Contacts of the helix formed by residues 980 - 1003 (chain B) in PDB entry 4TU6
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 MET 980 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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979B SER* 1.3 71.9 - - - +
981B GLN* 1.3 63.7 + - - +
983B GLU* 3.3 8.4 + - - +
984B ASP* 3.1 30.5 + - - +
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Residues in contact with GLN 981 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979B SER* 3.5 13.2 - - - +
980B MET* 1.3 78.4 - - + +
982B GLU* 1.3 65.1 + - + +
984B ASP* 3.2 24.0 + - - +
985B THR* 3.4 15.4 + - - -
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Residues in contact with GLU 982 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979B SER* 3.1 32.0 + - - +
981B GLN* 1.3 82.1 - - + +
983B GLU* 1.3 62.9 + - - +
985B THR* 3.2 10.4 + - - -
986B PHE* 3.2 27.5 + - + -
1104B ILE* 3.9 32.0 - - + +
1107B SER* 4.8 2.8 + - - -
1108B ARG* 2.7 48.6 + - - +
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Residues in contact with GLU 983 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979B SER 3.1 13.2 + - - +
980B MET* 3.3 9.1 + - - +
982B GLU* 1.3 76.2 - - - +
984B ASP* 1.3 56.4 + - - +
986B PHE* 4.1 15.3 - - - +
987B ARG* 2.9 39.9 + - - +
990B ARG* 2.7 40.6 + - - -
1041B HIS* 4.1 10.0 + - - -
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Residues in contact with ASP 984 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980B MET* 3.1 18.9 + - - +
981B GLN* 3.2 18.8 + - - +
983B GLU* 1.3 76.1 - - - +
985B THR* 1.3 58.4 + - - +
987B ARG* 2.7 37.1 + - - +
988B GLU* 3.0 31.0 + - - +
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Residues in contact with THR 985 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981B GLN* 3.4 9.8 + - - -
982B GLU* 3.2 9.8 + - - -
984B ASP* 1.3 78.6 - - - +
986B PHE* 1.3 59.5 + - + +
988B GLU* 3.3 5.3 + - - -
989B LEU* 3.0 23.7 + - - +
1097B PHE* 3.5 23.1 - - + -
1100B LEU* 3.6 27.0 - - + +
1101B CYS* 3.6 26.7 - - - -
1104B ILE* 4.0 15.5 - - + +
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Residues in contact with PHE 986 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982B GLU 3.2 18.3 + - - -
983B GLU* 3.9 18.8 - - - +
985B THR* 1.3 80.6 - - + +
987B ARG* 1.3 57.0 + - - +
989B LEU* 3.4 7.0 + - + +
990B ARG* 2.9 45.1 + - - +
1043B TYR 5.5 1.2 - - - +
1044B LEU* 3.4 64.6 - - + -
1101B CYS* 4.3 15.5 - - + -
1104B ILE* 3.3 38.4 - - + -
1105B GLN* 4.9 1.8 - - - -
1108B ARG* 4.3 12.6 - - + -
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Residues in contact with ARG 987 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983B GLU* 2.9 30.4 + - - +
984B ASP* 2.7 40.3 + - - +
985B THR 3.2 0.2 - - - -
986B PHE* 1.3 73.0 - - - +
988B GLU* 1.3 66.0 + - - +
990B ARG* 3.2 16.6 + - - +
991B ILE* 3.0 36.5 + - + +
1201B SO4 3.3 28.4 + - - +
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Residues in contact with GLU 988 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984B ASP* 3.0 17.0 + - - +
985B THR* 3.5 6.6 + - - +
987B ARG* 1.3 72.9 - - - +
989B LEU* 1.3 66.2 + - - +
991B ILE* 3.3 12.5 + - - +
992B PHE* 3.0 23.6 + - + +
1097B PHE* 3.5 32.9 - - + -
