Contacts of the helix formed by residues 1101 - 1122 (chain C) in PDB entry 3DLS
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 ASP1101 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099C ARG 4.1 1.0 + - - -
1100C LEU* 1.3 74.3 - - - +
1102C GLU* 1.3 59.4 + - - +
1103C PRO* 3.3 14.6 - - + +
1104C LEU* 3.3 21.3 + - - +
1105C ALA* 3.0 31.1 + - - +
1260C TYR* 2.7 34.3 + - - -
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Residues in contact with GLU1102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101C ASP* 1.3 71.0 - - - +
1103C PRO* 1.4 70.0 - - + +
1105C ALA* 4.4 1.6 - - - -
1106C SER* 2.9 31.9 + - - -
1197C VAL* 6.2 0.7 - - + -
1219C LEU 4.8 0.3 - - - +
1220C VAL* 3.2 21.5 - - + +
1221C SER* 2.6 49.2 + - - -
1224C LEU* 3.7 10.8 - - + +
1250C TRP* 2.8 35.3 + - - +
1253C GLN* 4.1 5.2 - - - +
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Residues in contact with PRO1103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101C ASP* 3.3 19.3 - - + +
1102C GLU* 1.4 94.1 - - + +
1104C LEU* 1.3 55.4 + - - +
1106C SER* 2.6 23.5 + - - +
1107C TYR 2.9 8.8 + - - -
1253C GLN* 3.7 20.4 - - + +
1254C PRO 4.2 7.4 - - - +
1255C VAL* 3.5 23.5 - - + +
1256C ASN 5.8 0.2 - - - +
1260C TYR* 3.4 12.6 - - - +
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Residues in contact with LEU1104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099C ARG 5.3 0.2 - - - +
1100C LEU* 3.6 27.8 - - + -
1101C ASP* 3.3 17.1 + - - +
1102C GLU 3.3 0.4 - - - -
1103C PRO* 1.3 74.0 - - - +
1105C ALA* 1.3 66.6 + - - +
1106C SER 3.1 1.1 - - - -
1107C TYR* 3.0 17.4 + - + +
1108C ILE* 3.0 16.4 + - + +
1140C PHE* 3.8 38.4 - - + -
1255C VAL* 4.6 1.6 - - - -
1257C LEU* 4.3 11.0 - - + -
1260C TYR* 3.8 34.5 + - + -
1265C VAL* 3.8 24.7 - - + -
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Residues in contact with ALA1105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100C LEU* 4.2 19.5 - - + +
1101C ASP 3.0 21.0 + - - +
1102C GLU* 3.9 3.6 - - - +
1104C LEU* 1.3 76.1 - - - +
1106C SER* 1.3 56.9 + - - +
1108C ILE* 3.5 1.6 + - - -
1109C PHE* 3.1 23.6 + - - +
1196C LEU* 3.2 22.7 - - + +
1197C VAL* 3.8 30.1 - - + -
1250C TRP* 3.8 4.7 - - + -
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Residues in contact with SER1106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102C GLU 2.9 16.8 + - - -
1103C PRO 2.6 18.4 + - - -
1105C ALA* 1.3 74.6 - - - +
1107C TYR* 1.3 63.2 + - - +
1109C PHE* 4.2 0.4 - - - +
1110C ARG* 2.8 47.6 + - - +
1250C TRP* 3.4 42.5 - - - -
1251C VAL* 4.3 1.8 - - - +
1253C GLN* 3.4 12.7 - - - +
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Residues in contact with TYR1107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103C PRO 2.9 13.9 + - - +
1104C LEU* 3.0 14.8 + - + +
1106C SER* 1.3 77.0 + - - +
1108C ILE* 1.3 61.2 + - - +
1110C ARG* 3.4 32.9 - - - +
1111C GLN* 3.2 39.7 + - + +
1139C ASP 4.2 2.6 + - - -
1140C PHE* 3.4 26.2 - - + -
1141C THR* 3.6 14.7 + - - -
1255C VAL* 4.2 23.8 - - + -
1257C LEU* 3.6 42.4 - - + +
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Residues in contact with ILE1108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090C LEU* 4.1 20.2 - - + -
1093C PHE* 4.4 4.5 - - + -
1100C LEU* 4.3 31.9 - - + -
1104C LEU* 3.0 19.9 + - + +
1105C ALA 3.7 5.4 - - - +
