
#######################################################
#                                                     #
#                        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   41 (   41),  selected   41 , name T0301TS464_3_1-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301TS464_3_1-D2.T0301_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D     187           -
LGA    -       -      G     188           -
LGA    -       -      G     189           -
LGA    -       -      A     190           -
LGA    -       -      I     191           -
LGA    -       -      F     192           -
LGA    -       -      P     193           -
LGA    -       -      T     194           -
LGA    -       -      G     195           -
LGA    -       -      N     196           -
LGA    -       -      L     197           -
LGA    G     207      V     198          1.632
LGA    T     208      D     199          4.540
LGA    F     209      D     200           -
LGA    -       -      L     201           -
LGA    -       -      E     202           -
LGA    -       -      V     203           -
LGA    -       -      P     204           -
LGA    -       -      G     205           -
LGA    -       -      V     206           -
LGA    -       -      G     207           -
LGA    -       -      T     208           -
LGA    -       -      F     209           -
LGA    -       -      K     210           -
LGA    K     210      A     211           #
LGA    A     211      T     212          3.835
LGA    T     212      M     213          3.927
LGA    M     213      I     214          1.142
LGA    I     214      N     215          4.836
LGA    N     215      -       -           -
LGA    A     216      -       -           -
LGA    G     217      A     216           #
LGA    I     218      G     217          4.181
LGA    -       -      I     218           -
LGA    -       -      P     219           -
LGA    P     219      T     220          3.856
LGA    T     220      V     221           #
LGA    V     221      F     222          5.050
LGA    F     222      V     223           #
LGA    -       -      N     224           -
LGA    -       -      A     225           -
LGA    -       -      E     226           -
LGA    -       -      E     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      Y     230           -
LGA    -       -      R     231           -
LGA    -       -      G     232           -
LGA    -       -      T     233           -
LGA    -       -      E     234           -
LGA    -       -      L     235           -
LGA    -       -      R     236           -
LGA    -       -      E     237           -
LGA    -       -      E     238           -
LGA    -       -      I     239           -
LGA    -       -      N     240           -
LGA    -       -      G     241           -
LGA    -       -      D     242           -
LGA    -       -      P     243           -
LGA    -       -      Q     244           -
LGA    -       -      Q     245           -
LGA    -       -      L     246           -
LGA    -       -      A     247           -
LGA    -       -      R     248           -
LGA    -       -      F     249           -
LGA    -       -      E     250           -
LGA    -       -      R     251           -
LGA    -       -      I     252           -
LGA    -       -      R     253           -
LGA    -       -      V     254           -
LGA    -       -      A     255           -
LGA    -       -      G     256           -
LGA    -       -      A     257           -
LGA    -       -      L     258           -
LGA    -       -      R     259           -
LGA    -       -      M     260           -
LGA    -       -      G     261           -
LGA    -       -      L     262           -
LGA    -       -      I     263           -
LGA    -       -      K     264           -
LGA    -       -      T     265           -
LGA    -       -      P     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      A     269           -
LGA    -       -      A     270           -
LGA    -       -      T     271           -
LGA    -       -      R     272           -
LGA    -       -      Q     273           -
LGA    -       -      H     274           -
LGA    -       -      T     275           -
LGA    -       -      P     276           -
LGA    -       -      K     277           -
LGA    -       -      I     278           -
LGA    -       -      A     279           -
LGA    -       -      F     280           -
LGA    -       -      V     281           -
LGA    -       -      A     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      R     285           -
LGA    -       -      D     286           -
LGA    -       -      Y     287           -
LGA    -       -      R     288           -
LGA    -       -      T     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      G     292           -
LGA    -       -      K     293           -
LGA    -       -      L     294           -
LGA    -       -      V     295           -
LGA    -       -      A     296           -
LGA    -       -      A     297           -
LGA    -       -      G     298           -
LGA    -       -      D     299           -
LGA    -       -      I     300           -
LGA    -       -      D     301           -
LGA    -       -      L     302           -
LGA    -       -      L     303           -
LGA    -       -      V     304           -
LGA    -       -      R     305           -
LGA    -       -      A     306           -
LGA    -       -      L     307           -
LGA    -       -      S     308           -
LGA    -       -      M     309           -
LGA    -       -      G     310           -
LGA    -       -      K     311           -
LGA    -       -      L     312           -
LGA    -       -      H     313           -
LGA    -       -      H     314           -
LGA    -       -      A     315           -
LGA    -       -      M     316           -
LGA    -       -      M     317           -
LGA    -       -      G     318           -
LGA    P     276      T     319          2.051
LGA    K     277      A     320          2.844
LGA    -       -      A     321           -
LGA    -       -      V     322           -
LGA    I     278      A     323          2.226
LGA    A     279      I     324          2.239
LGA    -       -      G     325           -
