Contacts of the helix formed by residues 1005 - 1038 (chain C) in PDB entry 7KHC
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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003C THR* 2.4 40.0 + - - +
1004C ASP* 1.3 81.1 - - - +
1006C GLU* 1.3 78.6 + - - +
1007C LYS* 3.1 27.7 + - - +
1008C GLN* 3.7 3.2 - - - +
1009C ASN* 3.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1006 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005C GLU* 1.3 80.7 - - - +
1007C LYS* 1.3 88.9 + - + +
1009C ASN* 3.1 11.1 + - - +
1010C GLN* 2.8 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1007 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
978C VAL* 4.7 10.2 - - + +
981C ALA* 4.8 16.4 - - + +
982C GLY* 4.8 14.7 - - - +
1002C LEU* 4.4 21.5 - - + -
1003C THR* 4.8 3.6 - - - +
1005C GLU* 3.1 21.9 + - + +
1006C GLU* 1.3 100.7 - - + +
1008C GLN* 1.3 63.0 + - - +
1010C GLN* 3.1 13.4 + - - +
1011C LEU* 3.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1008 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998C LEU 5.6 0.8 + - - -
1000C LEU 4.2 4.6 + - - -
1001C GLY* 4.0 10.5 - - - -
1002C LEU* 3.0 47.2 + - - +
1003C THR 3.8 13.1 + - - +
1004C ASP* 4.0 12.8 - - - +
1005C GLU 3.3 12.7 + - - +
1007C LYS* 1.3 77.9 - - - +
1009C ASN* 1.3 58.2 + - - +
1011C LEU* 3.3 20.6 + - - +
1012C GLU* 2.9 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1009 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005C GLU 3.1 13.2 + - - +
1006C GLU* 3.1 13.7 + - - +
1008C GLN* 1.3 78.3 - - - +
1010C GLN* 1.3 56.2 + - + +
1012C GLU* 3.1 12.5 + - - +
1013C GLN* 2.8 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1010 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743C PRO* 5.9 6.8 - - - +
974C ARG* 6.3 1.6 - - - -
978C VAL* 4.4 17.7 - - + +
1006C GLU* 2.8 27.6 + - - +
1007C LYS* 3.1 10.9 + - - +
1009C ASN* 1.3 74.5 - - + +
1011C LEU* 1.3 65.6 + - - +
1013C GLN* 3.1 12.1 + - + +
1014C LEU* 2.9 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1011 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975C ILE* 3.9 28.0 - - + +
978C VAL* 3.5 33.8 - - + +
979C LEU* 4.9 11.7 - - + +
997C TRP 5.5 4.9 - - - +
998C LEU* 5.5 6.5 - - + +
1000C LEU 5.0 7.9 - - - +
1001C GLY 5.3 0.2 - - - -
1002C LEU* 4.3 17.5 - - + +
1007C LYS 3.0 14.3 + - - +
1008C GLN* 3.3 38.3 + - - +
1010C GLN* 1.3 75.0 - - - +
1012C GLU* 1.3 57.5 + - - +
1014C LEU* 3.2 5.2 + - - +
1015C ALA* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1012 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008C GLN* 2.9 18.8 + - - +
1009C ASN* 3.1 19.3 + - - +
1011C LEU* 1.3 75.5 - - - +
1013C GLN* 1.3 63.7 + - - +
1015C ALA* 3.2 9.9 + - - +
1016C GLU* 2.9 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1013 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744C GLY* 5.0 16.4 - - - -
745C GLU 6.1 0.2 - - - +
1009C ASN* 2.8 28.9 + - - +
1010C GLN* 3.2 17.5 - - + +
1012C GLU* 1.3 76.3 - - - +
1014C LEU* 1.3 63.5 + - + +
1016C GLU* 3.2 13.8 + - - +
1017C GLN* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1014 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743C PRO 5.2 2.9 - - - +
745C GLU* 5.1 10.3 - - - +
971C LEU* 3.8 20.3 - - + +
974C ARG* 3.9 37.5 - - + +
975C ILE* 3.2 48.5 - - + +
978C VAL* 5.1 5.4 - - + -
1010C GLN* 2.9 33.7 + - + +
1011C LEU* 3.2 6.9 + - - +
1013C GLN* 1.3 83.0 - - + +
1015C ALA* 1.3 58.0 + - - +
1017C GLN* 3.3 8.1 + - + +
1018C TYR* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1015 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998C LEU* 3.5 31.6 - - + +
1011C LEU 2.9 12.7 + - - +
1012C GLU* 3.2 15.7 + - - +
1014C LEU* 1.3 76.8 - - - +
1016C GLU* 1.3 63.3 + - + +
1018C TYR* 3.1 4.0 + - - +
