Contacts of the helix formed by residues 1005 - 1038 (chain I) in PDB entry 6C6S
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU1005 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982I GLY* 5.5 5.7 - - - -
1002I LEU* 4.7 8.2 - - + +
1003I THR* 3.1 29.3 + - - +
1004I ASP* 1.3 82.5 - - - +
1006I GLU* 1.3 75.8 + - - +
1007I LYS* 3.2 15.8 + - - +
1008I GLN* 3.5 3.9 + - - +
1009I ASN* 3.3 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1006 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005I GLU* 1.3 81.9 - - - +
1007I LYS* 1.3 73.9 + - + +
1009I ASN* 3.4 13.9 - - + +
1010I GLN* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1007 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977I ALA 5.7 1.0 + - - -
978I VAL* 3.7 39.1 + - + +
981I ALA* 3.5 39.8 - - - +
982I GLY* 4.3 3.4 - - - +
1002I LEU* 3.7 16.6 - - + -
1005I GLU* 3.2 11.5 - - + +
1006I GLU* 1.3 87.9 - - + +
1008I GLN* 1.3 60.0 + - - +
1010I GLN* 3.2 11.4 + - - +
1011I LEU* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1008 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998I LEU* 3.6 36.0 + - - +
1000I LEU 4.7 0.3 - - - +
1002I LEU* 3.3 34.1 + - + +
1003I THR 3.5 23.3 - - - +
1004I ASP* 5.4 0.9 - - - -
1005I GLU 3.5 4.6 + - - +
1007I LYS* 1.3 75.6 - - - +
1009I ASN* 1.3 60.8 + - - +
1011I LEU* 3.2 21.1 + - - +
1012I GLU* 2.9 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1009 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005I GLU 3.3 12.8 + - - +
1006I GLU* 3.4 18.6 - - + +
1007I LYS 3.2 0.2 - - - -
1008I GLN* 1.3 78.6 - - - +
1010I GLN* 1.3 55.8 + - - +
1012I GLU* 3.3 8.3 + - - +
1013I GLN* 2.9 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1010 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743I PRO* 4.1 13.9 + - + +
974I ARG* 3.5 38.4 - - - +
978I VAL* 3.7 21.1 - - + +
1006I GLU 2.9 14.9 + - - +
1007I LYS* 3.2 13.5 + - - +
1009I ASN* 1.3 73.5 - - - +
1011I LEU* 1.3 60.8 + - - +
1013I GLN* 3.2 10.1 + - + +
1014I LEU* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1011 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975I ILE* 3.8 40.6 - - + +
978I VAL* 3.9 14.1 - - + -
979I LEU* 3.8 22.7 - - + -
998I LEU* 3.3 34.4 - - + +
1002I LEU* 3.8 14.4 - - + -
1007I LYS 2.9 14.7 + - - +
1008I GLN* 3.2 34.9 + - - +
1010I GLN* 1.3 77.5 - - - +
1012I GLU* 1.3 57.4 + - - +
1014I LEU* 3.4 5.1 + - + +
1015I ALA 2.9 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1012 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998I LEU* 4.2 11.2 - - + +
1008I GLN* 2.9 18.9 + - + +
1009I ASN* 3.7 9.6 - - - +
1010I GLN 3.3 0.2 - - - -
1011I LEU* 1.3 73.6 - - - +
1013I GLN* 1.3 60.4 + - - +
1015I ALA* 3.7 7.8 - - - +
1016I GLU* 2.9 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1013 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744I GLY* 5.1 14.0 - - - -
1009I ASN* 2.9 29.9 + - - +
1010I GLN* 3.3 16.2 - - + +
1012I GLU* 1.3 75.6 - - - +
1014I LEU* 1.3 61.5 + - + +
1016I GLU* 3.4 11.8 + - - +
1017I GLN* 2.9 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1014 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743I PRO 4.4 8.3 - - - +
744I GLY* 5.2 4.5 - - - -
745I GLU 5.5 0.4 - - - +
746I ALA* 4.4 8.3 - - + +
971I LEU* 3.4 49.8 - - + +
974I ARG* 3.7 35.4 - - + -
975I ILE* 3.7 18.8 - - + +
978I VAL* 6.4 0.7 - - + -
1010I GLN* 2.9 37.9 + - + +
1011I LEU* 3.9 4.7 - - + +
1013I GLN* 1.3 79.3 - - + +
1015I ALA* 1.3 56.0 + - - +
1017I GLN* 3.3 10.6 - - + +
1018I TYR* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1015 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971I LEU* 6.0 0.2 - - - -
996I ARG* 6.1 2.7 - - - +
998I LEU* 3.7 23.7 - - + +
1011I LEU 2.9 18.1 + - - +
