
#######################################################
#                                                     #
#                        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   19 (  184),  selected   19 , name T0386TS083_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS083_3-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     219           -
LGA    N     219      P     220          3.695
LGA    P     220      E     221          1.751
LGA    E     221      K     222          3.302
LGA    K     222      I     223          3.593
LGA    I     223      R     224          2.880
LGA    R     224      L     225          2.887
LGA    L     225      L     226          4.822
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    L     226      E     264          4.821
LGA    K     227      G     265          3.326
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    E     228      G     277          5.149
LGA    F     229      N     278          1.896
LGA    M     230      I     279          0.993
LGA    H     231      D     280          1.248
LGA    T     232      H     281          1.052
LGA    M     233      L     282          1.368
LGA    K     234      -       -           -
LGA    N     235      -       -           -
LGA    T     236      P     283          0.761
LGA    G     237      P     284          1.467
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19   81    5.0     17    3.00     5.88     14.063     0.548

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.921597 * X  +   0.090949 * Y  +   0.377343 * Z  +  19.808638
  Y_new =   0.242915 * X  +   0.623104 * Y  +  -0.743460 * Z  +  28.758224
  Z_new =  -0.302741 * X  +   0.776833 * Y  +   0.552158 * Z  +  36.689453 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.952871   -2.188721  [ DEG:    54.5955   -125.4045 ]
  Theta =   0.307567    2.834025  [ DEG:    17.6223    162.3777 ]
  Phi   =   0.257719   -2.883874  [ DEG:    14.7662   -165.2338 ]
 
# 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: T0386TS083_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS083_3-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   81   5.0   17   3.00    5.88  14.063
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS083_3-D2
PFRMAT TS
TARGET T0386
MODEL 3
PARENT 2F6S_A
ATOM   1197  H   ASN   219       0.350  54.961  79.365  1.00  1.00              
ATOM   1198  N   ASN   219       0.884  54.712  78.630  1.00  4.74              
ATOM   1199  CA  ASN   219       1.360  55.727  77.673  1.00  1.56              
ATOM   1200  CB  ASN   219       0.182  56.358  76.921  1.00  1.00              
ATOM   1201  C   ASN   219       2.231  56.831  78.279  1.00  7.22              
ATOM   1202  O   ASN   219       1.947  57.321  79.373  1.00  1.00              
ATOM   1203  CG  ASN   219      -0.507  55.397  75.972  1.00  1.00              
ATOM   1204  ND2 ASN   219      -1.777  55.655  75.682  1.00  1.00              
ATOM   1205 HD21 ASN   219      -2.184  56.410  76.073  1.00  1.00              
ATOM   1206 HD22 ASN   219      -2.244  55.084  75.096  1.00  1.00              
ATOM   1207  OD1 ASN   219       0.104  54.446  75.479  1.00  1.39              
ATOM   1208  N   PRO   220       3.280  57.274  77.562  1.00 15.93              
ATOM   1209  CA  PRO   220       4.182  58.327  78.033  1.00 16.80              
ATOM   1210  CB  PRO   220       5.505  57.640  77.710  1.00  4.08              
ATOM   1211  C   PRO   220       4.161  59.642  77.243  1.00 25.16              
ATOM   1212  O   PRO   220       3.249  60.467  77.329  1.00  1.00              
ATOM   1213  CG  PRO   220       5.251  57.041  76.351  1.00  3.16              
ATOM   1214  CD  PRO   220       3.766  56.739  76.281  1.00  1.00              
ATOM   1215  H   GLU   221       5.937  59.201  76.554  1.00  1.00              
ATOM   1216  N   GLU   221       5.253  59.852  76.514  1.00 35.88              
ATOM   1217  CA  GLU   221       5.465  61.018  75.659  1.00 28.45              
ATOM   1218  CB  GLU   221       4.383  62.085  75.848  1.00  4.68              
ATOM   1219  C   GLU   221       6.853  61.583  75.950  1.00 24.62              
ATOM   1220  O   GLU   221       7.649  60.909  76.600  1.00  1.00              
ATOM   1221  CG  GLU   221       3.438  62.201  74.660  1.00  4.84              
