
#######################################################
#                                                     #
#                        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   15 (  104),  selected   15 , name T0298TS319_4-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected  186 , name T0298_D2.pdb
# PARAMETERS: T0298TS319_4-D2.T0298_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      C     130           -
LGA    -       -      A     131           -
LGA    -       -      V     132           -
LGA    -       -      A     133           -
LGA    -       -      A     134           -
LGA    -       -      E     135           -
LGA    -       -      L     136           -
LGA    -       -      C     137           -
LGA    -       -      E     138           -
LGA    -       -      V     139           -
LGA    -       -      L     140           -
LGA    -       -      A     141           -
LGA    -       -      P     142           -
LGA    -       -      L     143           -
LGA    -       -      L     144           -
LGA    -       -      A     145           -
LGA    -       -      T     146           -
LGA    -       -      L     147           -
LGA    -       -      D     148           -
LGA    -       -      C     149           -
LGA    -       -      R     150           -
LGA    -       -      Q     151           -
LGA    -       -      L     152           -
LGA    -       -      N     153           -
LGA    -       -      L     154           -
LGA    -       -      T     155           -
LGA    -       -      A     156           -
LGA    -       -      C     157           -
LGA    -       -      L     158           -
LGA    C     130      S     159          4.737
LGA    A     131      V     160          1.099
LGA    V     132      S     161          3.515
LGA    -       -      S     162           -
LGA    -       -      L     163           -
LGA    -       -      G     164           -
LGA    -       -      R     165           -
LGA    -       -      E     166           -
LGA    -       -      G     167           -
LGA    -       -      V     168           -
LGA    A     133      K     169          1.904
LGA    A     134      E     170          0.916
LGA    E     135      L     171          1.402
LGA    L     136      A     172          1.416
LGA    C     137      R     173          0.891
LGA    E     138      Q     174          0.671
LGA    V     139      T     175          0.901
LGA    L     140      A     176          0.942
LGA    A     141      E     177          0.643
LGA    P     142      L     178          0.247
LGA    L     143      L     179          0.642
LGA    L     144      N     180          0.990
LGA    -       -      A     181           -
LGA    -       -      R     182           -
LGA    -       -      P     183           -
LGA    -       -      L     184           -
LGA    -       -      E     185           -
LGA    -       -      P     186           -
LGA    -       -      R     187           -
LGA    -       -      L     188           -
LGA    -       -      F     189           -
LGA    -       -      D     190           -
LGA    -       -      R     191           -
LGA    -       -      Q     192           -
LGA    -       -      I     193           -
LGA    -       -      A     194           -
LGA    -       -      F     195           -
LGA    -       -      N     196           -
LGA    -       -      L     197           -
LGA    -       -      L     198           -
LGA    -       -      A     199           -
LGA    -       -      Q     200           -
LGA    -       -      V     201           -
LGA    -       -      G     202           -
LGA    -       -      A     203           -
LGA    -       -      V     204           -
LGA    -       -      D     205           -
LGA    -       -      A     206           -
LGA    -       -      E     207           -
LGA    -       -      G     208           -
LGA    -       -      H     209           -
LGA    -       -      S     210           -
LGA    -       -      A     211           -
LGA    -       -      I     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
LGA    -       -      R     215           -
LGA    -       -      I     216           -
LGA    -       -      F     217           -
LGA    -       -      A     218           -
LGA    -       -      E     219           -
LGA    -       -      V     220           -
LGA    -       -      Q     221           -
LGA    -       -      A     222           -