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Residues in contact with LEU 989 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985B THR 3.0 13.5 + - - +
986B PHE* 3.5 11.0 - - + +
988B GLU* 1.3 76.7 - - - +
990B ARG* 1.3 63.6 + - - +
992B PHE* 3.1 10.6 + - + +
993B LEU* 2.9 41.0 + - + +
1043B TYR 3.7 9.4 - - - +
1044B LEU* 3.4 13.0 - - - +
1045B THR* 3.4 35.7 - - - +
1046B VAL* 3.7 27.1 - - + -
1093B LEU* 4.8 0.2 - - + -
1097B PHE* 3.8 20.6 - - + -
1101B CYS* 4.1 8.5 - - - -
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Residues in contact with ARG 990 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983B GLU* 2.7 30.3 + - - +
986B PHE* 2.9 24.5 + - - +
987B ARG* 3.2 20.7 + - - +
989B LEU* 1.3 78.1 - - - +
991B ILE* 1.3 61.0 + - - +
993B LEU* 3.4 4.8 + - + -
994B ARG* 3.1 35.7 + - - +
1038B ILE* 3.4 35.2 - - + +
1039B ASP* 5.0 0.7 - - - +
1041B HIS* 3.2 41.7 + - - +
1043B TYR 5.2 8.7 - - - +
1044B LEU* 6.1 1.8 - - - +
1201B SO4 2.5 46.9 + - - +
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Residues in contact with ILE 991 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987B ARG* 3.0 34.0 + - + +
988B GLU* 3.6 10.3 - - + +
989B LEU 3.3 0.2 - - - -
990B ARG* 1.3 72.2 - - - +
992B PHE* 1.3 70.9 + - - +
994B ARG* 3.5 19.6 + - - +
995B ASN* 3.4 19.7 + - + +
1201B SO4 5.5 2.0 - - - +
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Residues in contact with PHE 992 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988B GLU* 3.0 13.4 + - + +
989B LEU* 3.4 11.9 - - + +
991B ILE* 1.3 83.6 - - - +
993B LEU* 1.3 75.1 + - + +
995B ASN* 3.1 8.2 + - + +
996B VAL* 3.0 40.4 + - + +
999B ARG* 5.0 0.9 - - - -
1046B VAL* 5.3 0.2 - - + -
1088B ILE 4.7 1.8 - - - -
1089B ILE* 3.5 30.3 - - + -
1092B GLU* 3.6 43.1 - - + -
1093B LEU* 3.9 30.7 - - + -
1097B PHE* 6.0 1.6 - - + -
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Residues in contact with LEU 993 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989B LEU* 2.9 41.3 + - + +
990B ARG* 3.9 6.3 - - + +
991B ILE 3.3 0.2 - - - -
992B PHE* 1.3 94.1 - - + +
994B ARG* 1.3 55.2 + - - +
996B VAL* 3.4 4.4 + - + +
997B THR* 2.8 36.4 + - - -
1038B ILE* 3.8 15.5 - - + -
1043B TYR* 3.8 33.7 - - + +
1045B THR 4.9 0.4 - - - +
1046B VAL* 5.0 3.6 - - + -
1049B TYR* 3.6 42.8 - - + -
1089B ILE* 4.9 3.1 - - + -
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Residues in contact with ARG 994 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990B ARG* 3.1 31.5 + - - +
991B ILE* 3.7 28.5 - - - +
992B PHE 3.3 0.2 - - - -
993B LEU* 1.3 76.7 - - - +
995B ASN* 1.3 53.6 + - - +
997B THR* 3.5 1.7 + - - -
998B HIS* 2.8 34.8 + - - +
1035B ILE* 5.9 6.4 - - + +
1038B ILE* 3.9 20.3 - - + +
1039B ASP* 2.9 30.0 + - - +
1201B SO4 2.9 36.6 + - - -
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Residues in contact with ASN 995 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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991B ILE* 3.4 9.1 + - + +
992B PHE* 3.1 13.7 + - + +
994B ARG* 1.3 75.2 - - - +
996B VAL* 1.3 67.2 + - - +
998B HIS* 3.3 7.2 + - - +
999B ARG* 2.4 68.2 + - - +
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Residues in contact with VAL 996 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992B PHE* 3.0 52.6 + - + +