1019C ASP* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1016 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012C GLU* 2.9 38.6 + - + +
1013C GLN* 3.2 12.2 + - - +
1015C ALA* 1.3 77.8 - - + +
1017C GLN* 1.3 58.0 + - - +
1019C ASP* 3.4 7.3 + - - +
1020C GLU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1017 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745C GLU* 2.8 59.7 - - + +
971C LEU* 4.1 3.6 - - + -
1013C GLN 2.9 16.6 + - - +
1014C LEU* 3.6 8.5 - - + +
1015C ALA 3.2 0.2 - - - -
1016C GLU* 1.3 75.0 - - - +
1018C TYR* 1.3 60.2 + - - +
1020C GLU* 4.2 13.5 - - - +
1021C LEU* 2.9 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1018 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968C GLU* 2.9 34.5 - - + +
971C LEU* 4.0 13.6 - - + +
972C PHE* 3.4 40.5 - + - -
995C ASP* 4.7 13.9 + - - -
998C LEU* 4.4 8.3 - - + -
1014C LEU 2.9 14.0 + - - +
1015C ALA* 3.1 12.3 + - - +
1017C GLN* 1.3 77.0 - - - +
1019C ASP* 1.3 66.3 + - + +
1021C LEU* 3.4 2.5 + - - +
1022C LYS* 3.0 59.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1019 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015C ALA 3.0 12.0 + - - +
1016C GLU* 3.7 10.1 - - - +
1018C TYR* 1.3 84.2 - - + +
1020C GLU* 1.3 62.3 + - - +
1022C LYS* 3.1 8.3 + - - +
1023C HIS* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1020 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016C GLU 2.9 18.7 + - - +
1017C GLN* 3.9 14.6 - - - +
1019C ASP* 1.3 75.8 - - - +
1021C LEU* 1.3 64.7 + - + +
1023C HIS* 3.3 9.9 + - - +
1024C GLU* 2.9 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1021 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745C GLU* 3.6 24.5 - - + +
964C LEU* 4.2 9.3 - - + +
967C LEU* 4.9 28.5 - - + +
968C GLU* 4.0 15.5 - - - +
971C LEU* 4.0 12.3 - - + -
1017C GLN* 2.9 34.2 + - - +
1018C TYR 3.8 3.1 - - - +
1020C GLU* 1.3 76.3 - - + +
1022C LYS* 1.3 64.1 + - - +
1024C GLU* 3.1 20.0 - - + +
1025C PHE* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1022 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964C LEU* 3.8 24.9 - - + +
968C GLU* 3.7 17.8 - - + +
1018C TYR* 3.0 51.8 + - + +
1019C ASP* 3.1 11.6 + - - +
1021C LEU* 1.3 75.7 - - - +
1023C HIS* 1.3 63.4 + - - +
1025C PHE* 3.1 11.4 + - - +
1026C GLU* 3.0 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1023 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019C ASP* 3.0 19.8 + - - +
1020C GLU* 4.0 10.5 - - - +
1022C LYS* 1.3 77.7 - - - +
1024C GLU* 1.3 64.1 + - - +
1026C GLU* 3.1 12.0 + - + +
1027C LYS* 3.0 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1024 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963C GLU* 4.1 12.6 - - - +
964C LEU* 5.3 1.0 - - - +
1020C GLU* 2.9 26.0 + - + +
1021C LEU* 3.1 34.8 - - + +
1023C HIS* 1.3 73.6 - - - +
1025C PHE* 1.3 87.3 + - - +
1027C LYS* 3.3 13.9 - - + +
1028C LYS* 2.9 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1025 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957C LYS 5.3 0.2 - - - -
960C LEU* 3.2 43.6 - - + +
961C SER* 3.6 14.6 - - - -
963C GLU* 4.0 6.1 - - - -
964C LEU* 3.7 38.8 - - + -
1021C LEU 2.9 15.2 + - - +
1022C LYS* 3.2 12.6 - - - +
1024C GLU* 1.3 86.0 - - - +
1026C GLU* 1.3 89.5 + - - +
1028C LYS* 4.1 2.1 - - - +
1029C LEU* 2.9 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1026 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022C LYS* 3.0 20.2 + - - +
1023C HIS* 3.1 15.2 + - + +
1025C PHE* 1.3 104.7 - - - +
1027C LYS* 1.3 62.8 + - - +
1029C LEU* 3.5 7.1 - - - +
1030C GLU* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1027 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023C HIS* 3.0 29.0 + - + +
1024C GLU* 3.3 18.6 - - + +
1026C GLU* 1.3 78.9 - - - +
1028C LYS* 1.3 74.6 + - + +
