
#######################################################
#                                                     #
#                        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   42 (   42),  selected   42 , name T0356TS464_4-D3
# Molecule2: number of CA atoms  120 (  972),  selected  120 , name T0356_D3.pdb
# PARAMETERS: T0356TS464_4-D3.T0356_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D     353      F     348           -
LGA    -       -      P     349           -
LGA    -       -      E     350           -
LGA    -       -      I     351           -
LGA    -       -      V     352           -
LGA    F     354      D     353           #
LGA    Y     355      F     354           #
LGA    L     356      Y     355           #
LGA    P     357      L     356           #
LGA    P     358      P     357           #
LGA    E     359      P     358          4.429
LGA    G     360      E     359          4.791
LGA    C     361      G     360          3.300
LGA    S     362      C     361          2.893
LGA    Y     363      S     362          4.692
LGA    R     364      Y     363          4.207
LGA    L     365      R     364          3.479
LGA    A     366      L     365          2.715
LGA    V     367      A     366          2.667
LGA    V     368      -       -           -
LGA    T     369      V     367          4.465
LGA    I     370      V     368          4.510
LGA    K     371      -       -           -
LGA    K     372      -       -           -
LGA    Q     373      T     369           #
LGA    Y     374      -       -           -
LGA    A     375      -       -           -
LGA    K     396      -       -           -
LGA    F     397      -       -           -
LGA    V     398      -       -           -
LGA    I     399      -       -           -
LGA    V     400      -       -           -
LGA    S     445      I     370          2.081
LGA    G     446      K     371          1.848
LGA    L     447      -       -           -
LGA    G     448      K     372          2.192
LGA    S     449      -       -           -
LGA    K     450      Q     373          2.537
LGA    M     451      Y     374          2.647
LGA    G     452      A     375          2.875
LGA    L     453      G     376          4.275
LGA    D     454      H     377          3.920
LGA    -       -      A     378           -
LGA    -       -      K     379           -
LGA    A     455      R     380          1.845
LGA    T     456      V     381          1.169
LGA    -       -      M     382           -
LGA    -       -      M     383           -
LGA    N     457      G     384          0.683
LGA    -       -      V     385           -
LGA    -       -      W     386           -
LGA    -       -      S     387           -
LGA    -       -      F     388           -
LGA    -       -      L     389           -
LGA    -       -      R     390           -
LGA    -       -      Q     391           -
LGA    -       -      F     392           -
LGA    -       -      M     393           -
LGA    -       -      Y     394           -
LGA    -       -      T     395           -
LGA    -       -      K     396           -
LGA    -       -      F     397           -
LGA    -       -      V     398           -
LGA    -       -      I     399           -
LGA    -       -      V     400           -
LGA    -       -      C     401           -
LGA    -       -      D     402           -
LGA    -       -      D     403           -
LGA    -       -      D     404           -
LGA    -       -      V     405           -
LGA    -       -      N     406           -
LGA    -       -      A     407           -
LGA    -       -      R     408           -
LGA    -       -      D     409           -
LGA    -       -      W     410           -
LGA    -       -      N     411           -
LGA    -       -      D     412           -
LGA    -       -      V     413           -
LGA    -       -      I     414           -
LGA    -       -      W     415           -
LGA    -       -      A     416           -
LGA    -       -      I     417           -
LGA    -       -      T     418           -
LGA    -       -      T     419           -
LGA    -       -      R     420           -
LGA    -       -      M     421           -
LGA    -       -      D     422           -
LGA    -       -      P     423           -
LGA    -       -      A     424           -
LGA    -       -      R     425           -
LGA    -       -      D     426           -
LGA    -       -      T     427           -
LGA    -       -      V     428           -
LGA    -       -      L     429           -
LGA    -       -      V     430           -
LGA    W     467      E     431          2.125
LGA    -       -      N     432           -
LGA    -       -      T     433           -
LGA    -       -      P     434           -
LGA    -       -      I     435           -
LGA    -       -      D     436           -
LGA    -       -      Y     437           -
LGA    -       -      L     438           -
