
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0316AL044_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL044_3-D2.T0316_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    G     220      G     220           -
LGA    R     221      R     221           -
LGA    M     222      M     222           -
LGA    T     224      M     223           -
LGA    D     226      T     224           -
LGA    D     229      -       -           -
LGA    M     230      -       -           -
LGA    G     231      -       -           -
LGA    E     232      -       -           -
LGA    H     233      -       -           -
LGA    A     234      -       -           -
LGA    G     235      -       -           -
LGA    L     236      V     225           #
LGA    M     237      D     226          1.412
LGA    Y     238      G     227          1.590
LGA    Y     239      -       -           -
LGA    T     240      R     228          3.013
LGA    I     241      D     229          1.176
LGA    G     242      M     230           #
LGA    Q     243      G     231          4.114
LGA    G     246      E     232          3.451
LGA    L     247      H     233          2.176
LGA    G     254      A     234          4.641
LGA    G     255      G     235          4.576
LGA    D     256      L     236          3.515
LGA    N     257      M     237          1.197
LGA    A     258      Y     238          4.515
LGA    W     260      Y     239          0.741
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    F     261      G     245           #
LGA    V     262      G     246          3.082
LGA    V     263      L     247          3.579
LGA    G     264      -       -           -
LGA    K     265      G     248          2.288
LGA    D     266      I     249          2.760
LGA    L     267      G     250          3.601
LGA    S     268      -       -           -
LGA    K     269      G     251          3.686
LGA    N     270      D     256          4.458
LGA    I     271      N     257           -
LGA    -       -      A     258           -
LGA    -       -      P     259           -
LGA    -       -      W     260           -
LGA    L     272      F     261           #
LGA    Y     273      V     262          3.737
LGA    -       -      V     263           -
LGA    V     274      G     264          1.923
LGA    G     275      K     265          2.022
LGA    Q     276      D     266           #
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      Q     276           -
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    -       -      H     280           -
LGA    -       -      D     281           -
LGA    F     278      S     282           #
LGA    Y     279      L     283          4.545

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   60    5.0     24    3.23     4.17     22.743     0.722

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.845280 * X  +  -0.405167 * Y  +  -0.348342 * Z  +  75.279366
  Y_new =   0.197031 * X  +  -0.842340 * Y  +   0.501639 * Z  +  49.606533
  Z_new =  -0.496670 * X  +   0.355391 * Y  +   0.791843 * Z  + -36.685589 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.421868   -2.719724  [ DEG:    24.1713   -155.8287 ]
  Theta =   0.519758    2.621835  [ DEG:    29.7799    150.2201 ]
  Phi   =   2.912586   -0.229006  [ DEG:   166.8789    -13.1211 ]
 
# 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: T0316AL044_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL044_3-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   60   5.0   24   3.23    4.17  22.743
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL044_3-D2
REMARK Aligment from pdb entry: 1ni5_A
ATOM    621  N   GLY   220      20.200  -7.587 -32.583  1.00  0.00              