ATOM   1222  CD  GLU   221       2.337  63.230  74.854  1.00  1.00              
ATOM   1223  OE1 GLU   221       2.657  64.404  75.144  1.00  1.00              
ATOM   1224  OE2 GLU   221       1.148  62.871  74.697  1.00  1.00              
ATOM   1225  H   LYS   222       6.532  63.297  75.004  1.00  1.00              
ATOM   1226  N   LYS   222       7.150  62.813  75.539  1.00 15.99              
ATOM   1227  CA  LYS   222       8.435  63.422  75.889  1.00  2.29              
ATOM   1228  CB  LYS   222       8.816  64.476  74.846  1.00  1.00              
ATOM   1229  C   LYS   222       8.403  64.068  77.268  1.00  1.58              
ATOM   1230  O   LYS   222       9.243  63.788  78.128  1.00  1.00              
ATOM   1231  CG  LYS   222      10.139  65.171  75.130  1.00  1.01              
ATOM   1232  CD  LYS   222      10.480  66.182  74.043  1.00  1.00              
ATOM   1233  CE  LYS   222      11.801  66.885  74.327  1.00  1.00              
ATOM   1234  NZ  LYS   222      12.143  67.872  73.261  1.00  1.00              
ATOM   1235  H   ILE   223       6.802  65.113  76.786  1.00  1.00              
ATOM   1236  N   ILE   223       7.400  64.911  77.483  1.00  3.43              
ATOM   1237  CA  ILE   223       7.205  65.527  78.786  1.00  1.00              
ATOM   1238  CB  ILE   223       6.042  66.545  78.749  1.00  1.00              
ATOM   1239  C   ILE   223       6.904  64.403  79.760  1.00  1.00              
ATOM   1240  O   ILE   223       7.473  64.361  80.854  1.00  1.00              
ATOM   1241  CG1 ILE   223       6.411  67.717  77.834  1.00  2.24              
ATOM   1242  CD1 ILE   223       5.255  68.662  77.548  1.00  1.96              
ATOM   1243  CG2 ILE   223       5.720  67.042  80.157  1.00  1.22              
ATOM   1244  H   ARG   224       5.600  63.492  78.520  1.00  1.00              
ATOM   1245  N   ARG   224       6.032  63.470  79.377  1.00  5.85              
ATOM   1246  CA  ARG   224       5.774  62.363  80.268  1.00  2.71              
ATOM   1247  CB  ARG   224       4.490  61.603  79.951  1.00  1.47              
ATOM   1248  C   ARG   224       7.009  61.482  80.427  1.00  2.47              
ATOM   1249  O   ARG   224       7.148  60.904  81.488  1.00  1.00              
ATOM   1250  CG  ARG   224       3.250  62.434  80.260  1.00  1.00              
ATOM   1251  CD  ARG   224       1.942  61.710  79.963  1.00  1.00              
ATOM   1252  NE  ARG   224       0.793  62.557  80.281  1.00  1.00              
ATOM   1253  HE  ARG   224       0.972  63.399  80.682  1.00  1.00              
ATOM   1254  CZ  ARG   224      -0.482  62.251  80.049  1.00  1.00              
ATOM   1255  NH1 ARG   224      -0.805  61.110  79.450  1.00  1.00              
ATOM   1256  NH2 ARG   224      -1.443  63.095  80.409  1.00  1.00              
ATOM   1257  H   LEU   225       7.781  61.782  78.615  1.00  1.00              
ATOM   1258  N   LEU   225       7.931  61.388  79.463  1.00  2.20              
ATOM   1259  CA  LEU   225       9.155  60.609  79.708  1.00  1.35              
ATOM   1260  CB  LEU   225      10.129  60.751  78.533  1.00  1.00              
ATOM   1261  C   LEU   225       9.828  61.194  80.942  1.00  1.00              
ATOM   1262  O   LEU   225      10.243  60.463  81.845  1.00  1.00              
ATOM   1263  CG  LEU   225      11.503  60.095  78.693  1.00  2.51              
ATOM   1264  CD1 LEU   225      11.358  58.593  78.894  1.00  1.37              
ATOM   1265  CD2 LEU   225      12.368  60.389  77.475  1.00  1.57              
ATOM   1266  H   LEU   226       9.636  63.034  80.247  1.00  1.00              
ATOM   1267  N   LEU   226       9.911  62.519  80.992  1.00  1.00              
ATOM   1268  CA  LEU   226      10.453  63.192  82.165  1.00  1.00              
ATOM   1269  CB  LEU   226      10.603  64.693  81.899  1.00  1.00              
ATOM   1270  C   LEU   226       9.595  62.962  83.398  1.00  1.00              
ATOM   1271  O   LEU   226      10.113  62.635  84.468  1.00  1.00              
ATOM   1272  CG  LEU   226      11.649  65.088  80.854  1.00  1.39              
ATOM   1273  CD1 LEU   226      11.564  66.581  80.566  1.00  1.40              
ATOM   1274  CD2 LEU   226      13.043  64.718  81.343  1.00  1.57              