LGA    -       -      L     223           -
LGA    -       -      L     224           -
LGA    -       -      G     225           -
LGA    -       -      E     226           -
LGA    -       -      R     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      P     230           -
LGA    -       -      L     231           -
LGA    -       -      N     232           -
LGA    -       -      V     233           -
LGA    -       -      T     234           -
LGA    -       -      C     235           -
LGA    -       -      I     236           -
LGA    -       -      Q     237           -
LGA    -       -      A     238           -
LGA    -       -      P     239           -
LGA    -       -      V     240           -
LGA    -       -      F     241           -
LGA    -       -      F     242           -
LGA    -       -      G     243           -
LGA    -       -      D     244           -
LGA    -       -      S     245           -
LGA    -       -      L     246           -
LGA    -       -      S     247           -
LGA    -       -      V     248           -
LGA    -       -      T     249           -
LGA    -       -      L     250           -
LGA    -       -      Q     251           -
LGA    -       -      C     252           -
LGA    -       -      A     253           -
LGA    -       -      E     254           -
LGA    -       -      P     255           -
LGA    -       -      V     256           -
LGA    -       -      D     257           -
LGA    -       -      L     258           -
LGA    -       -      A     259           -
LGA    -       -      A     260           -
LGA    -       -      V     261           -
LGA    -       -      T     262           -
LGA    -       -      R     263           -
LGA    -       -      V     264           -
LGA    -       -      L     265           -
LGA    -       -      D     266           -
LGA    -       -      A     267           -
LGA    -       -      T     268           -
LGA    -       -      K     269           -
LGA    -       -      G     270           -
LGA    -       -      I     271           -
LGA    -       -      E     272           -
LGA    -       -      W     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      E     276           -
LGA    -       -      G     277           -
LGA    -       -      D     278           -
LGA    -       -      Y     279           -
LGA    -       -      P     280           -
LGA    -       -      T     281           -
LGA    -       -      V     282           -
LGA    -       -      V     283           -
LGA    -       -      G     284           -
LGA    -       -      D     285           -
LGA    -       -      A     286           -
LGA    -       -      L     287           -
LGA    -       -      G     288           -
LGA    -       -      Q     289           -
LGA    -       -      D     290           -
LGA    -       -      E     291           -
LGA    -       -      T     292           -
LGA    -       -      Y     293           -
LGA    -       -      V     294           -
LGA    -       -      G     295           -
LGA    -       -      R     296           -
LGA    -       -      V     297           -
LGA    -       -      R     298           -
LGA    -       -      A     299           -
LGA    -       -      G     300           -
LGA    -       -      Q     301           -
LGA    -       -      A     302           -
LGA    -       -      D     303           -
LGA    -       -      P     304           -
LGA    -       -      C     305           -
LGA    -       -      Q     306           -
LGA    -       -      V     307           -
LGA    -       -      N     308           -
LGA    -       -      L     309           -
LGA    -       -      W     310           -
LGA    -       -      I     311           -
LGA    -       -      V     312           -
LGA    -       -      S     313           -
LGA    -       -      D     314           -
LGA    -       -      N     315           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15  186    5.0     15    1.81     6.67      7.614     0.785

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.915795 * X  +  -0.343290 * Y  +  -0.208498 * Z  +  62.275970
  Y_new =   0.312262 * X  +  -0.935031 * Y  +   0.167956 * Z  +  73.542465
  Z_new =  -0.252610 * X  +   0.088708 * Y  +   0.963493 * Z  +  -0.709032 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.091810   -3.049783  [ DEG:     5.2603   -174.7397 ]
