
#######################################################
#                                                     #
#                        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 (  159),  selected   19 , name T0386TS319_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS319_1-D2.T0386_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    -       -      N     219           -
LGA    -       -      P     220           -
LGA    N     219      E     221          1.228
LGA    P     220      K     222          2.134
LGA    E     221      I     223          3.605
LGA    -       -      R     224           -
LGA    K     222      L     225          1.834
LGA    -       -      L     226           -
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    I     223      L     263          5.329
LGA    R     224      E     264          2.853
LGA    L     225      G     265          3.366
LGA    L     226      F     266          2.772
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    K     227      G     277           #
LGA    E     228      N     278          2.860
LGA    F     229      I     279          2.570
LGA    M     230      -       -           -
LGA    H     231      D     280          3.289
LGA    T     232      H     281          2.662
LGA    M     233      L     282          1.880
LGA    K     234      P     283          3.023
LGA    N     235      P     284          2.597
LGA    T     236      -       -           -
LGA    G     237      E     285          3.543
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     16    2.99     0.00     12.322     0.519

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.212503 * X  +   0.695217 * Y  +   0.686670 * Z  + -27.225220
  Y_new =   0.461534 * X  +   0.547986 * Y  +  -0.697637 * Z  +  24.689280
  Z_new =  -0.861295 * X  +   0.465171 * Y  +  -0.204417 * Z  +  48.172447 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.984838   -1.156754  [ DEG:   113.7229    -66.2771 ]
  Theta =   1.037813    2.103780  [ DEG:    59.4623    120.5377 ]
  Phi   =   1.139304   -2.002288  [ DEG:    65.2773   -114.7227 ]
 
# 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: T0386TS319_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS319_1-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   16   2.99    0.00  12.322
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS319_1-D2
PFRMAT TS
TARGET T0386
MODEL 1
PARENT N/A
ATOM   1462  N   ASN   219       2.260  58.919  77.755  1.00132.07       1SG1463
ATOM   1463  CA  ASN   219       3.416  58.212  78.217  1.00132.07       1SG1464
ATOM   1464  CB  ASN   219       3.404  56.682  77.955  1.00132.07       1SG1465
ATOM   1465  CG  ASN   219       3.324  56.336  76.478  1.00132.07       1SG1466
ATOM   1466  OD1 ASN   219       2.382  56.722  75.789  1.00132.07       1SG1467
ATOM   1467  ND2 ASN   219       4.343  55.589  75.976  1.00132.07       1SG1468
ATOM   1468  C   ASN   219       4.708  58.833  77.758  1.00132.07       1SG1469
ATOM   1469  O   ASN   219       5.708  58.629  78.444  1.00132.07       1SG1470
ATOM   1470  N   PRO   220       4.787  59.501  76.624  1.00114.70       1SG1471
ATOM   1471  CA  PRO   220       6.036  60.109  76.219  1.00114.70       1SG1472
ATOM   1472  CD  PRO   220       4.018  59.081  75.459  1.00114.70       1SG1473
ATOM   1473  CB  PRO   220       5.969  60.270  74.701  1.00114.70       1SG1474
ATOM   1474  CG  PRO   220       4.958  59.209  74.254  1.00114.70       1SG1475
ATOM   1475  C   PRO   220       6.404  61.410  76.877  1.00114.70       1SG1476
ATOM   1476  O   PRO   220       7.536  61.845  76.671  1.00114.70       1SG1477
ATOM   1477  N   GLU   221       5.502  62.059  77.643  1.00 82.87       1SG1478
ATOM   1478  CA  GLU   221       5.780  63.379  78.150  1.00 82.87       1SG1479