1012I GLU* 3.7 14.6 - - - +
1013I GLN 3.2 0.2 - - - -
1014I LEU* 1.3 75.0 - - - +
1016I GLU* 1.3 60.9 + - + +
1018I TYR* 3.1 9.7 + - - +
1019I ASP* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1016 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012I GLU* 2.9 44.8 + - - +
1013I GLN* 3.9 12.2 + - - +
1015I ALA* 1.3 73.1 - - + +
1017I GLN* 1.3 59.9 + - - +
1019I ASP* 4.0 6.6 - - - +
1020I GLU* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1017 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744I GLY* 5.2 3.4 - - - -
745I GLU* 3.4 51.6 + - - +
746I ALA 5.6 0.4 - - - +
971I LEU* 4.5 9.6 - - + -
1013I GLN* 2.9 27.2 + - + +
1014I LEU* 3.3 15.9 - - + +
1016I GLU* 1.3 77.7 - - - +
1018I TYR* 1.3 56.0 + - - +
1020I GLU* 3.3 26.9 + - - +
1021I LEU* 2.9 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1018 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964I LEU* 5.6 5.6 - - + -
968I GLU* 3.2 44.4 + - + -
971I LEU* 4.5 19.0 - - + +
972I PHE* 4.7 7.4 - + - -
995I ASP* 5.4 15.4 - - + +
1014I LEU 2.8 13.9 + - - +
1015I ALA* 3.1 13.0 + - - +
1017I GLN* 1.3 76.6 - - - +
1019I ASP* 1.3 60.9 + - + +
1021I LEU* 3.2 16.2 + - + +
1022I LYS* 2.9 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1019 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015I ALA 3.0 14.9 + - - +
1016I GLU* 4.0 7.2 - - - +
1018I TYR* 1.3 77.1 - - + +
1020I GLU* 1.3 64.4 + - - +
1022I LYS* 3.2 13.6 + - - +
1023I HIS* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1020 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745I GLU* 5.2 5.7 - - - +
1016I GLU 2.9 17.8 + - - +
1017I GLN* 3.3 34.9 + - - +
1019I ASP* 1.3 77.3 - - - +
1021I LEU* 1.3 58.0 + - + +
1023I HIS* 3.4 4.9 + - - +
1024I GLU* 2.8 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1021 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964I LEU* 3.7 27.6 - - + +
967I LEU* 3.8 37.2 - - + -
968I GLU* 5.5 1.1 - - - +
971I LEU* 4.0 23.8 - - + -
1017I GLN* 2.9 26.5 + - + +
1018I TYR* 3.2 15.2 + - + +
1020I GLU* 1.3 75.2 - - + +
1022I LYS* 1.3 59.8 + - - +
1024I GLU* 4.0 19.9 - - + +
1025I PHE* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1022 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964I LEU* 5.0 12.6 - - + +
1018I TYR* 2.9 46.9 + - + +
1019I ASP* 3.2 19.5 + - - +
1021I LEU* 1.3 77.4 - - + +
1023I HIS* 1.3 63.4 + - - +
1025I PHE* 3.3 13.4 + - + +
1026I GLU* 3.0 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1023 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019I ASP* 3.0 16.6 + - - +
1020I GLU* 4.1 4.7 - - - +
1022I LYS* 1.3 75.7 - - - +
1024I GLU* 1.3 58.3 + - - +
1026I GLU* 3.3 12.2 + - + +
1027I LYS* 3.0 54.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1024 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020I GLU* 2.8 30.4 + - + +
1021I LEU* 4.0 22.1 - - + +
1023I HIS* 1.3 75.6 - - + +
1025I PHE* 1.3 58.6 + - - +
1027I LYS* 3.6 13.9 - - + -
1028I LYS* 2.8 64.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1025 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957I LYS* 5.0 7.0 - - + -
960I LEU* 3.8 43.7 - - + -
961I SER* 3.9 13.7 - - - -
964I LEU* 3.6 28.3 - - + -
1021I LEU 2.8 20.2 + - - +
1022I LYS* 3.3 13.0 + - - +
1024I GLU* 1.3 76.6 - - - +
1026I GLU* 1.3 71.1 + - - +
1028I LYS* 4.4 2.6 - - - +
1029I LEU* 3.0 59.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1026 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022I LYS* 3.0 31.4 + - + +
1023I HIS* 3.5 15.3 - - + +
1025I PHE* 1.3 87.3 - - + +
1027I LYS* 1.3 58.2 + - - +
1029I LEU* 3.9 4.6 - - - +
1030I GLU* 3.0 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1027 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023I HIS* 3.0 48.2 + - + +