  Theta =   0.255376    2.886216  [ DEG:    14.6320    165.3680 ]
  Phi   =   2.812981   -0.328611  [ DEG:   161.1720    -18.8280 ]
 
# 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: T0298TS319_4-D2                               
REMARK     2: T0298_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS319_4-D2.T0298_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15  186   5.0   15   1.81    6.67   7.614
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS319_4-D2
PFRMAT TS
TARGET T0298
MODEL 4
PARENT N/A
ATOM    905  N   CYS   130      -4.082  59.834  10.181  1.00 85.90       1SG 906
ATOM    906  CA  CYS   130      -3.402  60.198   8.982  1.00 85.90       1SG 907
ATOM    907  CB  CYS   130      -2.972  58.991   8.129  1.00 85.90       1SG 908
ATOM    908  SG  CYS   130      -1.664  58.016   8.932  1.00 85.90       1SG 909
ATOM    909  C   CYS   130      -4.291  61.042   8.148  1.00 85.90       1SG 910
ATOM    910  O   CYS   130      -5.430  61.331   8.524  1.00 85.90       1SG 911
ATOM    911  N   ALA   131      -3.666  61.608   7.097  1.00158.83       1SG 912
ATOM    912  CA  ALA   131      -4.308  62.289   6.014  1.00158.83       1SG 913
ATOM    913  CB  ALA   131      -3.325  63.153   5.204  1.00158.83       1SG 914
ATOM    914  C   ALA   131      -4.998  61.328   5.012  1.00158.83       1SG 915
ATOM    915  O   ALA   131      -6.156  61.600   4.694  1.00158.83       1SG 916
ATOM    916  N   VAL   132      -4.341  60.205   4.515  1.00260.98       1SG 917
ATOM    917  CA  VAL   132      -4.848  59.209   3.549  1.00260.98       1SG 918
ATOM    918  CB  VAL   132      -4.482  59.595   2.128  1.00260.98       1SG 919
ATOM    919  CG1 VAL   132      -5.080  58.619   1.094  1.00260.98       1SG 920
ATOM    920  CG2 VAL   132      -4.952  61.048   1.922  1.00260.98       1SG 921
ATOM    921  C   VAL   132      -4.262  57.823   3.910  1.00260.98       1SG 922
ATOM    922  O   VAL   132      -3.690  57.675   4.982  1.00260.98       1SG 923
ATOM    923  N   ALA   133      -4.431  56.753   3.063  1.00115.36       1SG 924
ATOM    924  CA  ALA   133      -4.069  55.358   3.301  1.00115.36       1SG 925
ATOM    925  CB  ALA   133      -4.635  54.414   2.222  1.00115.36       1SG 926
ATOM    926  C   ALA   133      -2.594  55.030   3.438  1.00115.36       1SG 927
ATOM    927  O   ALA   133      -2.203  54.316   4.363  1.00115.36       1SG 928
ATOM    928  N   ALA   134      -1.716  55.567   2.568  1.00 53.22       1SG 929
ATOM    929  CA  ALA   134      -0.346  55.116   2.529  1.00 53.22       1SG 930
ATOM    930  CB  ALA   134       0.498  55.887   1.503  1.00 53.22       1SG 931
ATOM    931  C   ALA   134       0.312  55.275   3.863  1.00 53.22       1SG 932
ATOM    932  O   ALA   134       1.063  54.404   4.299  1.00 53.22       1SG 933
ATOM    933  N   GLU   135       0.038  56.385   4.559  1.00 95.64       1SG 934
ATOM    934  CA  GLU   135       0.662  56.635   5.824  1.00 95.64       1SG 935
ATOM    935  CB  GLU   135       0.280  58.003   6.410  1.00 95.64       1SG 936
ATOM    936  CG  GLU   135       0.990  59.181   5.733  1.00 95.64       1SG 937
ATOM    937  CD  GLU   135       0.558  59.245   4.273  1.00 95.64       1SG 938
ATOM    938  OE1 GLU   135       1.140  58.489   3.450  1.00 95.64       1SG 939
ATOM    939  OE2 GLU   135      -0.358  60.052   3.961  1.00 95.64       1SG 940
ATOM    940  C   GLU   135       0.266  55.580   6.815  1.00 95.64       1SG 941
ATOM    941  O   GLU   135       1.070  55.200   7.663  1.00 95.64       1SG 942
ATOM    942  N   LEU   136      -0.990  55.093   6.756  1.00 66.89       1SG 943
ATOM    943  CA  LEU   136      -1.444  54.110   7.706  1.00 66.89       1SG 944
ATOM    944  CB  LEU   136      -2.919  53.717   7.496  1.00 66.89       1SG 945
ATOM    945  CG  LEU   136      -3.902  54.890   7.649  1.00 66.89       1SG 946
ATOM    946  CD2 LEU   136      -3.637  55.664   8.948  1.00 66.89       1SG 947
ATOM    947  CD1 LEU   136      -5.360  54.427   7.513  1.00 66.89       1SG 948
ATOM    948  C   LEU   136      -0.654  52.856   7.523  1.00 66.89       1SG 949
ATOM    949  O   LEU   136      -0.139  52.267   8.473  1.00 66.89       1SG 950
ATOM    950  N   CYS   137      -0.494  52.442   6.260  1.00 48.19       1SG 951
ATOM    951  CA  CYS   137       0.167  51.208   5.969  1.00 48.19       1SG 952
ATOM    952  CB  CYS   137       0.285  50.983   4.455  1.00 48.19       1SG 953
ATOM    953  SG  CYS   137       1.077  49.410   4.026  1.00 48.19       1SG 954
