Contacts of the helix formed by residues 1181 - 1203 (chain A) in PDB entry 2X4Y
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 LYS1181 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180A ARG* 1.3 120.4 - - + +
1182A SER* 1.3 66.0 + - - +
1183A ASN* 3.3 17.9 - - - +
1184A ILE* 3.3 13.3 + - + +
1185A ARG* 3.0 27.9 + - - +
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Residues in contact with SER1182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181A LYS* 1.3 73.4 - - - +
1183A ASN* 1.3 56.1 + - - +
1185A ARG* 3.3 28.3 + - - +
1186A LYS* 2.8 30.7 + - - +
1185E ARG* 5.3 6.9 + - - -
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Residues in contact with ASN1183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181A LYS* 3.5 16.1 - - - +
1182A SER* 1.3 75.3 - - - +
1184A ILE* 1.3 86.6 + - - +
1186A LYS* 3.3 10.9 + - - +
1187A SER* 3.0 27.4 + - - -
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Residues in contact with ILE1184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096A TYR* 6.3 1.1 - - + -
1097A PRO* 3.7 35.7 - - + -
1099A TYR* 6.5 0.2 - - + -
1179A GLY* 4.3 6.3 - - - -
1180A ARG* 3.6 48.9 - - + +
1181A LYS* 3.3 18.1 + - + +
1183A ASN* 1.3 86.2 + - - +
1185A ARG* 1.3 66.7 + - - +
1187A SER* 3.2 9.1 + - - -
1188A VAL* 3.0 22.6 + - + +
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Residues in contact with ARG1185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176A MET 4.0 14.5 - - - +
1177A LEU* 4.0 21.2 - - - +
1179A GLY* 3.0 43.4 + - - +
1180A ARG 3.3 20.2 + - - -
1181A LYS* 3.0 9.1 + - - +
1182A SER* 3.3 35.5 + - - +
1184A ILE* 1.3 75.3 - - - +
1186A LYS* 1.3 58.7 + - - +
1188A VAL* 3.2 8.6 + - - +
1189A GLN* 2.9 40.8 + - - +
1182K SER* 5.0 9.1 + - - -
1186K LYS* 3.8 25.3 - - - +
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Residues in contact with LYS1186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182A SER* 2.8 18.0 + - - +
1183A ASN* 3.7 9.0 - - - +
1184A ILE 3.2 0.2 - - - -
1185A ARG* 1.3 77.0 - - - +
1187A SER* 1.3 52.5 + - - +
1189A GLN* 3.3 12.2 + - - +
1190A ILE* 2.8 50.2 + - - +
1177E LEU* 2.7 52.4 + - + +
1178E GLU* 3.5 8.3 + - - +
1179E GLY 3.1 17.0 + - - -
1180E ARG* 4.3 10.3 - - - +
1185E ARG* 4.0 19.9 - - - +
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Residues in contact with SER1187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1099A TYR* 3.1 10.8 + - - -
1183A ASN 3.0 13.2 + - - -
1184A ILE* 3.4 13.0 - - - -
1186A LYS* 1.3 71.9 - - - +
1188A VAL* 1.3 61.8 + - - +
1190A ILE* 3.5 9.5 + - - +
1191A ALA* 3.0 28.4 + - - +
1194A ARG* 5.7 0.5 + - - -
2207A SO4 2.4 42.5 + - - -
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Residues in contact with VAL1188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090A TRP* 3.6 33.7 - - + -
1097A PRO* 4.2 15.5 - - + -
1098A SER 3.9 10.8 - - - +
1099A TYR* 3.8 28.7 - - + -
1100A PRO* 3.9 2.7 - - + +
1175A LYS 4.6 2.5 - - - +
1176A MET* 4.0 16.6 - - + +
1179A GLY 6.0 1.6 - - - +
1184A ILE* 3.0 18.6 + - + +
1185A ARG* 3.2 10.7 + - - +
1187A SER* 1.3 76.0 - - - +
1189A GLN* 1.3 60.6 + - - +
1191A ALA* 3.2 5.3 + - - +
1192A TYR* 2.8 27.0 + - - +
