
#######################################################
#                                                     #
#                        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    8 (   68),  selected    8 , name T0316TS186_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS186_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           -
LGA    -       -      R     221           -
LGA    -       -      M     222           -
LGA    -       -      M     223           -
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    -       -      H     233           -
LGA    -       -      A     234           -
LGA    Q     276      G     235          2.172
LGA    G     277      L     236          1.961
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    -       -      P     259           -
LGA    -       -      W     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      V     263           -
LGA    -       -      G     264           -
LGA    -       -      K     265           -
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    F     278      I     271          2.922
LGA    Y     279      L     272          0.909
LGA    H     280      Y     273          0.662
LGA    D     281      V     274          0.792
LGA    S     282      G     275          0.944
LGA    L     283      Q     276          1.261
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    -       -      H     280           -
LGA    -       -      D     281           -
LGA    -       -      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    8   60    5.0      8    1.64     0.00     12.346     0.460

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.531516 * X  +  -0.742821 * Y  +   0.407073 * Z  +  51.685909
  Y_new =  -0.800960 * X  +  -0.284391 * Y  +   0.526863 * Z  +  -3.454333
  Z_new =  -0.275597 * X  +  -0.606085 * Y  +  -0.746128 * Z  +  60.754601 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.459392    0.682200  [ DEG:  -140.9128     39.0872 ]
  Theta =   0.279211    2.862382  [ DEG:    15.9976    164.0024 ]
  Phi   =  -0.984921    2.156672  [ DEG:   -56.4318    123.5682 ]
 
# 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: T0316TS186_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS186_3-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8   60   5.0    8   1.64    0.00  12.346
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS186_3-D2
PFRMAT TS
TARGET T0316
MODEL  3
PARENT 1j1z_A
ATOM   1295  N   GLN   276      44.636  24.500 -15.914  1.00  0.00
ATOM   1296  CA  GLN   276      44.864  23.912 -14.575  1.00  0.00
ATOM   1297  C   GLN   276      43.866  22.793 -14.277  1.00  0.00
ATOM   1298  O   GLN   276      43.748  22.345 -13.138  1.00  0.00
ATOM   1299  CB  GLN   276      44.712  24.979 -13.489  1.00  0.00
ATOM   1300  CG  GLN   276      45.859  25.976 -13.433  1.00  0.00
ATOM   1301  CD  GLN   276      45.594  27.115 -12.469  1.00  0.00
ATOM   1302  OE1 GLN   276      44.625  27.086 -11.710  1.00  0.00
ATOM   1303  NE2 GLN   276      46.457  28.123 -12.495  1.00  0.00
ATOM   1304  N   GLY   277      43.157  22.349 -15.310  1.00  0.00
ATOM   1305  CA  GLY   277      42.175  21.278 -15.179  1.00  0.00
ATOM   1306  C   GLY   277      41.715  20.822 -16.555  1.00  0.00
ATOM   1307  O   GLY   277      41.929  21.514 -17.551  1.00  0.00
ATOM   1308  N   PHE   278      41.077  19.656 -16.588  1.00  0.00
ATOM   1309  CA  PHE   278      40.562  19.044 -17.809  1.00  0.00
ATOM   1310  C   PHE   278      39.059  19.314 -17.984  1.00  0.00
