
#######################################################
#                                                     #
#                        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   29 (   29),  selected   29 , name T0372TS464_4_2-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372TS464_4_2-D2.T0372_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    -       -      R     118           -
LGA    -       -      A     119           -
LGA    -       -      Y     120           -
LGA    -       -      A     121           -
LGA    -       -      D     122           -
LGA    -       -      Y     123           -
LGA    -       -      I     124           -
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      R     127           -
LGA    -       -      S     128           -
LGA    -       -      D     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      T     132           -
LGA    -       -      L     133           -
LGA    -       -      K     134           -
LGA    -       -      G     135           -
LGA    -       -      K     136           -
LGA    -       -      K     137           -
LGA    -       -      F     138           -
LGA    -       -      Q     139           -
LGA    -       -      A     140           -
LGA    -       -      K     141           -
LGA    -       -      R     142           -
LGA    -       -      N     143           -
LGA    -       -      H     144           -
LGA    -       -      I     145           -
LGA    -       -      N     146           -
LGA    -       -      R     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      N     150           -
LGA    -       -      T     151           -
LGA    -       -      Y     152           -
LGA    -       -      P     153           -
LGA    -       -      D     154           -
LGA    -       -      Y     155           -
LGA    -       -      E     156           -
LGA    -       -      Y     157           -
LGA    -       -      T     158           -
LGA    -       -      P     159           -
LGA    -       -      I     160           -
LGA    -       -      T     161           -
LGA    -       -      P     162           -
LGA    -       -      D     163           -
LGA    -       -      R     164           -
LGA    -       -      I     165           -
LGA    -       -      Q     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      L     169           -
LGA    V     213      D     170          2.254
LGA    N     214      L     171          2.195
LGA    G     215      E     172          1.443
LGA    K     216      A     173          0.825
LGA    I     217      E     174          0.795
LGA    V     218      W     175          0.883
LGA    A     219      C     176          1.521
LGA    F     220      K     177          1.049
LGA    T     221      V     178          1.509
LGA    F     222      N     179          2.030
LGA    G     223      N     180          2.061
LGA    M     224      C     181          2.749
LGA    -       -      D     182           -
LGA    -       -      Q     183           -
LGA    -       -      Q     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    -       -      T     187           -
LGA    P     225      G     188          2.612
LGA    -       -      N     189           -
LGA    I     226      E     190          3.951
LGA    N     227      R     191          4.380
LGA    H     228      R     192          3.018
LGA    E     229      A     193          3.049
LGA    T     230      L     194          2.594
LGA    F     231      I     195          1.112
LGA    G     232      Y     196          1.788
LGA    V     233      A     197          1.234
LGA    H     234      L     198          4.174
LGA    V     235      H     199          4.979
LGA    E     236      N     200          4.866
LGA    -       -      F     201           -
LGA    -       -      E     202           -
LGA    -       -      A     203           -
LGA    -       -      L     204           -
LGA    -       -      G     205           -
LGA    -       -      L     206           -
LGA    K     237      T     207          4.305
LGA    A     238      G     208          3.758
LGA    D     239      G     209           #
LGA    T     240      I     210           #
LGA    S     241      L     211           -
LGA    -       -      H     212           -
LGA    -       -      V     213           -
LGA    -       -      N     214           -
LGA    -       -      G     215           -
LGA    -       -      K     216           -
LGA    -       -      I     217           -
LGA    -       -      V     218           -
LGA    -       -      A     219           -
LGA    -       -      F     220           -
LGA    -       -      T     221           -
LGA    -       -      F     222           -
LGA    -       -      G     223           -
LGA    -       -      M     224           -
LGA    -       -      P     225           -
LGA    -       -      I     226           -
LGA    -       -      N     227           -
LGA    -       -      H     228           -
LGA    -       -      E     229           -
LGA    -       -      T     230           -
LGA    -       -      F     231           -