LGA    -       -      D     439           -
LGA    -       -      F     440           -
LGA    -       -      A     441           -
LGA    -       -      S     442           -
LGA    -       -      P     443           -
LGA    -       -      V     444           -
LGA    -       -      S     445           -
LGA    -       -      G     446           -
LGA    -       -      L     447           -
LGA    -       -      G     448           -
LGA    -       -      S     449           -
LGA    -       -      K     450           -
LGA    -       -      M     451           -
LGA    -       -      G     452           -
LGA    -       -      L     453           -
LGA    -       -      D     454           -
LGA    -       -      A     455           -
LGA    -       -      T     456           -
LGA    -       -      N     457           -
LGA    -       -      K     458           -
LGA    -       -      W     459           -
LGA    -       -      P     460           -
LGA    -       -      G     461           -
LGA    -       -      E     462           -
LGA    -       -      T     463           -
LGA    -       -      Q     464           -
LGA    -       -      R     465           -
LGA    -       -      E     466           -
LGA    -       -      W     467           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42  120    5.0     23    3.27     0.00     12.124     0.682

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.488902 * X  +   0.452084 * Y  +  -0.746053 * Z  +  55.913349
  Y_new =   0.855242 * X  +   0.079914 * Y  +  -0.512031 * Z  +  71.154785
  Z_new =  -0.171861 * X  +  -0.888388 * Y  +  -0.425711 * Z  +  85.087990 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.017661    1.123931  [ DEG:  -115.6035     64.3965 ]
  Theta =   0.172719    2.968874  [ DEG:     9.8960    170.1040 ]
  Phi   =   2.090112   -1.051480  [ DEG:   119.7546    -60.2454 ]
 
# 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: T0356TS464_4-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_4-D3.T0356_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42  120   5.0   23   3.27    0.00  12.124
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_4-D3
PFRMAT TS
TARGET T0356
MODEL 4
PARENT N/A
ATOM    121  CA  ASP   353      57.305  68.546  66.674  1.00  0.00
ATOM    122  CA  PHE   354      54.583  71.079  67.384  1.00  0.00
ATOM    123  CA  TYR   355      51.970  68.340  67.937  1.00  0.00
ATOM    124  CA  LEU   356      54.072  66.710  70.706  1.00  0.00
ATOM    125  CA  PRO   357      54.513  70.141  72.287  1.00  0.00
ATOM    126  CA  PRO   358      50.932  71.401  72.371  1.00  0.00
ATOM    127  CA  GLU   359      49.485  67.979  73.335  1.00  0.00
ATOM    128  CA  GLY   360      52.376  66.234  75.062  1.00  0.00
ATOM    129  CA  CYS   361      52.283  63.236  72.715  1.00  0.00
ATOM    130  CA  SER   362      54.757  60.549  71.667  1.00  0.00
ATOM    131  CA  TYR   363      56.244  61.102  68.201  1.00  0.00
ATOM    132  CA  ARG   364      54.137  58.175  66.862  1.00  0.00
ATOM    133  CA  LEU   365      50.755  59.522  68.150  1.00  0.00
ATOM    134  CA  ALA   366      51.628  62.824  66.417  1.00  0.00
ATOM    135  CA  VAL   367      52.096  61.018  63.054  1.00  0.00
ATOM    136  CA  VAL   368      49.000  58.829  63.235  1.00  0.00
ATOM    137  CA  THR   369      46.841  61.843  64.192  1.00  0.00
ATOM    138  CA  ILE   370      48.323  63.206  60.958  1.00  0.00
ATOM    139  CA  LYS   371      47.201  60.256  58.886  1.00  0.00
ATOM    140  CA  LYS   372      43.623  60.638  60.095  1.00  0.00
ATOM    141  CA  GLN   373      43.360  64.434  60.148  1.00  0.00
ATOM    142  CA  TYR   374      44.289  63.986  56.276  1.00  0.00
ATOM    143  CA  ALA   375      41.759  61.159  56.033  1.00  0.00
ATOM    144  CA  LYS   396      44.085  57.051  52.249  1.00  0.00
ATOM    145  CA  PHE   397      46.876  59.600  52.813  1.00  0.00
ATOM    146  CA  VAL   398      49.993  57.710  53.961  1.00  0.00
ATOM    147  CA  ILE   399      52.544  58.609  56.647  1.00  0.00
ATOM    148  CA  VAL   400      56.225  57.769  56.317  1.00  0.00
ATOM    149  CA  SER   445      47.495  71.203  55.732  1.00  0.00
ATOM    150  CA  GLY   446      47.259  73.727  52.903  1.00  0.00
ATOM    151  CA  LEU   447      49.231  71.516  50.495  1.00  0.00
ATOM    152  CA  GLY   448      46.862  68.545  51.006  1.00  0.00
ATOM    153  CA  SER   449      43.806  70.550  49.922  1.00  0.00
ATOM    154  CA  LYS   450      45.384  71.951  46.769  1.00  0.00
ATOM    155  CA  MET   451      47.540  69.059  45.562  1.00  0.00
ATOM    156  CA  GLY   452      46.963  65.301  45.414  1.00  0.00
ATOM    157  CA  LEU   453      49.318  64.265  48.230  1.00  0.00
ATOM    158  CA  ASP   454      50.104  60.535  48.289  1.00  0.00
ATOM    159  CA  ALA   455      52.415  60.260  51.312  1.00  0.00
ATOM    160  CA  THR   456      53.843  62.699  53.880  1.00  0.00
ATOM    161  CA  ASN   457      57.354  61.808  55.021  1.00  0.00
ATOM    162  CA  TRP   467      53.267  44.285  58.164  1.00  0.00
TER
END