1030C GLU* 3.3 6.9 + - - +
1031C ALA* 2.9 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1028 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960C LEU* 5.1 18.6 - - + +
963C GLU* 5.9 2.6 + - - -
1024C GLU* 2.9 38.7 + - + +
1025C PHE* 4.1 2.0 - - - +
1027C LYS* 1.3 92.6 - - + +
1029C LEU* 1.3 57.4 + - - +
1031C ALA* 3.3 6.2 + - + +
1032C LYS* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1029 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953C LEU* 6.0 0.7 - - + -
956C ALA 6.1 0.4 - - - -
957C LYS* 4.4 26.5 - - + -
960C LEU* 4.3 19.6 - - + +
1025C PHE* 2.9 51.8 + - + +
1026C GLU* 3.5 10.1 - - - +
1028C LYS* 1.3 73.8 - - - +
1030C GLU* 1.3 68.2 + - - +
1032C LYS* 3.0 9.3 + - + +
1033C ARG* 3.0 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1030 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026C GLU 3.0 15.0 + - - +
1027C LYS* 3.7 9.6 - - - +
1029C LEU* 1.3 76.3 - - - +
1031C ALA* 1.3 63.0 + - - +
1033C ARG* 2.9 53.0 + - - +
1034C ARG* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1031 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027C LYS* 2.9 24.3 + - - +
1028C LYS* 3.5 10.3 - - + +
1030C GLU* 1.3 77.4 - - - +
1032C LYS* 1.3 57.4 + - - +
1034C ARG* 3.1 20.1 + - - +
1035C LYS* 2.9 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1032 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ASP* 5.1 5.1 + - - -
84C GLU* 3.9 23.6 - - - +
956C ALA* 4.0 17.2 - - + +
960C LEU* 4.3 21.1 - - + +
1028C LYS 2.8 14.9 + - - +
1029C LEU* 3.0 11.9 + - + +
1031C ALA* 1.3 75.6 - - - +
1033C ARG* 1.3 59.0 + - - +
1035C LYS* 3.3 16.5 + - + +
1036C ILE* 2.9 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1033 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953C LEU* 3.4 45.0 - - + +
957C LYS* 5.2 11.5 - - - +
1029C LEU* 3.0 38.5 + - + +
1030C GLU* 2.9 50.8 + - - +
1032C LYS* 1.3 77.1 - - - +
1034C ARG* 1.3 57.3 + - - +
1036C ILE* 3.3 10.7 + - - +
1037C THR* 3.0 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1034 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030C GLU* 3.0 36.2 + - - +
1031C ALA* 3.1 26.9 + - - +
1033C ARG* 1.3 80.5 - - + +
1035C LYS* 1.3 60.6 - - - +
1037C THR* 3.2 24.9 - - + +
1038C GLN* 3.2 16.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1035 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C VAL 4.4 15.5 - - - +
80C PHE* 4.3 19.1 - - + -
81C ASP 5.9 0.2 - - - +
84C GLU* 4.1 25.1 - - - +
88C ARG* 4.3 8.7 + - - -
1031C ALA* 2.9 47.7 + - - +
1032C LYS* 3.3 28.2 + - + +
1034C ARG* 1.3 78.7 - - - +
1036C ILE* 1.3 63.6 + - + +
1038C GLN* 3.4 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1036 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLU* 5.9 1.1 - - - +
88C ARG* 5.1 5.7 + - - +
949C GLU* 4.4 20.4 - - + +
952C GLN* 3.8 34.5 - - + +
953C LEU* 4.4 22.0 - - + +
956C ALA* 4.1 15.5 - - + -
1032C LYS* 2.9 47.5 + - + +
1033C ARG* 3.7 9.0 - - - +
1034C ARG 3.3 0.2 - - - -
1035C LYS* 1.3 80.2 - - + +
1037C THR* 1.3 65.6 + - - +
1038C GLN 3.9 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1037 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941C LYS* 4.8 7.4 + - - -
949C GLU* 4.0 22.8 + - - +
1033C ARG 3.0 14.8 + - - +
1034C ARG* 3.2 21.5 - - + +
1036C ILE* 1.3 78.9 - - - +
1038C GLN* 1.3 73.9 + - + +
1039C GLY* 3.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1038 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C PHE* 3.1 40.8 - - - -
88C ARG* 3.9 18.6 + - - +
1034C ARG* 3.2 15.4 + - + +
1035C LYS* 3.4 26.4 + - - +
1036C ILE 3.4 4.4 - - - +
1037C THR* 1.3 86.4 - - + +
1039C GLY* 1.3 69.3 + - - +
1040C ASP 3.6 1.4 + - - -
----------------------------------------------------------
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