LGA    -       -      T     326           -
LGA    F     280      A     327          2.105
LGA    -       -      A     328           -
LGA    -       -      A     329           -
LGA    -       -      I     330           -
LGA    -       -      P     331           -
LGA    -       -      G     332           -
LGA    -       -      T     333           -
LGA    -       -      L     334           -
LGA    -       -      V     335           -
LGA    V     281      N     336          1.071
LGA    A     282      L     337          2.593
LGA    -       -      A     338           -
LGA    -       -      A     339           -
LGA    -       -      G     340           -
LGA    -       -      G     341           -
LGA    -       -      G     342           -
LGA    -       -      E     343           -
LGA    -       -      R     344           -
LGA    -       -      S     345           -
LGA    -       -      A     346           -
LGA    -       -      V     347           -
LGA    -       -      R     348           -
LGA    -       -      F     349           -
LGA    -       -      G     350           -
LGA    -       -      H     351           -
LGA    -       -      P     352           -
LGA    -       -      S     353           -
LGA    -       -      G     354           -
LGA    -       -      T     355           -
LGA    -       -      L     356           -
LGA    D     299      R     357          4.139
LGA    I     300      V     358          3.220
LGA    D     301      G     359          3.603
LGA    L     302      -       -           -
LGA    L     303      -       -           -
LGA    V     304      -       -           -
LGA    A     327      -       -           -
LGA    A     328      -       -           -
LGA    A     329      -       -           -
LGA    I     330      -       -           -
LGA    P     331      -       -           -
LGA    L     356      A     360          1.580
LGA    R     357      E     361          2.152
LGA    V     358      A     362          2.041
LGA    G     359      S     363          2.369
LGA    A     360      Q     364           #
LGA    -       -      A     365           -
LGA    -       -      N     366           -
LGA    -       -      G     367           -
LGA    M     376      E     368           #
LGA    S     377      W     369          2.935
LGA    -       -      T     370           -
LGA    -       -      V     371           -
LGA    -       -      T     372           -
LGA    -       -      K     373           -
LGA    -       -      A     374           -
LGA    -       -      I     375           -
LGA    -       -      M     376           -
LGA    -       -      S     377           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41  191    5.0     24    3.14     0.00      8.007     0.741

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.539068 * X  +   0.345463 * Y  +  -0.768154 * Z  +  94.336578
  Y_new =   0.636730 * X  +   0.429853 * Y  +   0.640157 * Z  + -29.609814
  Z_new =   0.551343 * X  +  -0.834196 * Y  +   0.011753 * Z  +   1.539415 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.556708    1.584885  [ DEG:   -89.1928     90.8072 ]
  Theta =  -0.583974   -2.557619  [ DEG:   -33.4592   -146.5408 ]
  Phi   =   0.868268   -2.273324  [ DEG:    49.7481   -130.2519 ]
 
# 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: T0301TS464_3_1-D2                             
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_3_1-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41  191   5.0   24   3.14    0.00   8.007
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM     23  CA  GLY   207      99.935  -3.360   9.709  1.00  0.00
ATOM     24  CA  THR   208      99.158  -3.416   5.991  1.00  0.00
ATOM     25  CA  PHE   209      95.938  -1.310   6.178  1.00  0.00
ATOM     26  CA  LYS   210      97.556   1.209   8.570  1.00  0.00
ATOM     27  CA  ALA   211     100.309   2.006   6.057  1.00  0.00
ATOM     28  CA  THR   212      97.431   1.909   3.581  1.00  0.00
ATOM     29  CA  MET   213      95.682   4.855   5.249  1.00  0.00
ATOM     30  CA  ILE   214      98.991   6.783   5.549  1.00  0.00
ATOM     31  CA  ASN   215      99.587   6.570   1.764  1.00  0.00
ATOM     32  CA  ALA   216      96.101   8.040   1.390  1.00  0.00
ATOM     33  CA  GLY   217      96.610  10.959   3.788  1.00  0.00
ATOM     34  CA  ILE   218      94.254   9.361   6.335  1.00  0.00
ATOM     35  CA  PRO   219      94.921   9.411  10.071  1.00  0.00
ATOM     36  CA  THR   220      93.891   6.273  11.950  1.00  0.00
ATOM     37  CA  VAL   221      95.698   4.746  14.678  1.00  0.00
ATOM     38  CA  PHE   222      96.385   1.069  15.540  1.00  0.00
ATOM     39  CA  PRO   276      89.653  13.382  11.963  1.00  0.00
ATOM     40  CA  LYS   277      90.998  10.272  13.681  1.00  0.00
ATOM     41  CA  ILE   278      90.337   6.827  12.178  1.00  0.00
ATOM     42  CA  ALA   279      90.749   3.775  14.417  1.00  0.00
ATOM     43  CA  PHE   280      92.190   0.601  12.794  1.00  0.00
ATOM     44  CA  VAL   281      91.110  -2.400  14.897  1.00  0.00
ATOM     45  CA  ALA   282      93.617  -5.267  14.684  1.00  0.00
ATOM     46  CA  ASP   299      87.528   9.579  18.881  1.00  0.00
ATOM     47  CA  ILE   300      87.463   7.632  15.686  1.00  0.00
ATOM     48  CA  ASP   301      85.073   7.145  12.754  1.00  0.00
ATOM     49  CA  LEU   302      85.595   3.529  11.732  1.00  0.00
ATOM     50  CA  LEU   303      87.520   0.457  12.698  1.00  0.00
ATOM     51  CA  VAL   304      89.284  -2.032  10.561  1.00  0.00
ATOM     52  CA  ALA   327      83.066   3.950   5.529  1.00  0.00
ATOM     53  CA  ALA   328      85.144   6.441   3.543  1.00  0.00
ATOM     54  CA  ALA   329      88.125   7.607   5.637  1.00  0.00
ATOM     55  CA  ILE   330      89.169  11.235   4.874  1.00  0.00
ATOM     56  CA  PRO   331      92.502  13.131   5.207  1.00  0.00
ATOM     57  CA  LEU   356      82.262   2.871  10.023  1.00  0.00
ATOM     58  CA  ARG   357      83.057  -0.784   9.685  1.00  0.00
ATOM     59  CA  VAL   358      85.511  -1.390   6.818  1.00  0.00
ATOM     60  CA  GLY   359      83.778  -4.458   5.461  1.00  0.00
ATOM     61  CA  ALA   360      80.282  -5.541   4.366  1.00  0.00
ATOM     62  CA  MET   376      88.678  -1.895   4.845  1.00  0.00
ATOM     63  CA  SER   377      91.068  -1.007   1.998  1.00  0.00
TER
END