993B LEU* 3.7 9.0 - - + +
995B ASN* 1.3 77.4 + - - +
997B THR* 1.3 57.6 + - - +
999B ARG* 3.2 13.6 + - - +
1000B LEU* 3.1 33.1 + - + +
1049B TYR* 3.6 23.3 - - + +
1085B ALA* 5.1 4.5 - - - -
1088B ILE* 3.6 31.3 - - + +
1089B ILE* 4.3 5.4 - - + -
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Residues in contact with THR 997 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993B LEU 2.8 16.9 + - - -
994B ARG 3.9 2.9 - - - -
996B VAL* 1.3 72.8 - - - +
998B HIS* 1.3 61.8 + - - +
1000B LEU* 3.5 5.3 + - - +
1001B ALA* 2.8 27.8 + - - +
1031B LEU* 4.3 17.5 - - + +
1034B VAL* 4.2 15.5 - - + -
1035B ILE* 3.5 30.7 - - + -
1038B ILE* 3.6 7.6 - - - +
1049B TYR* 2.7 31.4 + - - +
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Residues in contact with HIS 998 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994B ARG 2.8 19.8 + - - +
995B ASN* 3.6 8.1 - - - +
996B VAL 3.3 0.2 - - - -
997B THR* 1.3 76.9 - - - +
999B ARG* 1.3 67.4 + - + +
1001B ALA* 3.2 7.6 + - - +
1002B ILE* 3.2 55.5 + - + +
1035B ILE* 5.2 5.3 - - - +
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Residues in contact with ARG 999 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992B PHE* 5.0 0.8 - - - -
995B ASN* 2.4 42.0 + - - +
996B VAL* 3.5 13.9 - - - +
997B THR 3.2 0.4 - - - -
998B HIS* 1.3 81.6 - - + +
1000B LEU* 1.3 66.3 + - - +
1002B ILE* 3.6 16.0 - - + +
1003B ASP* 3.5 20.3 + - - +
1088B ILE* 4.1 32.5 - - + +
1092B GLU* 2.7 42.8 + - - -
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Residues in contact with LEU1000 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996B VAL* 3.1 16.5 + - + +
997B THR* 3.7 7.9 - - - +
999B ARG* 1.3 79.2 - - - +
1001B ALA* 1.3 61.6 + - - +
1002B ILE 3.2 1.2 + - - -
1003B ASP* 3.3 9.1 + - - +
1006B PHE* 3.4 28.0 - - + +
1031B LEU* 4.4 9.6 - - + -
1049B TYR* 3.9 20.6 - - - +
1053B ILE* 4.3 9.9 - - + -
1081B LEU* 4.0 31.0 - - + -
1084B THR* 3.7 29.6 - - + -
1085B ALA* 4.1 23.3 - - + +
1088B ILE* 4.6 5.6 - - + -
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Residues in contact with ALA1001 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997B THR 2.8 21.4 + - - +
998B HIS* 3.2 10.0 + - - +
1000B LEU* 1.3 73.0 - - - +
1002B ILE* 1.3 61.5 + - + +
1003B ASP 4.8 2.2 - - - +
1006B PHE* 5.6 0.2 - - - -
1007B ARG* 5.4 0.9 - - - -
1010B THR* 3.5 32.2 - - + +
1031B LEU* 4.2 9.8 - - + +
1035B ILE* 4.5 16.4 - - + -
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Residues in contact with ILE1002 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998B HIS* 3.2 48.1 + - + +
999B ARG* 3.6 16.6 - - + +
1001B ALA* 1.3 78.8 - - + +
1003B ASP* 1.3 67.7 + - - +
1004B LYS* 3.3 4.2 + - - -
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Residues in contact with ASP1003 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999B ARG 3.5 12.1 + - - +
1000B LEU 3.3 4.8 + - - +
1001B ALA 4.8 1.0 - - - +
1002B ILE* 1.3 77.7 - - - +
1004B LYS* 1.3 71.0 + - - +
1005B ARG* 2.9 51.1 + - - +
1006B PHE* 2.9 41.9 + - + +
1007B ARG* 3.8 3.6 + - - +
1084B THR* 5.2 1.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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