LGA    -       -      G     232           -
LGA    -       -      V     233           -
LGA    -       -      H     234           -
LGA    -       -      V     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      A     238           -
LGA    -       -      D     239           -
LGA    -       -      T     240           -
LGA    -       -      S     241           -
LGA    -       -      I     242           -
LGA    -       -      D     243           -
LGA    -       -      G     244           -
LGA    -       -      A     245           -
LGA    -       -      Y     246           -
LGA    -       -      A     247           -
LGA    -       -      M     248           -
LGA    -       -      I     249           -
LGA    -       -      N     250           -
LGA    -       -      Y     251           -
LGA    -       -      E     252           -
LGA    -       -      F     253           -
LGA    -       -      A     254           -
LGA    -       -      N     255           -
LGA    -       -      R     256           -
LGA    -       -      I     257           -
LGA    -       -      P     258           -
LGA    -       -      E     259           -
LGA    -       -      Q     260           -
LGA    -       -      Y     261           -
LGA    -       -      I     262           -
LGA    -       -      Y     263           -
LGA    -       -      I     264           -
LGA    -       -      N     265           -
LGA    -       -      R     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      D     269           -
LGA    -       -      L     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      E     273           -
LGA    -       -      G     274           -
LGA    -       -      L     275           -
LGA    -       -      R     276           -
LGA    -       -      K     277           -
LGA    -       -      A     278           -
LGA    -       -      K     279           -
LGA    -       -      L     280           -
LGA    -       -      S     281           -
LGA    -       -      Y     282           -
LGA    -       -      Q     283           -
LGA    -       -      P     284           -
LGA    -       -      V     285           -
LGA    -       -      T     286           -
LGA    -       -      I     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   29  172    5.0     26    2.82     0.00     11.234     0.890

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.860451 * X  +   0.503170 * Y  +   0.080282 * Z  +  87.542610
  Y_new =  -0.230264 * X  +  -0.243437 * Y  +  -0.942187 * Z  + 117.467163
  Z_new =  -0.454537 * X  +  -0.829192 * Y  +   0.325327 * Z  + 105.712456 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.196909    1.944684  [ DEG:   -68.5778    111.4222 ]
  Theta =   0.471852    2.669741  [ DEG:    27.0351    152.9649 ]
  Phi   =  -2.880111    0.261481  [ DEG:  -165.0182     14.9818 ]
 
# 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: T0372TS464_4_2-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_4_2-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   29  172   5.0   26   2.82    0.00  11.234
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_4_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM     19  CA  VAL   213      51.706  30.946  24.237  1.00  0.00
ATOM     20  CA  ASN   214      48.351  31.580  25.787  1.00  0.00
ATOM     21  CA  GLY   215      46.836  32.408  22.438  1.00  0.00
ATOM     22  CA  LYS   216      48.251  29.068  21.162  1.00  0.00
ATOM     23  CA  ILE   217      46.297  27.113  23.792  1.00  0.00
ATOM     24  CA  VAL   218      42.696  28.417  23.689  1.00  0.00
ATOM     25  CA  ALA   219      42.412  28.001  19.906  1.00  0.00
ATOM     26  CA  PHE   220      44.228  24.515  20.259  1.00  0.00
ATOM     27  CA  THR   221      41.235  24.171  22.576  1.00  0.00
ATOM     28  CA  PHE   222      38.826  25.932  20.331  1.00  0.00
ATOM     29  CA  GLY   223      40.184  24.233  17.187  1.00  0.00
ATOM     30  CA  MET   224      40.143  27.590  15.409  1.00  0.00
ATOM     31  CA  PRO   225      43.414  29.078  14.274  1.00  0.00
ATOM     32  CA  ILE   226      44.432  32.697  13.859  1.00  0.00
ATOM     33  CA  ASN   227      46.262  34.953  11.425  1.00  0.00
ATOM     34  CA  HIS   228      49.429  36.744  12.223  1.00  0.00
ATOM     35  CA  GLU   229      47.487  39.900  12.194  1.00  0.00
ATOM     36  CA  THR   230      44.941  38.714  14.671  1.00  0.00
ATOM     37  CA  PHE   231      47.709  37.473  16.870  1.00  0.00
ATOM     38  CA  GLY   232      49.497  40.819  16.829  1.00  0.00
ATOM     39  CA  VAL   233      46.412  42.833  17.389  1.00  0.00
ATOM     40  CA  HIS   234      45.321  40.774  20.361  1.00  0.00
ATOM     41  CA  VAL   235      48.838  40.899  21.746  1.00  0.00
ATOM     42  CA  GLU   236      48.795  44.591  21.431  1.00  0.00
ATOM     43  CA  LYS   237      45.690  45.133  23.527  1.00  0.00
ATOM     44  CA  ALA   238      45.735  42.573  26.295  1.00  0.00
ATOM     45  CA  ASP   239      49.381  41.863  26.961  1.00  0.00
ATOM     46  CA  THR   240      49.885  44.435  29.686  1.00  0.00
ATOM     47  CA  SER   241      53.401  43.333  30.835  1.00  0.00
TER
END
