
#######################################################
#                                                     #
#                        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   21 (   21),  selected   21 , name T0321TS464_2_2-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS464_2_2-D1.T0321_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      W       2           -
LGA    -       -      E       3           -
LGA    -       -      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      D       6           -
LGA    -       -      A       7           -
LGA    -       -      M       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      G      11           -
LGA    -       -      I      12           -
LGA    -       -      P      13           -
LGA    -       -      E      14           -
LGA    -       -      D      15           -
LGA    -       -      F      16           -
LGA    -       -      L      17           -
LGA    -       -      V      18           -
LGA    -       -      D      19           -
LGA    -       -      E      20           -
LGA    -       -      L      21           -
LGA    -       -      V      22           -
LGA    -       -      C      23           -
LGA    -       -      G      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      H      27           -
LGA    -       -      S      28           -
LGA    -       -      V      29           -
LGA    -       -      I      30           -
LGA    -       -      R      31           -
LGA    -       -      S      32           -
LGA    -       -      G      33           -
LGA    -       -      N      34           -
LGA    -       -      G      35           -
LGA    -       -      V      36           -
LGA    -       -      G      37           -
LGA    E       3      L      38          3.845
LGA    I       4      G      39          2.867
LGA    Y       5      P      40           -
LGA    D       6      N      41           -
LGA    A       7      R      42           -
LGA    -       -      P      43           -
LGA    -       -      F      44           -
LGA    -       -      E      45           -
LGA    -       -      T      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      P      49           -
LGA    -       -      M      50           -
LGA    -       -      L      51           -
LGA    -       -      T      52           -
LGA    -       -      Q      53           -
LGA    -       -      N      54           -
LGA    -       -      L      55           -
LGA    -       -      L      56           -
LGA    -       -      G      57           -
LGA    -       -      L      58           -
LGA    -       -      P      59           -
LGA    V      18      L      60           #
LGA    D      19      R      61          1.932
LGA    E      20      V      62          2.396
LGA    L      21      A      63          2.346
LGA    -       -      A      64           -
LGA    -       -      G      65           -
LGA    -       -      C      66           -
LGA    -       -      V      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      W      70           -
LGA    -       -      N      71           -
LGA    -       -      Y      72           -
LGA    -       -      V      73           -
LGA    -       -      E      74           -
LGA    V      22      A      75          4.654
LGA    -       -      S      76           -
LGA    -       -      I      77           -
LGA    C      23      G      78           #
LGA    G      24      L      79           -
LGA    N      87      A      80          1.781
LGA    N      88      A      81          0.889
LGA    P      89      I      82          1.518
LGA    Q      90      N      83          1.691
LGA    V      91      A      84          0.341
LGA    A      92      Y      85          1.548
LGA    R      93      Y      86          1.844
LGA    E      94      N      87          1.493
LGA    H      95      N      88          2.131
LGA    -       -      P      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      A      92           -
LGA    -       -      R      93           -
LGA    -       -      E      94           -
LGA    -       -      H      95           -
LGA    -       -      G      96           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21   96    5.0     15    2.33     0.00     12.249     0.617

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.269476 * X  +  -0.134128 * Y  +   0.953621 * Z  + -44.488384
  Y_new =  -0.918867 * X  +  -0.260555 * Y  +  -0.296302 * Z  + 118.006432
  Z_new =   0.288213 * X  +  -0.956097 * Y  +  -0.053033 * Z  +  75.225731 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.626208    1.515385  [ DEG:   -93.1748     86.8252 ]
  Theta =  -0.292360   -2.849233  [ DEG:   -16.7510   -163.2490 ]
  Phi   =  -1.856067    1.285526  [ DEG:  -106.3448     73.6552 ]
 
# 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: T0321TS464_2_2-D1                             
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_2_2-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21   96   5.0   15   2.33    0.00  12.249
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      1  CA  GLU     3       1.026  54.093  67.759  1.00  0.00
ATOM      2  CA  ILE     4      -1.804  52.006  66.281  1.00  0.00
ATOM      3  CA  TYR     5      -0.380  48.585  67.198  1.00  0.00
ATOM      4  CA  ASP     6       1.039  49.888  70.497  1.00  0.00
ATOM      5  CA  ALA     7      -2.153  51.678  71.399  1.00  0.00
ATOM      6  CA  VAL    18     -17.496  44.683  59.512  1.00  0.00
ATOM      7  CA  ASP    19     -17.029  47.120  62.409  1.00  0.00
ATOM      8  CA  GLU    20     -14.419  49.563  61.146  1.00  0.00
ATOM      9  CA  LEU    21     -12.361  50.344  58.110  1.00  0.00
ATOM     10  CA  VAL    22      -8.778  51.327  57.834  1.00  0.00
ATOM     11  CA  CYS    23      -8.182  53.206  54.590  1.00  0.00
ATOM     12  CA  GLY    24      -4.546  54.179  54.152  1.00  0.00
ATOM     13  CA  ASN    87      -7.330  53.680  64.162  1.00  0.00
ATOM     14  CA  ASN    88      -9.866  50.871  64.723  1.00  0.00
ATOM     15  CA  PRO    89      -6.992  48.653  65.895  1.00  0.00
ATOM     16  CA  GLN    90      -5.763  51.131  68.518  1.00  0.00
ATOM     17  CA  VAL    91      -9.357  51.666  69.617  1.00  0.00
ATOM     18  CA  ALA    92      -9.955  47.900  70.002  1.00  0.00
ATOM     19  CA  ARG    93      -6.675  47.186  71.790  1.00  0.00
ATOM     20  CA  GLU    94      -7.146  50.021  74.286  1.00  0.00
ATOM     21  CA  HIS    95     -10.871  49.432  74.893  1.00  0.00
TER
END