ATOM    622  CA  GLY   220      20.966  -7.211 -31.404  1.00  0.00              
ATOM    623  C   GLY   220      22.450  -7.011 -31.702  1.00  0.00              
ATOM    624  O   GLY   220      23.128  -6.243 -31.021  1.00  0.00              
ATOM    625  N   ARG   221      22.952  -7.696 -32.722  1.00  0.00              
ATOM    626  CA  ARG   221      24.353  -7.585 -33.085  1.00  0.00              
ATOM    627  C   ARG   221      24.584  -6.260 -33.808  1.00  0.00              
ATOM    628  O   ARG   221      25.595  -5.589 -33.603  1.00  0.00              
ATOM    629  N   MET   222      23.629  -5.881 -34.645  1.00  0.00              
ATOM    630  CA  MET   222      23.719  -4.633 -35.393  1.00  0.00              
ATOM    631  C   MET   222      23.707  -3.433 -34.450  1.00  0.00              
ATOM    632  O   MET   222      24.373  -2.425 -34.698  1.00  0.00              
ATOM    633  N   THR   224      22.948  -3.559 -33.366  1.00  0.00              
ATOM    634  CA  THR   224      22.803  -2.497 -32.385  1.00  0.00              
ATOM    635  C   THR   224      24.075  -2.224 -31.601  1.00  0.00              
ATOM    636  O   THR   224      24.381  -1.073 -31.291  1.00  0.00              
ATOM    637  N   ASP   226      24.817  -3.279 -31.283  1.00  0.00              
ATOM    638  CA  ASP   226      26.077  -3.125 -30.557  1.00  0.00              
ATOM    639  C   ASP   226      27.030  -2.420 -31.506  1.00  0.00              
ATOM    640  O   ASP   226      27.863  -1.614 -31.095  1.00  0.00              
ATOM    641  N   ASP   229      26.886  -2.738 -32.786  1.00  0.00              
ATOM    642  CA  ASP   229      27.704  -2.139 -33.821  1.00  0.00              
ATOM    643  C   ASP   229      27.445  -0.639 -33.816  1.00  0.00              
ATOM    644  O   ASP   229      28.385   0.156 -33.816  1.00  0.00              
ATOM    645  N   MET   230      26.174  -0.246 -33.803  1.00  0.00              
ATOM    646  CA  MET   230      25.853   1.175 -33.775  1.00  0.00              
ATOM    647  C   MET   230      26.370   1.800 -32.484  1.00  0.00              
ATOM    648  O   MET   230      26.976   2.872 -32.501  1.00  0.00              
ATOM    649  N   GLY   231      28.812   0.957 -30.716  1.00  0.00              
ATOM    650  CA  GLY   231      30.252   1.078 -30.862  1.00  0.00              
ATOM    651  C   GLY   231      30.651   2.247 -31.728  1.00  0.00              
ATOM    652  O   GLY   231      31.631   2.934 -31.436  1.00  0.00              
ATOM    653  N   GLU   232      29.905   2.480 -32.801  1.00  0.00              
ATOM    654  CA  GLU   232      30.231   3.583 -33.700  1.00  0.00              
ATOM    655  C   GLU   232      29.973   4.941 -33.050  1.00  0.00              
ATOM    656  O   GLU   232      30.707   5.900 -33.290  1.00  0.00              
ATOM    657  N   HIS   233      28.932   5.022 -32.228  1.00  0.00              
ATOM    658  CA  HIS   233      28.631   6.260 -31.549  1.00  0.00              
ATOM    659  C   HIS   233      29.784   6.550 -30.620  1.00  0.00              
ATOM    660  O   HIS   233      30.241   7.689 -30.512  1.00  0.00              
ATOM    661  N   ALA   234      30.258   5.510 -29.948  1.00  0.00              
ATOM    662  CA  ALA   234      31.373   5.657 -29.032  1.00  0.00              
ATOM    663  C   ALA   234      32.618   6.136 -29.786  1.00  0.00              
ATOM    664  O   ALA   234      33.278   7.077 -29.354  1.00  0.00              
ATOM    665  N   GLY   235      32.934   5.511 -30.915  1.00  0.00              
ATOM    666  CA  GLY   235      34.102   5.931 -31.672  1.00  0.00              