ATOM   1275  H   LYS   227       7.930  63.318  82.390  1.00  1.00              
ATOM   1276  N   LYS   227       8.282  63.071  83.239  1.00  1.00              
ATOM   1277  CA  LYS   227       7.390  62.853  84.364  1.00  1.00              
ATOM   1278  CB  LYS   227       5.925  63.061  83.972  1.00  1.00              
ATOM   1279  C   LYS   227       7.616  61.433  84.884  1.00  1.00              
ATOM   1280  O   LYS   227       7.715  61.203  86.092  1.00  1.00              
ATOM   1281  CG  LYS   227       5.565  64.515  83.706  1.00  1.00              
ATOM   1282  CD  LYS   227       4.092  64.674  83.355  1.00  1.00              
ATOM   1283  CE  LYS   227       3.728  66.136  83.125  1.00  1.00              
ATOM   1284  NZ  LYS   227       2.285  66.304  82.787  1.00  1.17              
ATOM   1285  H   GLU   228       7.723  60.756  83.045  1.00  1.00              
ATOM   1286  N   GLU   228       7.767  60.496  83.953  1.00  1.28              
ATOM   1287  CA  GLU   228       7.972  59.087  84.261  1.00  1.24              
ATOM   1288  CB  GLU   228       8.096  58.342  82.935  1.00  1.75              
ATOM   1289  C   GLU   228       9.256  58.855  85.054  1.00  1.00              
ATOM   1290  O   GLU   228       9.245  58.204  86.104  1.00  1.00              
ATOM   1291  CG  GLU   228       8.318  56.847  82.994  1.00  1.00              
ATOM   1292  CD  GLU   228       8.405  56.294  81.586  1.00  1.00              
ATOM   1293  OE1 GLU   228       8.383  57.100  80.628  1.00  1.00              
ATOM   1294  OE2 GLU   228       8.467  55.062  81.424  1.00  1.00              
ATOM   1295  H   PHE   229      10.316  59.908  83.762  1.00  1.00              
ATOM   1296  N   PHE   229      10.355  59.432  84.582  1.00  1.00              
ATOM   1297  CA  PHE   229      11.632  59.313  85.276  1.00  1.00              
ATOM   1298  CB  PHE   229      12.780  59.937  84.474  1.00  1.00              
ATOM   1299  C   PHE   229      11.556  59.938  86.662  1.00  1.00              
ATOM   1300  O   PHE   229      12.028  59.359  87.648  1.00  1.00              
ATOM   1301  CG  PHE   229      14.109  59.845  85.179  1.00  1.54              
ATOM   1302  CD1 PHE   229      14.800  58.640  85.230  1.00  1.16              
ATOM   1303  CE1 PHE   229      16.013  58.543  85.910  1.00  1.00              
ATOM   1304  CZ  PHE   229      16.559  59.668  86.511  1.00  1.42              
ATOM   1305  CD2 PHE   229      14.654  60.960  85.807  1.00  1.58              
ATOM   1306  CE2 PHE   229      15.884  60.880  86.455  1.00  1.45              
ATOM   1307  H   MET   230      10.577  61.529  85.978  1.00  1.00              
ATOM   1308  N   MET   230      10.946  61.117  86.747  1.00  1.00              
ATOM   1309  CA  MET   230      10.877  61.803  88.026  1.00  1.00              
ATOM   1310  CB  MET   230      10.139  63.139  87.906  1.00  1.00              
ATOM   1311  C   MET   230      10.174  60.892  89.027  1.00  1.00              
ATOM   1312  O   MET   230      10.646  60.728  90.155  1.00  1.00              
ATOM   1313  CG  MET   230      10.917  64.195  87.134  1.00  1.00              
ATOM   1314  SD  MET   230      12.511  64.569  87.900  1.00  1.34              
ATOM   1315  CE  MET   230      11.975  65.308  89.435  1.00  1.17              
ATOM   1316  H   HIS   231       8.745  60.423  87.742  1.00  1.00              
ATOM   1317  N   HIS   231       9.090  60.244  88.606  1.00  1.16              
ATOM   1318  CA  HIS   231       8.411  59.298  89.485  1.00  1.52              
ATOM   1319  CB  HIS   231       7.059  58.809  88.965  1.00  1.15              
ATOM   1320  C   HIS   231       9.325  58.128  89.850  1.00  1.00              
ATOM   1321  O   HIS   231       9.387  57.716  91.014  1.00  1.00              
ATOM   1322  CG  HIS   231       6.305  58.085  90.040  1.00  1.00              
ATOM   1323  ND1 HIS   231       5.378  58.719  90.838  1.00  1.63              
ATOM   1324  HD1 HIS   231       5.155  59.643  90.811  1.00  1.00              
ATOM   1325  CE1 HIS   231       4.907  57.856  91.723  1.00  1.00              
ATOM   1326  NE2 HIS   231       5.560  56.716  91.581  1.00  1.00              
ATOM   1327  HE2 HIS   231       5.418  55.939  92.111  1.00  1.00              