ATOM   1479  CB  GLU   221       4.711  63.917  79.121  1.00 82.87       1SG1480
ATOM   1480  CG  GLU   221       3.387  64.283  78.446  1.00 82.87       1SG1481
ATOM   1481  CD  GLU   221       3.604  65.532  77.602  1.00 82.87       1SG1482
ATOM   1482  OE1 GLU   221       4.615  66.243  77.847  1.00 82.87       1SG1483
ATOM   1483  OE2 GLU   221       2.758  65.795  76.705  1.00 82.87       1SG1484
ATOM   1484  C   GLU   221       7.085  63.409  78.879  1.00 82.87       1SG1485
ATOM   1485  O   GLU   221       7.377  62.555  79.716  1.00 82.87       1SG1486
ATOM   1486  N   LYS   222       7.908  64.428  78.552  1.00175.99       1SG1487
ATOM   1487  CA  LYS   222       9.204  64.612  79.136  1.00175.99       1SG1488
ATOM   1488  CB  LYS   222       9.988  65.767  78.486  1.00175.99       1SG1489
ATOM   1489  CG  LYS   222       9.314  67.137  78.618  1.00175.99       1SG1490
ATOM   1490  CD  LYS   222       7.929  67.215  77.970  1.00175.99       1SG1491
ATOM   1491  CE  LYS   222       7.965  67.329  76.444  1.00175.99       1SG1492
ATOM   1492  NZ  LYS   222       8.482  68.657  76.045  1.00175.99       1SG1493
ATOM   1493  C   LYS   222       9.063  64.927  80.593  1.00175.99       1SG1494
ATOM   1494  O   LYS   222       9.782  64.374  81.423  1.00175.99       1SG1495
ATOM   1495  N   ILE   223       8.114  65.818  80.941  1.00118.17       1SG1496
ATOM   1496  CA  ILE   223       7.948  66.241  82.304  1.00118.17       1SG1497
ATOM   1497  CB  ILE   223       6.912  67.325  82.451  1.00118.17       1SG1498
ATOM   1498  CG2 ILE   223       5.559  66.788  81.953  1.00118.17       1SG1499
ATOM   1499  CG1 ILE   223       6.887  67.854  83.894  1.00118.17       1SG1500
ATOM   1500  CD1 ILE   223       8.157  68.604  84.296  1.00118.17       1SG1501
ATOM   1501  C   ILE   223       7.545  65.075  83.149  1.00118.17       1SG1502
ATOM   1502  O   ILE   223       8.070  64.874  84.244  1.00118.17       1SG1503
ATOM   1503  N   ARG   224       6.602  64.259  82.652  1.00129.52       1SG1504
ATOM   1504  CA  ARG   224       6.122  63.141  83.402  1.00129.52       1SG1505
ATOM   1505  CB  ARG   224       5.007  62.386  82.657  1.00129.52       1SG1506
ATOM   1506  CG  ARG   224       3.762  63.248  82.425  1.00129.52       1SG1507
ATOM   1507  CD  ARG   224       2.537  62.824  83.236  1.00129.52       1SG1508
ATOM   1508  NE  ARG   224       1.505  63.885  83.064  1.00129.52       1SG1509
ATOM   1509  CZ  ARG   224       0.735  63.922  81.938  1.00129.52       1SG1510
ATOM   1510  NH1 ARG   224       0.947  63.021  80.934  1.00129.52       1SG1511
ATOM   1511  NH2 ARG   224      -0.242  64.867  81.811  1.00129.52       1SG1512
ATOM   1512  C   ARG   224       7.264  62.199  83.612  1.00129.52       1SG1513
ATOM   1513  O   ARG   224       7.418  61.621  84.686  1.00129.52       1SG1514
ATOM   1514  N   LEU   225       8.085  62.014  82.564  1.00121.20       1SG1515
ATOM   1515  CA  LEU   225       9.211  61.121  82.572  1.00121.20       1SG1516
ATOM   1516  CB  LEU   225       9.863  61.127  81.179  1.00121.20       1SG1517
ATOM   1517  CG  LEU   225      10.951  60.084  80.843  1.00121.20       1SG1518
ATOM   1518  CD2 LEU   225      11.969  59.825  81.965  1.00121.20       1SG1519
ATOM   1519  CD1 LEU   225      11.615  60.492  79.523  1.00121.20       1SG1520
ATOM   1520  C   LEU   225      10.257  61.596  83.551  1.00121.20       1SG1521
ATOM   1521  O   LEU   225      10.696  60.846  84.419  1.00121.20       1SG1522
ATOM   1522  N   LEU   226      10.705  62.860  83.451  1.00100.15       1SG1523
ATOM   1523  CA  LEU   226      11.810  63.272  84.276  1.00100.15       1SG1524
ATOM   1524  CB  LEU   226      12.369  64.648  83.845  1.00100.15       1SG1525
ATOM   1525  CG  LEU   226      13.739  65.061  84.436  1.00100.15       1SG1526
ATOM   1526  CD2 LEU   226      13.793  65.003  85.971  1.00100.15       1SG1527
