Contacts of the helix formed by residues 942 - 972 (chain C) in PDB entry 3H2V
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 GLY 942 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941C SER* 1.3 74.8 + - - +
943C THR* 1.3 59.1 + - - +
944C LYS* 3.1 38.8 + - - +
946C ALA* 4.1 6.8 + - - +
117G ARG* 3.2 22.3 + - - -
122G GLU* 4.3 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 943 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936C LEU* 3.8 31.2 - - + +
939C GLY* 2.9 40.4 - - - +
941C SER 2.7 7.2 + - - +
942C GLY 1.3 82.8 - - - +
944C LYS* 1.3 54.1 + - - +
945C ARG 3.4 0.2 - - - -
946C ALA* 3.0 5.2 + - - -
947C LEU* 2.5 39.5 + - - +
1006C LEU* 2.9 32.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 944 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941C SER* 4.8 8.5 - - - +
942C GLY* 3.1 40.1 + - - +
943C THR* 1.3 80.3 + - - +
945C ARG* 1.3 83.4 + - + +
947C LEU* 3.5 2.1 - - - +
948C ILE* 3.1 29.7 + - + +
1003C ALA* 4.1 29.8 - - + +
1006C LEU* 4.7 6.3 - - + +
117G ARG* 3.0 32.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 945 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944C LYS* 1.3 92.2 - - + +
946C ALA* 1.3 64.0 + - - +
948C ILE* 3.5 6.0 + - - +
949C GLN* 3.0 20.3 + - - +
117G ARG* 2.8 61.6 - - - +
120G GLU* 2.9 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 946 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932C GLU* 4.9 0.4 - - - +
936C LEU* 3.7 25.4 - - + -
942C GLY 4.1 11.3 + - - +
943C THR 3.0 6.9 + - - +
945C ARG* 1.3 76.7 - - - +
947C LEU* 1.3 54.9 + - - +
949C GLN* 3.1 4.0 + - - +
950C CYS* 2.6 37.2 + - - +
120G GLU 3.3 16.6 + - - +
121G ARG* 4.3 20.5 + - + +
122G GLU 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 947 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933C MET* 3.3 52.2 - - + +
936C LEU* 3.6 25.3 - - + +
937C VAL* 4.9 9.4 - - + +
943C THR 2.5 21.3 + - - +
944C LYS* 3.5 5.8 - - - +
946C ALA* 1.3 72.0 - - - +
948C ILE* 1.3 63.0 + - - +
951C ALA* 3.0 19.9 + - - +
999C SER* 4.2 20.1 - - - +
1002C LYS* 4.0 26.9 - - + -
1003C ALA* 4.3 11.0 - - + +
1006C LEU* 4.6 12.6 - - + -
1023C LEU* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 948 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944C LYS* 3.1 26.0 + - + +
945C ARG* 3.7 6.5 - - - +
947C LEU* 1.3 76.9 - - - +
949C GLN* 1.3 70.1 + - - +
951C ALA* 3.0 7.6 + - - +
952C LYS* 2.9 46.1 + - + +
999C SER* 4.8 3.8 - - - +
1000C THR* 4.1 28.3 - - + +
1003C ALA* 3.4 25.8 - - + -
1004C THR* 6.1 0.2 - - + -
120G GLU* 5.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 949 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945C ARG 3.0 8.8 + - - +
946C ALA 3.6 2.7 - - - +
948C ILE* 1.3 78.8 - - - +
950C CYS* 1.3 58.4 + - - +
952C LYS* 3.1 34.4 + - - +
953C ASP* 2.8 39.7 + - - +
956C LYS* 5.6 0.2 + - - -
119G ARG* 3.2 12.3 - - + +
120G GLU* 2.9 48.0 + - + +
121G ARG* 3.4 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 950 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929C LEU* 3.3 30.5 - - - -
932C GLU* 3.9 25.6 - - - -
933C MET* 3.6 18.8 - - + -
936C LEU* 3.8 10.3 - - + -
946C ALA 2.6 20.6 + - - +
947C LEU 3.5 5.2 - - - +
949C GLN* 1.3 75.2 - - - +
951C ALA* 1.3 61.1 + - - +
953C ASP* 3.2 4.2 + - - +
954C ILE* 3.0 22.5 + - - +
121G ARG* 4.0 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 951 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933C MET* 3.5 12.8 - - + +
947C LEU 3.0 9.0 + - - +
948C ILE 3.0 8.9 + - - +
950C CYS* 1.3 73.6 - - - +
952C LYS* 1.3 66.0 + - - +
954C ILE* 3.1 9.8 + - - +
955C ALA* 3.0 23.2 + - - +
995C LEU* 4.3 9.6 - - + +
996C LYS* 4.1 17.8 - - + +
999C SER* 3.4 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 952 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948C ILE* 2.9 38.6 + - + +