ATOM   1328  CD2 HIS   231       6.472  56.846  90.564  1.00  1.00              
ATOM   1329  H   THR   232      10.025  57.960  88.000  1.00  1.00              
ATOM   1330  N   THR   232      10.079  57.622  88.876  1.00  1.00              
ATOM   1331  CA  THR   232      10.965  56.487  89.133  1.00  1.00              
ATOM   1332  CB  THR   232      11.798  56.179  87.869  1.00  1.00              
ATOM   1333  C   THR   232      11.922  56.845  90.270  1.00  1.00              
ATOM   1334  O   THR   232      12.102  56.077  91.228  1.00  1.00              
ATOM   1335  CG2 THR   232      12.886  55.149  88.135  1.00  1.00              
ATOM   1336  OG1 THR   232      10.935  55.734  86.815  1.00  1.00              
ATOM   1337  H   MET   233      12.355  58.572  89.428  1.00  1.00              
ATOM   1338  N   MET   233      12.491  58.041  90.205  1.00  1.00              
ATOM   1339  CA  MET   233      13.351  58.543  91.273  1.00  1.00              
ATOM   1340  CB  MET   233      13.751  59.979  90.911  1.00  1.00              
ATOM   1341  C   MET   233      12.548  58.631  92.566  1.00  1.00              
ATOM   1342  O   MET   233      13.042  58.289  93.645  1.00  1.00              
ATOM   1343  CG  MET   233      14.652  60.119  89.693  1.00  1.00              
ATOM   1344  SD  MET   233      16.299  59.424  89.952  1.00  1.00              
ATOM   1345  CE  MET   233      16.998  60.645  91.052  1.00  1.01              
ATOM   1346  H   LYS   234      10.984  59.393  91.616  1.00  1.00              
ATOM   1347  N   LYS   234      11.314  59.121  92.467  1.00  1.00              
ATOM   1348  CA  LYS   234      10.477  59.304  93.649  1.00  1.00              
ATOM   1349  CB  LYS   234       9.126  59.940  93.308  1.00  1.00              
ATOM   1350  C   LYS   234      10.275  57.976  94.366  1.00  1.00              
ATOM   1351  O   LYS   234      10.245  57.934  95.597  1.00  1.00              
ATOM   1352  CG  LYS   234       9.211  61.406  92.913  1.00  1.00              
ATOM   1353  CD  LYS   234       7.838  61.975  92.584  1.00  1.00              
ATOM   1354  CE  LYS   234       7.918  63.446  92.196  1.00  1.00              
ATOM   1355  NZ  LYS   234       6.574  64.006  91.867  1.00  1.00              
ATOM   1356  H   ASN   235      10.212  56.969  92.671  1.00  1.00              
ATOM   1357  N   ASN   235      10.208  56.887  93.612  1.00  1.00              
ATOM   1358  CA  ASN   235      10.066  55.564  94.214  1.00  1.00              
ATOM   1359  CB  ASN   235      10.007  54.496  93.118  1.00  1.00              
ATOM   1360  C   ASN   235      11.227  55.296  95.170  1.00  1.00              
ATOM   1361  O   ASN   235      11.040  54.677  96.220  1.00  2.08              
ATOM   1362  CG  ASN   235       8.715  54.572  92.329  1.00  1.00              
ATOM   1363  ND2 ASN   235       8.827  54.579  91.007  1.00  1.00              
ATOM   1364 HD21 ASN   235       9.689  54.542  90.627  1.00  1.00              
ATOM   1365 HD22 ASN   235       8.050  54.627  90.475  1.00  1.00              
ATOM   1366  OD1 ASN   235       7.626  54.659  92.902  1.00  1.00              
ATOM   1367  H   THR   236      12.561  56.060  93.928  1.00  1.00              
ATOM   1368  N   THR   236      12.434  55.716  94.798  1.00  1.00              
ATOM   1369  CA  THR   236      13.591  55.590  95.691  1.00  1.00              
ATOM   1370  CB  THR   236      14.895  56.030  94.991  1.00  1.00              
ATOM   1371  C   THR   236      13.428  56.376  96.989  1.00  1.00              
ATOM   1372  O   THR   236      13.804  55.888  98.060  1.00  1.00              
ATOM   1373  CG2 THR   236      16.083  55.929  95.940  1.00  1.00              
ATOM   1374  OG1 THR   236      15.136  55.194  93.852  1.00  1.00              
ATOM   1375  H   GLY   237      12.755  57.982  96.065  1.00  1.00              
ATOM   1376  N   GLY   237      12.939  57.610  96.901  1.00  1.00              
ATOM   1377  CA  GLY   237      12.714  58.402  98.101  1.00  1.00              
ATOM   1378  C   GLY   237      12.461  59.876  97.813  1.00  1.00              
ATOM   1379  O   GLY   237      11.375  60.370  98.177  1.00  1.00              
ATOM   1380  OXT GLY   237      13.422  60.581  97.438  1.00  1.00              
TER
END