1106C SER 3.3 0.2 - - - -
1107C TYR* 1.3 76.6 - - + +
1109C PHE* 1.3 61.3 + - - +
1111C GLN* 3.5 11.6 + - - +
1136C ILE* 3.9 18.2 - - + -
1140C PHE* 4.0 22.4 - - + +
1142C ILE* 3.0 49.0 - - + +
1196C LEU* 4.2 13.9 - - + -
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Residues in contact with PHE1109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1105C ALA 3.1 16.8 + - - +
1106C SER 3.5 3.1 + - - +
1107C TYR 3.4 0.4 - - - -
1108C ILE* 1.3 75.0 - - - +
1110C ARG* 1.3 61.3 + - - +
1112C LEU* 3.2 17.8 + - + +
1113C VAL* 3.0 44.8 + - + +
1189C LEU* 3.5 45.3 - - + -
1192C THR* 5.3 2.5 - - + -
1193C LEU* 3.7 43.5 - - + -
1196C LEU* 4.4 7.0 - - + -
1227C LEU* 4.6 0.7 - - + -
1231C LEU* 4.3 9.4 - - + -
1245C LEU* 4.0 17.3 - - + -
1250C TRP* 4.2 11.0 - + + -
1251C VAL* 4.2 14.1 - - + -
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Residues in contact with ARG1110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106C SER* 2.8 47.0 + - - +
1107C TYR* 3.4 25.0 - - + +
1109C PHE* 1.3 74.9 - - - +
1111C GLN* 1.3 61.7 + - + +
1113C VAL* 3.4 12.1 + - - +
1114C SER* 2.7 36.7 + - - +
1251C VAL* 3.2 37.7 + - + +
1252C THR* 3.8 8.3 + - - +
1253C GLN* 3.1 29.1 + - - +
1255C VAL* 3.8 20.8 - - - +
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Residues in contact with GLN1111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063C ASN* 3.0 40.5 + - - +
1107C TYR* 3.2 41.3 + - + +
1108C ILE* 3.5 7.7 + - - +
1109C PHE 3.2 0.4 - - - -
1110C ARG* 1.3 78.0 - - + +
1112C LEU* 1.3 64.8 + - - +
1114C SER* 3.5 6.1 + - - -
1115C ALA 3.2 16.3 + - - -
1140C PHE 3.0 25.1 + - - -
1141C THR* 3.3 12.5 + - - +
1142C ILE* 2.9 35.7 + - + +
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Residues in contact with LEU1112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063C ASN* 5.5 0.2 - - - -
1108C ILE 3.7 2.0 + - - +
1109C PHE* 3.2 20.3 + - + +
1111C GLN* 1.3 78.6 - - - +
1113C VAL* 1.3 59.8 + - - +
1115C ALA* 3.2 5.1 + - + +
1116C VAL* 3.0 45.1 + - + +
1129C ILE* 3.8 15.7 - - + -
1134C ILE* 3.8 30.5 - - + -
1142C ILE* 3.7 15.6 - - + +
1144C LEU* 4.1 22.7 - - + -
1189C LEU* 3.6 27.1 - - + -
1192C THR* 4.0 11.9 - - + -
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Residues in contact with VAL1113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109C PHE* 3.0 47.0 + - + +
1110C ARG* 3.6 12.3 - - - +
1111C GLN 3.3 0.2 - - - -
1112C LEU* 1.3 75.3 - - - +
1114C SER* 1.3 52.8 + - - +
1116C VAL* 3.7 5.1 - - - +
1117C GLY* 2.8 31.9 + - - -
1189C LEU* 5.6 2.9 - - + -
1242C LEU* 4.4 3.3 - - + +
1245C LEU* 3.8 24.9 - - + -
1246C VAL* 3.7 39.5 - - + +
1251C VAL* 4.5 8.5 - - + -
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Residues in contact with SER1114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061C HIS* 3.6 19.3 + - - -
1063C ASN* 4.2 4.2 + - - -
1110C ARG* 2.7 24.1 + - - +
1111C GLN* 3.6 10.0 - - - -
1112C LEU 3.3 0.2 - - - -
1113C VAL* 1.3 76.1 - - - +
1115C ALA* 1.3 56.8 + - - +
1117C GLY* 3.5 1.7 + - - -
1118C TYR* 2.9 29.5 + - - +
1246C VAL* 6.4 1.8 - - - -
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Residues in contact with ALA1115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061C HIS* 3.7 11.4 - - - -
1063C ASN* 3.8 24.7 - - + +
1064C ILE* 4.1 12.8 - - + +
1111C GLN 3.2 10.4 + - - +
