I think there might be something going wrong with the hydrophobe feature
definition, or to be more precise, with the implementation.
Using the linking amino acid Alanine as an example, the C atom will be
labelled as Hydrophobe - ChainTwoWayAttach, although it is bound to the
main-chain oxygen and has a negative charge. In addition, only the CA atom
is identified as polar carbon, not the C bound to the oxygen.
Adrian
ALA_LL
-ISIS- 3D
10 9 0 0 0 0 0 0 0 0 0
2.2810 26.2130 12.8040 N 0 5 0 0 0
1.1690 26.9420 13.4110 C 0 0 0 0 0
1.5390 28.3440 13.8740 C 0 5 0 0 0
2.7090 28.6470 14.1140 O 0 0 0 0 0
0.6010 26.1430 14.5740 C 0 0 0 0 0
2.0330 25.2730 12.4930 H 0 0 0 0 0
0.3990 27.0670 12.6130 H 0 0 0 0 0
-0.2470 26.6990 15.0370 H 0 0 0 0 0
0.3080 25.1100 14.2700 H 0 0 0 0 0
1.3840 25.8760 15.3210 H 0 0 0 0 0
1 2 1 0 0 0
1 6 1 0 0 0
2 3 1 0 0 0
2 5 1 0 0 0
2 7 1 0 0 0
3 4 2 0 0 0
5 8 1 0 0 0
5 9 1 0 0 0
5 10 1 0 0 0
M END
$$$$