ATOM    667  C   GLY   235      34.049   7.413 -31.999  1.00  0.00              
ATOM    668  O   GLY   235      35.061   8.105 -31.952  1.00  0.00              
ATOM    669  N   LEU   236      32.867   7.904 -32.334  1.00  0.00              
ATOM    670  CA  LEU   236      32.722   9.311 -32.678  1.00  0.00              
ATOM    671  C   LEU   236      32.909  10.217 -31.467  1.00  0.00              
ATOM    672  O   LEU   236      33.525  11.277 -31.567  1.00  0.00              
ATOM    673  N   MET   237      32.373   9.810 -30.318  1.00  0.00              
ATOM    674  CA  MET   237      32.514  10.630 -29.117  1.00  0.00              
ATOM    675  C   MET   237      33.984  10.712 -28.741  1.00  0.00              
ATOM    676  O   MET   237      34.444  11.733 -28.242  1.00  0.00              
ATOM    677  N   TYR   238      36.521  13.721 -28.451  1.00  0.00              
ATOM    678  CA  TYR   238      37.405  13.843 -27.295  1.00  0.00              
ATOM    679  C   TYR   238      38.772  14.325 -27.778  1.00  0.00              
ATOM    680  O   TYR   238      39.366  15.265 -27.232  1.00  0.00              
ATOM    681  N   TYR   239      39.262  13.672 -28.818  1.00  0.00              
ATOM    682  CA  TYR   239      40.540  14.019 -29.394  1.00  0.00              
ATOM    683  C   TYR   239      40.444  15.451 -29.889  1.00  0.00              
ATOM    684  O   TYR   239      41.147  16.333 -29.417  1.00  0.00              
ATOM    685  N   THR   240      39.530  15.680 -30.816  1.00  0.00              
ATOM    686  CA  THR   240      39.336  16.990 -31.414  1.00  0.00              
ATOM    687  C   THR   240      39.106  18.157 -30.482  1.00  0.00              
ATOM    688  O   THR   240      39.424  19.294 -30.838  1.00  0.00              
ATOM    689  N   ILE   241      38.549  17.904 -29.302  1.00  0.00              
ATOM    690  CA  ILE   241      38.274  18.994 -28.368  1.00  0.00              
ATOM    691  C   ILE   241      39.320  19.182 -27.272  1.00  0.00              
ATOM    692  O   ILE   241      39.325  20.216 -26.597  1.00  0.00              
ATOM    693  N   GLY   242      40.199  18.193 -27.106  1.00  0.00              
ATOM    694  CA  GLY   242      41.251  18.224 -26.086  1.00  0.00              
ATOM    695  C   GLY   242      41.784  19.624 -25.766  1.00  0.00              
ATOM    696  O   GLY   242      41.689  20.093 -24.626  1.00  0.00              
ATOM    697  N   GLN   243      42.342  20.303 -26.760  1.00  0.00              
ATOM    698  CA  GLN   243      42.864  21.642 -26.526  1.00  0.00              
ATOM    699  C   GLN   243      41.795  22.554 -25.933  1.00  0.00              
ATOM    700  O   GLN   243      41.997  23.140 -24.873  1.00  0.00              
ATOM    701  N   GLY   246      40.655  22.665 -26.607  1.00  0.00              
ATOM    702  CA  GLY   246      39.577  23.509 -26.118  1.00  0.00              
ATOM    703  C   GLY   246      39.288  23.210 -24.661  1.00  0.00              
ATOM    704  O   GLY   246      39.063  24.116 -23.855  1.00  0.00              
ATOM    705  N   LEU   247      42.229  24.391 -22.272  1.00  0.00              
ATOM    706  CA  LEU   247      42.181  25.833 -22.120  1.00  0.00              
ATOM    707  C   LEU   247      41.048  26.323 -21.236  1.00  0.00              
ATOM    708  O   LEU   247      41.278  27.118 -20.327  1.00  0.00              
ATOM    709  N   GLY   254      39.829  25.855 -21.487  1.00  0.00              
ATOM    710  CA  GLY   254      38.681  26.309 -20.695  1.00  0.00              
ATOM    711  C   GLY   254      38.555  25.688 -19.304  1.00  0.00              
ATOM    712  O   GLY   254      37.864  26.226 -18.434  1.00  0.00              