1112C LEU* 3.2 11.7 + - - +
1114C SER* 1.3 78.2 - - - +
1116C VAL* 1.3 59.3 + - - +
1118C TYR* 3.6 3.1 + - - +
1119C LEU* 3.1 33.1 + - - +
1144C LEU* 4.5 13.2 - - + -
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Residues in contact with VAL1116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112C LEU* 3.0 37.6 + - + +
1113C VAL* 4.0 4.9 - - - +
1115C ALA* 1.3 79.2 - - - +
1117C GLY* 1.3 57.1 + - - +
1119C LEU* 3.5 8.1 + - + +
1120C ARG* 3.1 27.7 + - - +
1124C ILE 5.3 0.2 - - - +
1129C ILE* 3.8 20.6 - - + -
1144C LEU* 4.5 7.6 - - + -
1185C GLU* 3.4 38.3 - - + +
1189C LEU* 4.1 16.4 - - + -
1242C LEU* 4.1 9.8 - - + +
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Residues in contact with GLY1117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113C VAL 2.8 16.3 + - - -
1114C SER* 3.8 2.0 - - - -
1116C VAL* 1.3 75.3 - - - +
1118C TYR* 1.3 62.8 + - - +
1120C ARG* 3.6 3.1 + - - +
1121C LEU* 3.2 22.0 + - - +
1242C LEU* 3.6 22.3 - - - +
1246C VAL* 5.6 4.0 - - - -
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Residues in contact with TYR1118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058C ARG 4.4 1.4 + - - -
1059C VAL* 3.4 28.8 - - + -
1060C GLU* 3.0 37.3 + - - +
1061C HIS* 3.5 22.9 - + + +
1064C ILE* 3.6 21.8 - - + -
1114C SER 2.9 17.4 + - - +
1115C ALA 3.8 2.5 - - - +
1116C VAL 3.4 0.2 - - - -
1117C GLY* 1.3 73.5 - - - +
1119C LEU* 1.3 67.9 + - + +
1121C LEU* 3.3 21.3 - - + +
1122C LYS* 3.1 51.9 + - + +
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Residues in contact with LEU1119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059C VAL* 3.9 18.4 - - + -
1064C ILE* 3.8 20.9 - - + -
1115C ALA 3.1 23.2 + - - +
1116C VAL* 3.9 8.5 - - + +
1117C GLY 3.4 0.2 - - - -
1118C TYR* 1.3 75.7 - - + +
1120C ARG* 1.3 60.2 + - - +
1122C LYS* 2.9 16.3 + - - +
1124C ILE* 2.8 56.7 + - + +
1126C HIS* 4.3 13.0 - - + +
1144C LEU* 4.0 21.1 - - + -
1147C PHE* 3.9 25.1 - - + -
1185C GLU* 5.9 2.5 - - - +
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Residues in contact with ARG1120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116C VAL 3.1 16.6 + - - +
1117C GLY 3.8 5.4 - - - +
1118C TYR 3.4 0.2 - - - -
1119C LEU* 1.3 73.7 - - - +
1121C LEU* 1.3 57.7 + - - +
1123C ASP* 2.8 26.4 + - - +
1124C ILE 3.8 6.3 + - - +
1125C ILE* 4.1 5.9 - - - +
1153C LEU* 3.7 23.5 - - - +
1182C PRO* 3.6 33.6 - - - +
1185C GLU* 2.6 29.9 + - - -
1186C MET* 3.6 25.3 - - - -
1241C THR* 5.3 1.4 + - - -
1242C LEU* 3.8 32.8 - - + +
1243C GLU* 4.7 13.7 + - - +
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Residues in contact with LEU1121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1117C GLY 3.2 11.1 + - - +
1118C TYR* 3.3 23.6 - - + +
1120C ARG* 1.3 77.9 - - - +
1122C LYS* 1.3 69.3 + - + +
1123C ASP* 3.2 5.8 + - - +
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Residues in contact with LYS1122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058C ARG* 4.4 22.4 + - + +
1059C VAL* 4.9 7.2 - - + +
1118C TYR* 3.1 52.2 + - + +
1119C LEU* 2.9 11.8 + - - +
1121C LEU* 1.3 84.1 + - + +
1123C ASP* 1.3 69.8 + - - +
1124C ILE* 3.9 20.7 - - + +
1152C TYR* 4.6 1.9 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
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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