ATOM   1311  O   PHE   278      38.342  19.518 -17.009  1.00  0.00
ATOM   1312  CB  PHE   278      40.767  17.528 -17.776  1.00  0.00
ATOM   1313  CG  PHE   278      42.209  17.111 -17.789  1.00  0.00
ATOM   1314  CD1 PHE   278      43.202  18.008 -18.146  1.00  0.00
ATOM   1315  CD2 PHE   278      42.575  15.821 -17.444  1.00  0.00
ATOM   1316  CE1 PHE   278      44.529  17.624 -18.158  1.00  0.00
ATOM   1317  CE2 PHE   278      43.903  15.438 -17.456  1.00  0.00
ATOM   1318  CZ  PHE   278      44.878  16.333 -17.810  1.00  0.00
ATOM   1319  N   TYR   279      38.588  19.294 -19.228  1.00  0.00
ATOM   1320  CA  TYR   279      37.181  19.540 -19.525  1.00  0.00
ATOM   1321  C   TYR   279      36.603  18.622 -20.591  1.00  0.00
ATOM   1322  O   TYR   279      37.318  18.147 -21.470  1.00  0.00
ATOM   1323  CB  TYR   279      36.982  20.972 -20.026  1.00  0.00
ATOM   1324  CG  TYR   279      37.689  21.268 -21.329  1.00  0.00
ATOM   1325  CD1 TYR   279      37.041  21.096 -22.546  1.00  0.00
ATOM   1326  CD2 TYR   279      39.002  21.719 -21.339  1.00  0.00
ATOM   1327  CE1 TYR   279      37.679  21.365 -23.741  1.00  0.00
ATOM   1328  CE2 TYR   279      39.657  21.994 -22.525  1.00  0.00
ATOM   1329  CZ  TYR   279      38.982  21.812 -23.732  1.00  0.00
ATOM   1330  OH  TYR   279      39.621  22.080 -24.921  1.00  0.00
ATOM   1331  N   HIS   280      35.298  18.373 -20.492  1.00  0.00
ATOM   1332  CA  HIS   280      34.565  17.594 -21.488  1.00  0.00
ATOM   1333  C   HIS   280      33.188  18.230 -21.564  1.00  0.00
ATOM   1334  O   HIS   280      32.429  18.216 -20.584  1.00  0.00
ATOM   1335  CB  HIS   280      34.470  16.129 -21.059  1.00  0.00
ATOM   1336  CG  HIS   280      35.798  15.476 -20.840  1.00  0.00
ATOM   1337  ND1 HIS   280      36.550  14.952 -21.869  1.00  0.00
ATOM   1338  CD2 HIS   280      36.641  15.198 -19.685  1.00  0.00
ATOM   1339  CE1 HIS   280      37.685  14.437 -21.364  1.00  0.00
ATOM   1340  NE2 HIS   280      37.746  14.581 -20.055  1.00  0.00
ATOM   1341  N   ASP   281      32.864  18.779 -22.731  1.00  0.00
ATOM   1342  CA  ASP   281      31.601  19.464 -22.903  1.00  0.00
ATOM   1343  C   ASP   281      30.719  18.943 -24.019  1.00  0.00
ATOM   1344  O   ASP   281      31.192  18.538 -25.070  1.00  0.00
ATOM   1345  CB  ASP   281      31.831  20.943 -23.215  1.00  0.00
ATOM   1346  CG  ASP   281      30.550  21.753 -23.183  1.00  0.00
ATOM   1347  OD1 ASP   281      29.498  21.185 -22.819  1.00  0.00
ATOM   1348  OD2 ASP   281      30.596  22.954 -23.523  1.00  0.00
ATOM   1349  N   SER   282      29.420  18.965 -23.759  1.00  0.00
ATOM   1350  CA  SER   282      28.422  18.544 -24.724  1.00  0.00
ATOM   1351  C   SER   282      27.086  19.205 -24.360  1.00  0.00
ATOM   1352  O   SER   282      26.991  19.932 -23.371  1.00  0.00
ATOM   1353  CB  SER   282      28.262  17.022 -24.700  1.00  0.00
ATOM   1354  OG  SER   282      27.677  16.590 -23.484  1.00  0.00
ATOM   1355  N   LEU   283      26.062  18.937 -25.161  1.00  0.00
ATOM   1356  CA  LEU   283      24.746  19.521 -24.960  1.00  0.00
ATOM   1357  C   LEU   283      24.128  19.291 -23.573  1.00  0.00
ATOM   1358  O   LEU   283      23.263  20.055 -23.152  1.00  0.00
ATOM   1359  CB  LEU   283      23.796  19.010 -26.046  1.00  0.00
ATOM   1360  CG  LEU   283      22.675  19.948 -26.485  1.00  0.00
ATOM   1361  CD1 LEU   283      23.243  21.340 -26.760  1.00  0.00
ATOM   1362  CD2 LEU   283      22.010  19.386 -27.739  1.00  0.00
TER
END