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Residues in contact with GLN1189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176A MET* 4.1 36.0 + - + +
1185A ARG* 2.9 28.2 + - - +
1186A LYS* 3.3 19.8 + - - +
1188A VAL* 1.3 76.3 - - - +
1190A ILE* 1.3 62.3 + - - +
1192A TYR* 3.1 1.9 + - - +
1193A HIS* 3.0 34.9 + - + +
1177E LEU* 3.8 26.9 - - + +
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Residues in contact with ILE1190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186A LYS* 2.8 35.0 + - - +
1187A SER* 3.8 7.9 - - - +
1189A GLN* 1.3 71.6 - - - +
1191A ALA* 1.3 57.1 + - - +
1193A HIS* 3.2 7.1 + - - +
1194A ARG* 2.8 64.4 + - - +
1174E GLU* 4.1 20.5 - - + +
1177E LEU* 3.8 42.4 - - + +
1178E GLU* 5.4 2.5 - - - -
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Residues in contact with ALA1191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099A TYR* 3.5 31.4 - - + +
1100A PRO* 3.8 10.0 - - + +
1148A PHE* 3.6 25.1 - - + +
1187A SER 3.0 18.7 + - - +
1188A VAL 3.4 4.9 - - - +
1190A ILE* 1.3 77.4 - - - +
1192A TYR* 1.3 57.6 + - - +
1194A ARG* 3.2 5.1 + - - +
1195A ALA* 2.8 28.9 + - - +
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Residues in contact with TYR1192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090A TRP* 3.7 17.7 - + - -
1100A PRO* 3.6 10.9 - - + +
1165A LEU* 3.8 22.4 - - + -
1166A GLY* 4.4 2.3 - - - -
1169A GLN* 4.8 11.1 + - - +
1172A ASP* 2.7 46.8 + - + +
1176A MET* 3.7 28.5 - - + -
1188A VAL 2.8 13.9 + - - +
1189A GLN 3.1 7.8 + - - +
1191A ALA* 1.3 78.8 - - - +
1193A HIS* 1.3 80.1 + + - +
1195A ALA* 3.2 5.1 + - - +
1196A LEU* 3.0 53.9 + - + +
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Residues in contact with HIS1193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176A MET* 5.2 3.4 - - + -
1189A GLN* 3.0 28.9 + - - +
1190A ILE* 3.8 4.7 - - - +
1192A TYR* 1.3 100.1 - + - +
1194A ARG* 1.3 56.7 + - - +
1196A LEU 3.4 0.4 + - - +
1197A GLN* 3.0 35.7 + - - +
1170E ASP* 2.8 46.9 + - + +
1173E LYS* 3.5 40.5 - - + +
1174E GLU* 4.2 8.3 - - + +
1177E LEU* 4.2 14.9 - - + +
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Residues in contact with ARG1194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099A TYR* 5.0 0.4 + - - -
1148A PHE* 2.9 40.8 + - + -
1149A ASP* 3.5 3.0 + - - +
1150A ASN* 2.5 42.6 + - - +
1152A ARG* 6.5 0.4 - - - +
1187A SER 5.7 0.2 + - - -
1190A ILE* 2.8 38.4 + - - +
1191A ALA* 3.5 7.9 - - - +
1193A HIS* 1.3 74.8 - - - +
1195A ALA* 1.3 64.9 + - - +
1197A GLN* 3.2 10.8 + - - +
1198A HIS* 3.0 21.1 + - - +
2207A SO4 4.0 3.6 + - - -
1174E GLU* 3.3 32.0 + - - +
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Residues in contact with ALA1195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088A LEU* 3.5 13.0 - - + +
1100A PRO* 4.2 6.3 - - + -
1101A ALA 5.5 0.4 - - - +
1148A PHE* 3.7 32.2 - - + -
1165A LEU* 4.1 22.2 - - + -
1191A ALA 2.8 16.7 + - - +
1192A TYR 3.2 10.1 + - - +
1194A ARG* 1.3 73.3 - - - +
1196A LEU* 1.3 58.9 + - - +
1198A HIS* 3.2 4.5 + - - +
1199A ARG 3.0 22.5 + - - -
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Residues in contact with LEU1196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088A LEU* 4.3 8.3 - - + -
1165A LEU* 3.9 24.9 - - + -
1166A GLY* 4.3 13.2 - - - -
1192A TYR* 3.0 46.4 + - + +
