331     -22.041  68.179  -6.629  1.00  0.00
ATOM   2411  CD2 LEU   331     -22.641  68.520  -4.262  1.00  0.00
ATOM   2412  N   ILE   332     -18.140  67.099  -6.606  1.00  0.00
ATOM   2413  CA  ILE   332     -16.947  67.891  -6.534  1.00  0.00
ATOM   2414  C   ILE   332     -17.215  69.158  -7.275  1.00  0.00
ATOM   2415  O   ILE   332     -17.834  69.148  -8.339  1.00  0.00
ATOM   2416  CB  ILE   332     -15.747  67.164  -7.168  1.00  0.00
ATOM   2417  CG1 ILE   332     -15.461  65.858  -6.423  1.00  0.00
ATOM   2418  CG2 ILE   332     -14.502  68.036  -7.107  1.00  0.00
ATOM   2419  CD1 ILE   332     -14.467  64.960  -7.126  1.00  0.00
ATOM   2420  N   LYS   333     -16.763  70.295  -6.711  1.00  0.00
ATOM   2421  CA  LYS   333     -17.019  71.538  -7.371  1.00  0.00
ATOM   2422  C   LYS   333     -15.731  72.070  -7.913  1.00  0.00
ATOM   2423  O   LYS   333     -14.756  72.247  -7.184  1.00  0.00
ATOM   2424  CB  LYS   333     -17.613  72.552  -6.391  1.00  0.00
ATOM   2425  CG  LYS   333     -18.975  72.159  -5.841  1.00  0.00
ATOM   2426  CD  LYS   333     -19.498  73.203  -4.868  1.00  0.00
ATOM   2427  CE  LYS   333     -20.869  72.821  -4.333  1.00  0.00
ATOM   2428  NZ  LYS   333     -21.432  73.875  -3.445  1.00  0.00
ATOM   2429  N   HIS   334     -15.711  72.307  -9.237  1.00  0.00
ATOM   2430  CA  HIS   334     -14.626  72.957  -9.913  1.00  0.00
ATOM   2431  C   HIS   334     -13.347  72.241  -9.613  1.00  0.00
ATOM   2432  O   HIS   334     -12.281  72.851  -9.572  1.00  0.00
ATOM   2433  CB  HIS   334     -14.500  74.410  -9.449  1.00  0.00
ATOM   2434  CG  HIS   334     -15.745  75.217  -9.649  1.00  0.00
ATOM   2435  ND1 HIS   334     -16.236  75.532 -10.897  1.00  0.00
ATOM   2436  CD2 HIS   334     -16.721  75.854  -8.776  1.00  0.00
ATOM   2437  CE1 HIS   334     -17.357  76.261 -10.756  1.00  0.00
ATOM   2438  NE2 HIS   334     -17.653  76.458  -9.486  1.00  0.00
ATOM   2439  N   TYR   335     -13.397  70.915  -9.401  1.00  0.00
ATOM   2440  CA  TYR   335     -12.160  70.245  -9.126  1.00  0.00
ATOM   2441  C   TYR   335     -12.121  68.976  -9.909  1.00  0.00
ATOM   2442  O   TYR   335     -13.113  68.252  -9.997  1.00  0.00
ATOM   2443  CB  TYR   335     -12.045  69.926  -7.634  1.00  0.00
ATOM   2444  CG  TYR   335     -10.768  69.207  -7.259  1.00  0.00
ATOM   2445  CD1 TYR   335      -9.566  69.896  -7.166  1.00  0.00
ATOM   2446  CD2 TYR   335     -10.771  67.842  -6.998  1.00  0.00
ATOM   2447  CE1 TYR   335      -8.394  69.248  -6.824  1.00  0.00
ATOM   2448  CE2 TYR   335      -9.608  67.178  -6.654  1.00  0.00
ATOM   2449  CZ  TYR   335      -8.415  67.894  -6.568  1.00  0.00
ATOM   2450  OH  TYR   335      -7.250  67.246  -6.227  1.00  0.00
ATOM   2451  N   LEU   336     -10.955  68.687 -10.514  1.00  0.00
ATOM   2452  CA  LEU   336     -10.798  67.469 -11.249  1.00  0.00
ATOM   2453  C   LEU   336      -9.360  67.021 -11.027  1.00  0.00
ATOM   2454  O   LEU   336      -9.018  65.890 -11.463  1.00  0.00
ATOM   2455  CB  LEU   336     -11.064  67.704 -12.738  1.00  0.00
ATOM   2456  CG  LEU   336     -12.492  68.102 -13.116  1.00  0.00
ATOM   2457  CD1 LEU   336     -12.573  68.481 -14.587  1.00  0.00
ATOM   2458  CD2 LEU   336     -13.455  66.952 -12.868  1.00  0.00
TER
END