ATOM    713  N   GLY   255      39.226  24.561 -19.098  1.00  0.00              
ATOM    714  CA  GLY   255      39.166  23.866 -17.823  1.00  0.00              
ATOM    715  C   GLY   255      40.297  24.342 -16.946  1.00  0.00              
ATOM    716  O   GLY   255      41.461  24.211 -17.304  1.00  0.00              
ATOM    717  N   ASP   256      42.528  24.650 -13.181  1.00  0.00              
ATOM    718  CA  ASP   256      43.161  23.617 -12.356  1.00  0.00              
ATOM    719  C   ASP   256      42.209  23.250 -11.216  1.00  0.00              
ATOM    720  O   ASP   256      42.152  22.097 -10.778  1.00  0.00              
ATOM    721  N   ASN   257      41.452  24.244 -10.760  1.00  0.00              
ATOM    722  CA  ASN   257      40.492  24.070  -9.671  1.00  0.00              
ATOM    723  C   ASN   257      39.418  23.047 -10.016  1.00  0.00              
ATOM    724  O   ASN   257      38.952  22.313  -9.148  1.00  0.00              
ATOM    725  N   ALA   258      39.021  23.008 -11.283  1.00  0.00              
ATOM    726  CA  ALA   258      37.997  22.071 -11.700  1.00  0.00              
ATOM    727  C   ALA   258      36.738  22.784 -12.143  1.00  0.00              
ATOM    728  O   ALA   258      35.634  22.242 -12.068  1.00  0.00              
ATOM    729  N   TRP   260      36.911  24.020 -12.595  1.00  0.00              
ATOM    730  CA  TRP   260      35.797  24.818 -13.081  1.00  0.00              
ATOM    731  C   TRP   260      35.989  25.022 -14.576  1.00  0.00              
ATOM    732  O   TRP   260      36.993  24.586 -15.147  1.00  0.00              
ATOM    733  N   PHE   261      35.030  25.694 -15.203  1.00  0.00              
ATOM    734  CA  PHE   261      35.098  25.956 -16.632  1.00  0.00              
ATOM    735  C   PHE   261      35.079  27.466 -16.900  1.00  0.00              
ATOM    736  O   PHE   261      34.154  28.171 -16.486  1.00  0.00              
ATOM    737  N   VAL   262      36.109  27.952 -17.591  1.00  0.00              
ATOM    738  CA  VAL   262      36.220  29.368 -17.930  1.00  0.00              
ATOM    739  C   VAL   262      35.143  29.744 -18.938  1.00  0.00              
ATOM    740  O   VAL   262      35.081  29.169 -20.018  1.00  0.00              
ATOM    741  N   VAL   263      34.310  30.719 -18.598  1.00  0.00              
ATOM    742  CA  VAL   263      33.259  31.149 -19.506  1.00  0.00              
ATOM    743  C   VAL   263      33.768  32.000 -20.674  1.00  0.00              
ATOM    744  O   VAL   263      33.442  31.742 -21.829  1.00  0.00              
ATOM    745  N   GLY   264      34.584  33.004 -20.381  1.00  0.00              
ATOM    746  CA  GLY   264      35.079  33.899 -21.425  1.00  0.00              
ATOM    747  C   GLY   264      35.576  33.254 -22.721  1.00  0.00              
ATOM    748  O   GLY   264      35.201  33.693 -23.812  1.00  0.00              
ATOM    749  N   LYS   265      36.419  32.210 -22.626  1.00  0.00              
ATOM    750  CA  LYS   265      36.928  31.568 -23.844  1.00  0.00              
ATOM    751  C   LYS   265      35.861  30.872 -24.676  1.00  0.00              
ATOM    752  O   LYS   265      36.102  30.529 -25.831  1.00  0.00              
ATOM    753  N   ASP   266      34.686  30.670 -24.091  1.00  0.00              
ATOM    754  CA  ASP   266      33.610  29.985 -24.786  1.00  0.00              
ATOM    755  C   ASP   266      32.578  30.904 -25.408  1.00  0.00              
ATOM    756  O   ASP   266      31.861  30.507 -26.325  1.00  0.00              
ATOM    757  N   LEU   267      32.496  32.126 -24.898  1.00  0.00              
ATOM    758  CA  LEU   267      31.543  33.108 -25.389  1.00  0.00              