949C GLN* 3.1 34.6 + - - +
951C ALA* 1.3 75.2 - - + +
953C ASP* 1.3 61.9 + - - +
955C ALA* 3.6 2.9 + - - +
956C LYS* 3.2 22.1 + - - +
996C LYS* 4.5 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 953 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929C LEU* 3.6 21.9 - - + +
949C GLN* 2.8 19.6 + - - +
950C CYS 3.3 9.6 - - - +
951C ALA 3.0 0.2 - - - -
952C LYS* 1.3 75.0 - - - +
954C ILE* 1.3 65.7 + - - +
956C LYS* 3.1 37.3 + - - +
957C ALA* 3.1 12.3 + - - +
69G ASP* 4.2 7.2 - - - +
119G ARG* 3.3 14.0 + - - -
121G ARG* 2.3 40.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 954 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926C MET* 4.0 9.3 - - + +
929C LEU* 3.8 34.1 - - + +
930C MET* 3.3 32.5 - - + -
933C MET* 4.1 14.6 - - - -
950C CYS* 3.0 26.4 + - - +
951C ALA* 3.1 8.5 + - - +
953C ASP* 1.3 77.1 - - - +
955C ALA* 1.3 53.0 + - + +
957C ALA* 3.2 6.8 + - - +
958C SER* 2.7 34.1 + - - +
992C SER* 5.2 1.1 - - - -
995C LEU* 3.9 9.9 - - + -
1030C LEU* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 955 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951C ALA 3.0 14.0 + - - +
952C LYS 3.8 5.4 - - - +
954C ILE* 1.3 74.0 - - + +
956C LYS* 1.3 57.1 - - - +
958C SER* 2.9 8.7 + - - -
959C ASP* 2.7 45.1 + - - +
992C SER* 4.2 17.9 + - - +
996C LYS* 4.1 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 956 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925C ARG* 5.6 0.4 - - - -
952C LYS 3.2 9.2 + - - +
953C ASP* 3.1 36.7 + - - +
955C ALA* 1.3 78.0 - - - +
957C ALA* 1.3 61.5 + - - +
959C ASP* 3.3 8.7 + - - +
960C GLU* 3.2 39.6 + - + +
69G ASP* 5.2 5.3 + - - -
119G ARG* 6.0 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 957 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922C ALA* 3.9 9.1 - - + +
925C ARG* 4.2 23.8 - - + +
926C MET* 3.4 31.0 - - + +
929C LEU* 4.9 4.9 - - + -
953C ASP 3.1 10.0 + - - +
954C ILE* 3.4 4.9 - - - +
955C ALA 3.1 0.6 - - - -
956C LYS* 1.3 79.1 - - - +
958C SER* 1.3 60.8 + - - +
960C GLU* 3.3 5.8 + - - +
961C VAL* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 958 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926C MET* 3.8 21.4 - - - +
954C ILE* 2.7 20.6 + - - +
955C ALA* 2.9 7.0 + - - -
957C ALA* 1.3 71.7 - - - +
959C ASP* 1.3 66.7 + - - +
960C GLU 3.0 1.8 - - - -
961C VAL* 3.0 4.9 + - - +
962C THR* 2.7 30.8 + - - -
988C ILE* 3.4 26.7 - - - -
989C PRO* 6.1 0.7 - - - -
992C SER* 3.8 15.7 - - - -
1030C LEU* 4.5 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 959 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955C ALA* 2.7 32.8 + - - +
956C LYS* 3.5 10.4 - - - +
957C ALA 3.3 0.2 - - - -
958C SER* 1.3 73.9 - - - +
960C GLU* 1.3 67.5 + - - +
962C THR* 3.9 6.0 - - - -
963C ARG* 3.1 27.7 + - - +
989C PRO* 5.0 14.2 - - - +
992C SER* 5.1 2.8 + - - -
996C LYS* 5.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 960 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922C ALA* 5.0 7.0 - - + -
925C ARG* 5.5 6.3 - - - +
956C LYS* 3.2 30.9 + - + +
957C ALA* 3.8 7.2 - - - +
958C SER 3.0 1.0 - - - -
959C ASP* 1.3 90.0 - - - +
961C VAL* 1.3 61.9 + - - +
963C ARG* 3.0 39.5 + - - +
964C LEU* 3.1 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 961 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919C ILE* 4.2 22.6 - - + +
922C ALA* 3.5 22.2 - - + -
923C ALA 4.5 0.4 - - - +
926C MET* 4.5 2.9 - - - -
957C ALA 3.2 16.7 + - - +
958C SER* 3.0 10.2 + - - +
960C GLU* 1.3 74.2 - - - +
962C THR* 1.3 62.0 + - - +
964C LEU* 3.9 1.1 - - - +
965C ALA* 2.9 31.7 + - - +
988C ILE* 4.4 10.5 - - + -
1034C VAL* 4.3 26.9 - - + -
1037C THR* 3.8 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 962 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958C SER 2.7 16.9 + - - -
959C ASP* 3.9 6.6 - - - -