1024I GLU* 3.4 17.3 - - + +
1026I GLU* 1.3 76.9 - - - +
1028I LYS* 1.3 67.0 + - + +
1030I GLU* 3.5 5.0 + - - +
1031I ALA* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1028 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960I LEU* 3.8 24.3 - - + +
1024I GLU* 2.8 50.1 + - + +
1027I LYS* 1.3 79.7 - - + +
1029I LEU* 1.3 61.6 + - - +
1031I ALA* 3.8 4.7 - - - +
1032I LYS* 2.9 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1029 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957I LYS* 3.7 42.0 - - + -
960I LEU* 3.6 11.2 - - + +
1025I PHE* 3.0 45.7 + - + +
1026I GLU* 3.9 4.0 - - - +
1028I LYS* 1.3 74.4 - - - +
1030I GLU* 1.3 62.6 + - + +
1032I LYS* 3.4 4.4 + - - +
1033I ARG* 2.9 70.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1030 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026I GLU 3.0 18.5 + - - +
1027I LYS* 3.9 5.4 - - - +
1029I LEU* 1.3 79.6 - - + +
1031I ALA* 1.3 60.5 + - - +
1033I ARG* 3.2 29.9 + - - +
1034I ARG* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1031 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027I LYS 2.9 19.1 + - - +
1028I LYS* 4.0 5.8 - - - +
1030I GLU* 1.3 75.8 - - - +
1032I LYS* 1.3 57.7 + - - +
1034I ARG* 3.2 23.1 + - - +
1035I LYS* 2.9 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1032 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I GLU* 5.5 15.4 + - - +
953I LEU* 5.3 0.7 - - + -
956I ALA* 3.7 35.7 - - + +
960I LEU* 5.0 14.6 - - + +
1028I LYS 2.9 19.7 + - - +
1029I LEU* 3.8 5.6 - - - +
1031I ALA* 1.3 73.0 - - - +
1033I ARG* 1.3 61.4 + - - +
1035I LYS* 3.3 19.7 + - + +
1036I ILE* 2.9 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1033 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953I LEU* 3.7 37.8 - - + +
957I LYS* 4.3 20.2 - - - +
1029I LEU* 2.9 43.3 + - + +
1030I GLU* 3.2 29.4 + - - +
1032I LYS* 1.3 77.3 - - - +
1034I ARG* 1.3 56.9 + - - +
1036I ILE* 4.5 0.4 - - - +
1037I THR* 2.5 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1034 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030I GLU* 3.0 14.4 + - - +
1031I ALA* 3.2 21.0 + - - +
1033I ARG* 1.3 77.7 - - - +
1035I LYS* 1.3 84.1 + - - +
1037I THR* 4.4 2.6 - - - -
1038I GLN* 3.2 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1035 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I VAL 3.3 25.0 + - - -
80I PHE* 4.9 15.7 - - + +
81I ASP* 5.3 6.9 + - - +
88I ARG* 4.9 18.6 + - - +
1031I ALA* 2.9 21.4 + - - +
1032I LYS* 3.3 26.3 + - + +
1034I ARG* 1.3 98.0 - - - +
1036I ILE* 1.3 62.4 + - + +
1038I GLN* 3.3 32.4 + - - +
1040I ASP* 5.1 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1036 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941I LYS* 4.5 1.7 + - - -
949I GLU* 3.8 38.6 - - + +
952I GLN* 3.7 42.2 - - + +
953I LEU* 3.9 18.4 - - + +
956I ALA* 3.8 18.4 - - + -
1032I LYS* 2.9 34.3 + - + +
1033I ARG* 4.2 3.1 - - - +
1035I LYS* 1.3 77.5 - - + +
1037I THR* 1.3 65.6 + - - +
1038I GLN 3.4 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1037 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941I LYS* 3.1 18.5 + - - -
949I GLU* 3.4 16.9 + - - +
953I LEU* 5.5 5.0 - - - +
1033I ARG* 2.5 29.0 + - - +
1034I ARG* 4.4 3.1 - - - -
1036I ILE* 1.3 78.8 - - - +
1038I GLN* 1.3 63.1 + - - +
1039I GLY 3.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1038 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I PHE* 5.0 14.6 - - - -
88I ARG* 5.5 2.0 - - - +
937I ASP* 5.1 6.5 - - - +
941I LYS* 4.5 3.9 + - - -
1034I ARG* 3.2 35.9 + - + +
1035I LYS* 3.3 30.3 + - - +
1036I ILE 3.5 7.8 - - - +
1037I THR* 1.3 81.5 - - - +
1039I GLY* 1.3 72.1 + - - +
1040I ASP* 4.1 14.5 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il