ATOM    759  C   LEU   267      31.470  33.139 -26.905  1.00  0.00              
ATOM    760  O   LEU   267      30.405  33.368 -27.475  1.00  0.00              
ATOM    761  N   SER   268      32.602  32.896 -27.556  1.00  0.00              
ATOM    762  CA  SER   268      32.676  32.937 -29.014  1.00  0.00              
ATOM    763  C   SER   268      32.302  31.653 -29.760  1.00  0.00              
ATOM    764  O   SER   268      31.961  31.690 -30.946  1.00  0.00              
ATOM    765  N   LYS   269      32.368  30.522 -29.070  1.00  0.00              
ATOM    766  CA  LYS   269      32.075  29.234 -29.677  1.00  0.00              
ATOM    767  C   LYS   269      30.640  29.036 -30.102  1.00  0.00              
ATOM    768  O   LYS   269      29.765  29.844 -29.800  1.00  0.00              
ATOM    769  N   ASN   270      30.411  27.941 -30.811  1.00  0.00              
ATOM    770  CA  ASN   270      29.082  27.607 -31.288  1.00  0.00              
ATOM    771  C   ASN   270      28.389  26.733 -30.266  1.00  0.00              
ATOM    772  O   ASN   270      29.032  26.090 -29.429  1.00  0.00              
ATOM    773  N   ILE   271      31.675  17.163 -21.628  1.00  0.00              
ATOM    774  CA  ILE   271      32.928  16.526 -21.256  1.00  0.00              
ATOM    775  C   ILE   271      33.433  17.028 -19.895  1.00  0.00              
ATOM    776  O   ILE   271      34.014  16.272 -19.122  1.00  0.00              
ATOM    777  N   LEU   272      33.200  18.304 -19.601  1.00  0.00              
ATOM    778  CA  LEU   272      33.625  18.894 -18.330  1.00  0.00              
ATOM    779  C   LEU   272      32.863  18.238 -17.182  1.00  0.00              
ATOM    780  O   LEU   272      33.471  17.818 -16.191  1.00  0.00              
ATOM    781  N   TYR   273      31.541  18.152 -17.325  1.00  0.00              
ATOM    782  CA  TYR   273      30.692  17.541 -16.311  1.00  0.00              
ATOM    783  C   TYR   273      31.078  16.080 -16.091  1.00  0.00              
ATOM    784  O   TYR   273      30.940  15.546 -14.990  1.00  0.00              
ATOM    785  N   VAL   274      31.573  15.435 -17.137  1.00  0.00              
ATOM    786  CA  VAL   274      31.990  14.044 -17.028  1.00  0.00              
ATOM    787  C   VAL   274      33.197  13.982 -16.115  1.00  0.00              
ATOM    788  O   VAL   274      33.345  13.037 -15.343  1.00  0.00              
ATOM    789  N   GLY   275      34.059  14.993 -16.220  1.00  0.00              
ATOM    790  CA  GLY   275      35.261  15.056 -15.408  1.00  0.00              
ATOM    791  C   GLY   275      34.984  15.086 -13.917  1.00  0.00              
ATOM    792  O   GLY   275      35.732  14.497 -13.136  1.00  0.00              
ATOM    793  N   GLN   276      33.923  15.780 -13.515  1.00  0.00              
ATOM    794  CA  GLN   276      33.557  15.852 -12.105  1.00  0.00              
ATOM    795  C   GLN   276      32.841  14.542 -11.781  1.00  0.00              
ATOM    796  O   GLN   276      32.286  14.378 -10.691  1.00  0.00              
ATOM    797  N   PHE   278      32.858  13.615 -12.739  1.00  0.00              
ATOM    798  CA  PHE   278      32.195  12.320 -12.595  1.00  0.00              
ATOM    799  C   PHE   278      30.776  12.610 -12.184  1.00  0.00              
ATOM    800  O   PHE   278      30.296  12.100 -11.179  1.00  0.00              
ATOM    801  N   TYR   279      30.119  13.450 -12.975  1.00  0.00              
ATOM    802  CA  TYR   279      28.751  13.855 -12.719  1.00  0.00              
ATOM    803  C   TYR   279      27.782  13.019 -13.537  1.00  0.00              
ATOM    804  O   TYR   279      28.178  12.365 -14.499  1.00  0.00              
END