1193A HIS 4.0 0.2 - - - +
1194A ARG 3.3 0.2 - - - -
1195A ALA* 1.3 72.8 - - - +
1197A GLN* 1.3 60.5 - - - +
1199A ARG* 3.3 16.3 + - - +
1200A SER* 2.9 27.5 + - - -
1170E ASP* 3.4 37.8 - - - +
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Residues in contact with GLN1197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193A HIS 3.0 28.2 + - - +
1194A ARG* 3.2 10.1 + - - +
1196A LEU* 1.3 74.8 - - - +
1198A HIS* 1.3 64.4 + - - +
1200A SER* 3.3 7.4 + - - -
1201A LYS* 2.9 38.2 + - + +
1168E ASN* 3.8 20.9 - - - +
1170E ASP* 3.6 6.5 + - + -
1171E LEU* 3.5 40.9 - - - +
1174E GLU* 2.8 27.3 + - - +
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Residues in contact with HIS1198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086A LEU* 5.3 1.0 + - - +
1088A LEU* 4.2 18.4 - - + -
1102A LEU* 3.9 30.6 - - + +
1115A HIS* 5.1 4.0 - - - -
1118A VAL* 4.0 27.2 - - + +
1119A PRO 5.8 0.2 - - - -
1120A ILE* 4.0 11.7 - - + +
1148A PHE* 3.8 19.6 - + + -
1152A ARG* 5.4 2.6 + - - -
1194A ARG 3.0 12.2 + - - +
1195A ALA 3.2 8.0 + - - +
1197A GLN* 1.3 75.1 - - - +
1199A ARG* 1.3 68.3 + - - +
1201A LYS* 3.1 10.6 + - - +
1202A VAL* 2.9 38.5 + - + +
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Residues in contact with ARG1199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088A LEU* 3.6 28.7 + - + +
1165A LEU 2.9 24.9 + - - -
1166A GLY* 2.8 33.1 + - - -
1167A VAL* 4.7 5.5 - - - +
1195A ALA 3.0 13.5 + - - +
1196A LEU* 3.5 19.0 - - - +
1198A HIS* 1.3 83.6 - - - +
1200A SER* 1.3 57.9 + - - +
1202A VAL* 3.2 6.1 + - - +
1203A GLN* 2.9 62.8 + - + +
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Residues in contact with SER1200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196A LEU 2.9 16.7 + - - -
1197A GLN* 3.6 6.1 - - - -
1198A HIS 3.3 0.2 - - - -
1199A ARG* 1.3 76.2 - - - +
1201A LYS* 1.3 60.6 + - - +
1203A GLN* 3.2 11.3 + - - +
1204A GLY 3.1 5.0 + - - -
1205A GLU* 2.9 64.4 + - - +
1168E ASN* 3.6 18.5 + - - -
1170E ASP* 6.0 0.9 - - - -
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Residues in contact with LYS1201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116A HIS 4.8 2.9 - - - +
1118A VAL* 3.9 25.5 - - + +
1197A GLN* 2.9 28.8 + - - +
1198A HIS* 3.1 11.9 + - - +
1200A SER* 1.3 74.8 - - - +
1202A VAL* 1.3 65.2 + - - +
1204A GLY* 3.1 14.6 + - - -
1205A GLU* 4.4 9.5 - - - +
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Residues in contact with VAL1202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115A HIS* 3.5 38.8 - - + +
1116A HIS* 3.4 36.1 - - + +
1118A VAL* 3.8 24.5 - - + -
1198A HIS* 2.9 38.2 + - + +
1199A ARG* 3.7 9.6 - - - +
1201A LYS* 1.3 74.8 - - - +
1203A GLN* 1.4 63.4 + - + +
1204A GLY* 3.3 4.2 + - - -
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Residues in contact with GLN1203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199A ARG* 2.9 46.1 + - + +
1200A SER* 3.2 9.1 + - - +
1202A VAL* 1.4 79.7 - - + +
1204A GLY* 1.3 59.9 + - - +
1205A GLU* 3.5 8.7 + - + +
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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
------------------------------------------------------------
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