ATOM   1527  CD1 LEU   226      14.156  66.443  83.915  1.00100.15       1SG1528
ATOM   1528  C   LEU   226      11.394  63.332  85.714  1.00100.15       1SG1529
ATOM   1529  O   LEU   226      12.102  62.842  86.590  1.00100.15       1SG1530
ATOM   1530  N   LYS   227      10.225  63.931  85.991  1.00115.43       1SG1531
ATOM   1531  CA  LYS   227       9.767  64.101  87.339  1.00115.43       1SG1532
ATOM   1532  CB  LYS   227       8.464  64.915  87.428  1.00115.43       1SG1533
ATOM   1533  CG  LYS   227       8.633  66.378  87.003  1.00115.43       1SG1534
ATOM   1534  CD  LYS   227       9.642  67.152  87.857  1.00115.43       1SG1535
ATOM   1535  CE  LYS   227       9.132  67.497  89.258  1.00115.43       1SG1536
ATOM   1536  NZ  LYS   227      10.175  68.232  90.012  1.00115.43       1SG1537
ATOM   1537  C   LYS   227       9.519  62.749  87.920  1.00115.43       1SG1538
ATOM   1538  O   LYS   227       9.695  62.531  89.118  1.00115.43       1SG1539
ATOM   1539  N   GLU   228       9.080  61.806  87.071  1.00108.04       1SG1540
ATOM   1540  CA  GLU   228       8.748  60.491  87.521  1.00108.04       1SG1541
ATOM   1541  CB  GLU   228       8.206  59.614  86.381  1.00108.04       1SG1542
ATOM   1542  CG  GLU   228       9.223  58.861  85.530  1.00108.04       1SG1543
ATOM   1543  CD  GLU   228       8.555  58.538  84.201  1.00108.04       1SG1544
ATOM   1544  OE1 GLU   228       7.325  58.789  84.087  1.00108.04       1SG1545
ATOM   1545  OE2 GLU   228       9.265  58.055  83.279  1.00108.04       1SG1546
ATOM   1546  C   GLU   228       9.980  59.829  88.047  1.00108.04       1SG1547
ATOM   1547  O   GLU   228       9.951  59.209  89.110  1.00108.04       1SG1548
ATOM   1548  N   PHE   229      11.110  59.955  87.320  1.00 98.13       1SG1549
ATOM   1549  CA  PHE   229      12.295  59.287  87.762  1.00 98.13       1SG1550
ATOM   1550  CB  PHE   229      13.486  59.339  86.795  1.00 98.13       1SG1551
ATOM   1551  CG  PHE   229      14.442  58.374  87.404  1.00 98.13       1SG1552
ATOM   1552  CD1 PHE   229      14.262  57.023  87.219  1.00 98.13       1SG1553
ATOM   1553  CD2 PHE   229      15.498  58.811  88.170  1.00 98.13       1SG1554
ATOM   1554  CE1 PHE   229      15.125  56.113  87.780  1.00 98.13       1SG1555
ATOM   1555  CE2 PHE   229      16.367  57.907  88.734  1.00 98.13       1SG1556
ATOM   1556  CZ  PHE   229      16.181  56.558  88.539  1.00 98.13       1SG1557
ATOM   1557  C   PHE   229      12.739  59.881  89.059  1.00 98.13       1SG1558
ATOM   1558  O   PHE   229      13.185  59.162  89.951  1.00 98.13       1SG1559
ATOM   1559  N   MET   230      12.639  61.215  89.206  1.00 57.28       1SG1560
ATOM   1560  CA  MET   230      13.081  61.814  90.434  1.00 57.28       1SG1561
ATOM   1561  CB  MET   230      12.948  63.347  90.470  1.00 57.28       1SG1562
ATOM   1562  CG  MET   230      13.990  64.070  89.618  1.00 57.28       1SG1563
ATOM   1563  SD  MET   230      13.895  65.883  89.686  1.00 57.28       1SG1564
ATOM   1564  CE  MET   230      15.313  66.156  88.585  1.00 57.28       1SG1565
ATOM   1565  C   MET   230      12.258  61.271  91.559  1.00 57.28       1SG1566
ATOM   1566  O   MET   230      12.784  60.984  92.634  1.00 57.28       1SG1567
ATOM   1567  N   HIS   231      10.939  61.110  91.355  1.00 46.13       1SG1568
ATOM   1568  CA  HIS   231      10.125  60.609  92.425  1.00 46.13       1SG1569
ATOM   1569  ND1 HIS   231       7.692  60.647  94.458  1.00 46.13       1SG1570
ATOM   1570  CG  HIS   231       7.816  60.027  93.234  1.00 46.13       1SG1571
ATOM   1571  CB  HIS   231       8.625  60.561  92.090  1.00 46.13       1SG1572
ATOM   1572  NE2 HIS   231       6.507  58.769  94.574  1.00 46.13       1SG1573
ATOM   1573  CD2 HIS   231       7.084  58.883  93.322  1.00 46.13       1SG1574