961C VAL* 1.3 79.5 - - - +
963C ARG* 1.3 63.0 - - - +
965C ALA* 3.2 6.0 + - - +
966C LYS* 3.0 44.3 + - - +
985C CYS* 3.3 26.7 - - - +
986C GLU* 5.3 0.2 - - - +
988C ILE* 3.6 20.1 - - - +
989C PRO* 4.2 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 963 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918C ASP* 5.3 3.6 + - - -
959C ASP 3.1 17.0 + - - +
960C GLU* 3.0 32.9 + - - +
961C VAL 3.3 0.4 - - - -
962C THR* 1.3 79.9 - - - +
964C LEU* 1.3 97.1 + - - +
966C LYS* 3.7 7.6 + - - +
967C GLU* 3.5 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 964 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918C ASP* 3.5 41.1 - - + +
919C ILE* 3.9 16.2 - - + +
960C GLU* 3.1 25.9 + - + +
963C ARG* 1.3 111.8 - - - +
965C ALA* 1.3 67.4 + - - +
966C LYS 3.0 1.8 - - - -
967C GLU* 3.1 11.1 + - + +
968C VAL* 3.0 25.9 + - - +
1056C LEU* 5.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 965 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919C ILE* 4.1 9.1 - - + +
961C VAL 2.9 20.0 + - - +
962C THR 3.2 4.2 + - - +
964C LEU* 1.3 77.4 - - - +
966C LYS* 1.3 58.0 + - - +
968C VAL* 3.5 6.0 - - - +
969C ALA* 3.1 19.6 + - - +
981C LEU* 3.3 21.9 - - + +
985C CYS* 4.1 16.8 - - + -
1037C THR* 3.9 24.0 - - + -
1041C ALA* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 966 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962C THR* 3.0 31.0 + - + +
963C ARG* 3.8 8.3 - - - +
964C LEU 3.0 0.4 - - - -
965C ALA* 1.3 75.4 - - - +
967C GLU* 1.3 56.3 + - - +
968C VAL 3.1 1.3 - - - -
969C ALA* 3.1 6.0 + - - +
970C LYS* 2.7 34.5 + - - +
982C LEU* 3.8 14.1 - - + +
985C CYS* 3.2 25.1 - - - -
986C GLU* 3.6 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 967 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963C ARG* 3.5 12.4 + - - +
964C LEU* 3.1 14.9 + - + +
966C LYS* 1.3 78.1 - - - +
968C VAL* 1.3 61.9 + - - +
970C LYS* 2.8 37.5 + - - +
971C GLN* 3.0 46.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 968 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919C ILE* 4.9 0.2 - - + -
964C LEU 3.0 18.3 + - - +
965C ALA* 3.5 12.8 - - - +
967C GLU* 1.3 79.1 - - + +
969C ALA* 1.3 57.6 + - - +
971C GLN* 3.3 7.6 + - - +
972C CYS* 3.1 22.9 + - - +
981C LEU* 3.6 16.8 - - + -
1041C ALA* 3.9 18.8 - - + +
1044C ALA* 3.8 22.5 - - + +
1045C SER* 4.5 6.5 - - - +
1055C THR* 6.3 2.2 - - - +
1056C LEU* 4.2 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 969 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965C ALA 3.1 14.6 + - - +
966C LYS 3.1 4.9 + - - +
968C VAL* 1.3 76.9 - - - +
970C LYS* 1.3 61.4 + - - +
971C GLN 3.0 6.0 + - - -
972C CYS* 3.2 13.2 + - - +
978C ARG* 3.1 32.2 + - + +
981C LEU* 3.7 15.9 - - + -
982C LEU* 3.9 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 970 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966C LYS 2.7 16.2 + - - +
967C GLU* 2.8 34.4 + - - +
968C VAL 3.3 0.2 - - - -
969C ALA* 1.3 76.2 - - - +
971C GLN* 1.3 68.7 + - - +
972C CYS 4.5 2.0 - - - +
978C ARG* 5.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 971 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967C GLU* 3.0 39.0 + - - +
968C VAL* 3.8 6.5 - - - +
969C ALA 3.0 0.6 - - - -
970C LYS* 1.3 92.0 + - - +
972C CYS* 1.3 67.0 + - - +
973C THR* 3.6 13.3 + - - +
1044C ALA 5.6 0.2 - - - -
1055C THR* 5.5 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 972 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968C VAL 3.1 13.3 + - - +
969C ALA* 3.2 17.1 + - - +
970C LYS 4.5 2.4 - - - +
971C GLN* 1.3 80.9 - - - +
973C THR* 1.3 62.0 + - - +
974C ASP* 3.4 31.4 - - - -
977C ILE* 4.4 1.6 - - - -
978C ARG* 2.9 36.0 + - + -
1044C ALA* 4.0 32.5 + - + +
----------------------------------------------------------
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