
#######################################################
#                                                     #
#                        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_1-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS186_1-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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          1.231
LGA    G     277      L     236          1.727
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          2.416
LGA    Y     279      L     272          0.740
LGA    H     280      Y     273          0.819
LGA    D     281      V     274          0.523
LGA    S     282      G     275          0.761
LGA    L     283      Q     276          1.076
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    1.30     0.00     12.697     0.571

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.897121 * X  +  -0.441772 * Y  +  -0.003411 * Z  +  63.462132
  Y_new =  -0.092646 * X  +   0.195678 * Y  +  -0.976282 * Z  +  32.466080
  Z_new =   0.431961 * X  +  -0.875527 * Y  +  -0.216476 * Z  + -21.213478 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.813187    1.328406  [ DEG:  -103.8880     76.1120 ]
  Theta =  -0.446666   -2.694927  [ DEG:   -25.5921   -154.4079 ]
  Phi   =  -3.038687    0.102906  [ DEG:  -174.1039      5.8961 ]
 
# 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_1-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS186_1-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   1.30    0.00  12.697
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS186_1-D2
PFRMAT TS
TARGET T0316
MODEL  1
PARENT 1vl2_A
ATOM   1352  N   GLN   276      43.247  25.104 -15.680  1.00  0.00
ATOM   1353  CA  GLN   276      44.057  24.041 -15.137  1.00  0.00
ATOM   1354  C   GLN   276      43.325  22.764 -14.723  1.00  0.00
ATOM   1355  O   GLN   276      43.655  22.168 -13.682  1.00  0.00
ATOM   1356  CB  GLN   276      44.785  24.512 -13.877  1.00  0.00
ATOM   1357  CG  GLN   276      45.834  25.582 -14.128  1.00  0.00
ATOM   1358  CD  GLN   276      46.473  26.084 -12.848  1.00  0.00
ATOM   1359  OE1 GLN   276      46.114  25.653 -11.753  1.00  0.00
ATOM   1360  NE2 GLN   276      47.426  27.000 -12.983  1.00  0.00
ATOM   1361  N   GLY   277      42.338  22.379 -15.516  1.00  0.00
ATOM   1362  CA  GLY   277      41.598  21.127 -15.336  1.00  0.00
ATOM   1363  C   GLY   277      41.422  20.470 -16.702  1.00  0.00
ATOM   1364  O   GLY   277      41.456  21.172 -17.727  1.00  0.00
ATOM   1365  N   PHE   278      41.244  19.151 -16.703  1.00  0.00
ATOM   1366  CA  PHE   278      40.820  18.422 -17.913  1.00  0.00
ATOM   1367  C   PHE   278      39.309  18.537 -18.017  1.00  0.00
ATOM   1368  O   PHE   278      38.626  18.080 -17.135  1.00  0.00
ATOM   1369  CB  PHE   278      41.224  16.948 -17.820  1.00  0.00
ATOM   1370  CG  PHE   278      40.859  16.142 -19.034  1.00  0.00
ATOM   1371  CD1 PHE   278      41.567  16.282 -20.214  1.00  0.00
ATOM   1372  CD2 PHE   278      39.805  15.245 -18.995  1.00  0.00
ATOM   1373  CE1 PHE   278      41.230  15.540 -21.331  1.00  0.00
ATOM   1374  CE2 PHE   278      39.469  14.503 -20.112  1.00  0.00
ATOM   1375  CZ  PHE   278      40.176  14.647 -21.276  1.00  0.00
ATOM   1376  N   TYR   279      38.794  19.135 -19.094  1.00  0.00
ATOM   1377  CA  TYR   279      37.371  19.432 -19.189  1.00  0.00
ATOM   1378  C   TYR   279      36.828  18.882 -20.504  1.00  0.00
ATOM   1379  O   TYR   279      37.537  18.929 -21.520  1.00  0.00
ATOM   1380  CB  TYR   279      37.134  20.943 -19.144  1.00  0.00
ATOM   1381  CG  TYR   279      37.559  21.590 -17.845  1.00  0.00
ATOM   1382  CD1 TYR   279      38.851  22.074 -17.679  1.00  0.00
ATOM   1383  CD2 TYR   279      36.666  21.717 -16.788  1.00  0.00
ATOM   1384  CE1 TYR   279      39.246  22.667 -16.496  1.00  0.00
ATOM   1385  CE2 TYR   279      37.044  22.308 -15.598  1.00  0.00
ATOM   1386  CZ  TYR   279      38.347  22.784 -15.459  1.00  0.00
ATOM   1387  OH  TYR   279      38.739  23.375 -14.279  1.00  0.00
ATOM   1388  N   HIS   280      35.642  18.283 -20.441  1.00  0.00
ATOM   1389  CA  HIS   280      34.909  17.809 -21.644  1.00  0.00
ATOM   1390  C   HIS   280      33.570  18.487 -21.589  1.00  0.00
ATOM   1391  O   HIS   280      32.962  18.500 -20.549  1.00  0.00
ATOM   1392  CB  HIS   280      34.755  16.287 -21.612  1.00  0.00
ATOM   1393  CG  HIS   280      34.068  15.724 -22.816  1.00  0.00
ATOM   1394  ND1 HIS   280      32.699  15.580 -22.895  1.00  0.00
ATOM   1395  CD2 HIS   280      34.495  15.214 -24.112  1.00  0.00
ATOM   1396  CE1 HIS   280      32.383  15.051 -24.090  1.00  0.00
ATOM   1397  NE2 HIS   280      33.455  14.829 -24.825  1.00  0.00
ATOM   1398  N   ASP   281      33.063  18.976 -22.702  1.00  0.00
ATOM   1399  CA  ASP   281      31.770  19.642 -22.671  1.00  0.00
ATOM   1400  C   ASP   281      30.884  19.233 -23.854  1.00  0.00
ATOM   1401  O   ASP   281      31.371  19.032 -24.980  1.00  0.00
ATOM   1402  CB  ASP   281      31.949  21.160 -22.729  1.00  0.00
ATOM   1403  CG  ASP   281      30.660  21.910 -22.452  1.00  0.00
ATOM   1404  OD1 ASP   281      29.654  21.255 -22.111  1.00  0.00
ATOM   1405  OD2 ASP   281      30.657  23.153 -22.576  1.00  0.00
ATOM   1406  N   SER   282      29.607  19.082 -23.591  1.00  0.00
ATOM   1407  CA  SER   282      28.636  18.819 -24.659  1.00  0.00
ATOM   1408  C   SER   282      27.314  19.363 -24.192  1.00  0.00
ATOM   1409  O   SER   282      27.230  20.011 -23.106  1.00  0.00
ATOM   1410  CB  SER   282      28.526  17.316 -24.925  1.00  0.00
ATOM   1411  OG  SER   282      27.963  16.642 -23.813  1.00  0.00
ATOM   1412  N   LEU   283      26.259  19.111 -24.959  1.00  0.00
ATOM   1413  CA  LEU   283      24.954  19.605 -24.615  1.00  0.00
ATOM   1414  C   LEU   283      24.413  19.081 -23.301  1.00  0.00
ATOM   1415  O   LEU   283      23.529  19.674 -22.716  1.00  0.00
ATOM   1416  CB  LEU   283      23.954  19.212 -25.738  1.00  0.00
ATOM   1417  CG  LEU   283      22.718  20.050 -25.875  1.00  0.00
ATOM   1418  CD1 LEU   283      23.038  21.452 -26.393  1.00  0.00
ATOM   1419  CD2 LEU   283      21.758  19.285 -26.826  1.00  0.00
TER
END