ATOM   1574  CE1 HIS   231       6.901  59.851  95.221  1.00 46.13       1SG1575
ATOM   1575  C   HIS   231      10.548  59.217  92.776  1.00 46.13       1SG1576
ATOM   1576  O   HIS   231      10.674  58.882  93.953  1.00 46.13       1SG1577
ATOM   1577  N   THR   232      10.790  58.375  91.753  1.00118.77       1SG1578
ATOM   1578  CA  THR   232      11.137  56.997  91.964  1.00118.77       1SG1579
ATOM   1579  CB  THR   232      11.278  56.227  90.687  1.00118.77       1SG1580
ATOM   1580  OG1 THR   232      12.367  56.718  89.923  1.00118.77       1SG1581
ATOM   1581  CG2 THR   232       9.978  56.379  89.889  1.00118.77       1SG1582
ATOM   1582  C   THR   232      12.448  56.896  92.679  1.00118.77       1SG1583
ATOM   1583  O   THR   232      12.636  56.007  93.507  1.00118.77       1SG1584
ATOM   1584  N   MET   233      13.409  57.778  92.346  1.00148.34       1SG1585
ATOM   1585  CA  MET   233      14.690  57.742  92.989  1.00148.34       1SG1586
ATOM   1586  CB  MET   233      15.688  58.790  92.456  1.00148.34       1SG1587
ATOM   1587  CG  MET   233      15.401  60.216  92.933  1.00148.34       1SG1588
ATOM   1588  SD  MET   233      16.690  61.440  92.554  1.00148.34       1SG1589
ATOM   1589  CE  MET   233      16.062  62.722  93.677  1.00148.34       1SG1590
ATOM   1590  C   MET   233      14.454  58.056  94.419  1.00148.34       1SG1591
ATOM   1591  O   MET   233      15.069  57.480  95.313  1.00148.34       1SG1592
ATOM   1592  N   LYS   234      13.543  59.004  94.678  1.00209.11       1SG1593
ATOM   1593  CA  LYS   234      13.256  59.258  96.044  1.00209.11       1SG1594
ATOM   1594  CB  LYS   234      12.560  60.609  96.286  1.00209.11       1SG1595
ATOM   1595  CG  LYS   234      12.802  61.162  97.691  1.00209.11       1SG1596
ATOM   1596  CD  LYS   234      12.547  62.668  97.797  1.00209.11       1SG1597
ATOM   1597  CE  LYS   234      13.166  63.316  99.039  1.00209.11       1SG1598
ATOM   1598  NZ  LYS   234      12.928  64.778  99.017  1.00209.11       1SG1599
ATOM   1599  C   LYS   234      12.350  58.131  96.383  1.00209.11       1SG1600
ATOM   1600  O   LYS   234      11.968  57.359  95.515  1.00209.11       1SG1601
ATOM   1601  N   ASN   235      11.997  57.983  97.654  1.00269.02       1SG1602
ATOM   1602  CA  ASN   235      11.212  56.891  98.149  1.00269.02       1SG1603
ATOM   1603  CB  ASN   235      10.032  56.497  97.231  1.00269.02       1SG1604
ATOM   1604  CG  ASN   235       8.996  55.700  98.015  1.00269.02       1SG1605
ATOM   1605  OD1 ASN   235       9.299  54.905  98.903  1.00269.02       1SG1606
ATOM   1606  ND2 ASN   235       7.701  55.927  97.669  1.00269.02       1SG1607
ATOM   1607  C   ASN   235      12.123  55.719  98.309  1.00269.02       1SG1608
ATOM   1608  O   ASN   235      11.822  54.798  99.064  1.00269.02       1SG1609
ATOM   1609  N   THR   236      13.297  55.748  97.646  1.00130.36       1SG1610
ATOM   1610  CA  THR   236      14.234  54.683  97.841  1.00130.36       1SG1611
ATOM   1611  CB  THR   236      15.338  54.634  96.814  1.00130.36       1SG1612
ATOM   1612  OG1 THR   236      16.016  53.389  96.897  1.00130.36       1SG1613
ATOM   1613  CG2 THR   236      16.334  55.783  97.049  1.00130.36       1SG1614
ATOM   1614  C   THR   236      14.839  54.852  99.191  1.00130.36       1SG1615
ATOM   1615  O   THR   236      15.064  53.886  99.918  1.00130.36       1SG1616
ATOM   1616  N   GLY   237      15.104  56.119  99.562  1.00 21.34       1SG1617
ATOM   1617  CA  GLY   237      15.712  56.397 100.824  1.00 21.34       1SG1618
ATOM   1618  C   GLY   237      16.538  57.663 100.647  1.00 21.34       1SG1619
ATOM   1619  O   GLY   237      16.151  58.706 101.240  1.00 21.34       1SG1620
ATOM   1620  OXT GLY   237      17.564  57.607  99.917  1.00 21.34       1SG1621
TER
END