ATOM    954  C   CYS   137       1.545  51.279   6.544  1.00 48.19       1SG 955
ATOM    955  O   CYS   137       2.031  50.319   7.142  1.00 48.19       1SG 956
ATOM    956  N   GLU   138       2.211  52.435   6.378  1.00 49.49       1SG 957
ATOM    957  CA  GLU   138       3.544  52.605   6.876  1.00 49.49       1SG 958
ATOM    958  CB  GLU   138       4.199  53.929   6.442  1.00 49.49       1SG 959
ATOM    959  CG  GLU   138       4.511  54.000   4.949  1.00 49.49       1SG 960
ATOM    960  CD  GLU   138       5.173  55.342   4.678  1.00 49.49       1SG 961
ATOM    961  OE1 GLU   138       5.547  56.030   5.667  1.00 49.49       1SG 962
ATOM    962  OE2 GLU   138       5.319  55.695   3.480  1.00 49.49       1SG 963
ATOM    963  C   GLU   138       3.562  52.585   8.371  1.00 49.49       1SG 964
ATOM    964  O   GLU   138       4.435  51.955   8.949  1.00 49.49       1SG 965
ATOM    965  N   VAL   139       2.604  53.241   9.053  1.00 96.16       1SG 966
ATOM    966  CA  VAL   139       2.675  53.332  10.490  1.00 96.16       1SG 967
ATOM    967  CB  VAL   139       1.578  54.153  11.104  1.00 96.16       1SG 968
ATOM    968  CG1 VAL   139       0.244  53.421  10.919  1.00 96.16       1SG 969
ATOM    969  CG2 VAL   139       1.951  54.437  12.571  1.00 96.16       1SG 970
ATOM    970  C   VAL   139       2.602  51.959  11.067  1.00 96.16       1SG 971
ATOM    971  O   VAL   139       3.270  51.648  12.053  1.00 96.16       1SG 972
ATOM    972  N   LEU   140       1.794  51.091  10.440  1.00 59.64       1SG 973
ATOM    973  CA  LEU   140       1.612  49.758  10.924  1.00 59.64       1SG 974
ATOM    974  CB  LEU   140       0.741  48.907   9.983  1.00 59.64       1SG 975
ATOM    975  CG  LEU   140       0.579  47.436  10.415  1.00 59.64       1SG 976
ATOM    976  CD2 LEU   140      -0.093  46.602   9.311  1.00 59.64       1SG 977
ATOM    977  CD1 LEU   140      -0.153  47.320  11.759  1.00 59.64       1SG 978
ATOM    978  C   LEU   140       2.945  49.080  10.972  1.00 59.64       1SG 979
ATOM    979  O   LEU   140       3.248  48.380  11.937  1.00 59.64       1SG 980
ATOM    980  N   ALA   141       3.795  49.280   9.946  1.00 47.92       1SG 981
ATOM    981  CA  ALA   141       5.021  48.533   9.903  1.00 47.92       1SG 982
ATOM    982  CB  ALA   141       5.862  48.813   8.645  1.00 47.92       1SG 983
ATOM    983  C   ALA   141       5.867  48.813  11.114  1.00 47.92       1SG 984
ATOM    984  O   ALA   141       6.327  47.858  11.734  1.00 47.92       1SG 985
ATOM    985  N   PRO   142       6.104  50.036  11.522  1.00159.08       1SG 986
ATOM    986  CA  PRO   142       6.881  50.184  12.720  1.00159.08       1SG 987
ATOM    987  CD  PRO   142       6.511  51.052  10.566  1.00159.08       1SG 988
ATOM    988  CB  PRO   142       7.306  51.645  12.778  1.00159.08       1SG 989
ATOM    989  CG  PRO   142       7.480  51.996  11.295  1.00159.08       1SG 990
ATOM    990  C   PRO   142       6.234  49.671  13.958  1.00159.08       1SG 991
ATOM    991  O   PRO   142       6.949  49.351  14.906  1.00159.08       1SG 992
ATOM    992  N   LEU   143       4.895  49.611  13.998  1.00 48.32       1SG 993
ATOM    993  CA  LEU   143       4.236  49.116  15.166  1.00 48.32       1SG 994
ATOM    994  CB  LEU   143       2.709  49.282  15.098  1.00 48.32       1SG 995
ATOM    995  CG  LEU   143       2.271  50.757  15.049  1.00 48.32       1SG 996
ATOM    996  CD2 LEU   143       3.006  51.588  16.114  1.00 48.32       1SG 997
ATOM    997  CD1 LEU   143       0.740  50.885  15.126  1.00 48.32       1SG 998
ATOM    998  C   LEU   143       4.536  47.659  15.303  1.00 48.32       1SG 999
ATOM    999  O   LEU   143       4.745  47.158  16.408  1.00 48.32       1SG1000
ATOM   1000  N   LEU   144       4.578  46.939  14.167  1.00 75.36       1SG1001
ATOM   1001  CA  LEU   144       4.754  45.517  14.210  1.00 75.36       1SG1002
ATOM   1002  CB  LEU   144       6.101  45.033  14.790  1.00 75.36       1SG1003
ATOM   1003  CG  LEU   144       7.350  45.370  13.950  1.00 75.36       1SG1004
ATOM   1004  CD2 LEU   144       7.631  46.877  13.936  1.00 75.36       1SG1005
ATOM   1005  CD1 LEU   144       7.289  44.733  12.551  1.00 75.36       1SG1006
ATOM   1006  C   LEU   144       3.661  44.972  15.120  1.00 75.36       1SG1007
ATOM   1007  O   LEU   144       2.472  45.318  14.888  1.00 75.36       1SG1008
ATOM   1008  OXT LEU   144       3.997  44.206  16.062  1.00 75.36       1SG1009
TER
END
