Contacts of the helix formed by residues 1181 - 1199 (chain A) 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 GLY1181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1125A ILE* 3.7 13.8 - - - +
1153A LEU* 4.2 6.5 - - - -
1159A PHE* 4.8 2.2 - - - -
1179A TYR* 3.5 21.1 - - - +
1180A ARG* 1.3 79.9 - - - +
1182A PRO* 1.4 65.8 - - - +
1183A GLU* 3.4 3.6 + - - -
1184A LEU* 3.4 7.3 + - - +
1185A GLU* 3.0 22.7 + - - +
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Residues in contact with PRO1182 (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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1120A ARG* 3.7 39.4 + - - +
1125A ILE* 3.7 2.9 - - + -
1153A LEU* 4.0 14.1 - - + -
1180A ARG* 3.2 41.3 - - + +
1181A GLY* 1.4 87.6 - - - +
1183A GLU* 1.3 69.5 + - + +
1185A GLU* 3.4 3.6 + - - +
1186A MET* 3.1 28.9 + - + +
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Residues in contact with GLU1183 (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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1172A GLU* 4.2 6.5 - - - +
1180A ARG* 3.5 45.7 + - - +
1181A GLY 4.2 1.9 + - - -
1182A PRO* 1.3 76.8 - - + +
1184A LEU* 1.3 58.3 + - - +
1186A MET* 3.3 10.0 + - - +
1187A TRP 3.1 17.7 + - - -
1236A PRO* 3.8 30.2 - - + +
1237A GLU* 5.8 0.2 - - - -
1239A ARG* 3.0 30.3 + - - +
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Residues in contact with LEU1184 (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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1127A ARG* 6.1 6.5 - - + +
1162A PHE* 3.7 31.9 - - + -
1168A TYR 4.8 1.6 - - - +
1169A CYS* 4.2 2.0 - - - -
1170A ALA* 3.4 44.2 - - + +
1172A GLU* 4.3 1.9 + - - +
1173A VAL* 3.8 15.3 - - + -
1179A TYR* 3.5 44.6 - - + +
1181A GLY 3.4 6.5 + - - +
1182A PRO 3.3 0.2 - - - -
1183A GLU* 1.3 77.4 - - - +
1185A GLU* 1.3 65.1 + - - +
1187A TRP* 3.3 3.1 + - - +
1188A SER* 3.1 24.2 + - - -
1239A ARG* 4.2 0.2 - - - +
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Residues in contact with GLU1185 (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 VAL* 3.1 30.2 - - + +
1119A LEU* 5.8 1.8 - - - +
1120A ARG* 2.7 33.0 + - - +
1124A ILE 4.8 2.9 - - - +
1125A ILE* 3.4 23.8 - - + +
1126A HIS* 3.7 11.1 + - - +
1127A ARG* 4.7 2.0 + - - +
1129A ILE* 3.7 21.7 - - + +
1181A GLY 3.0 13.6 + - - +
1182A PRO 3.4 8.5 - - - +
1184A LEU* 1.3 76.7 - - - +
1186A MET* 1.3 56.4 + - - +
1188A SER* 2.9 22.5 + - - -
1189A LEU* 3.1 19.8 + - + +
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Residues in contact with MET1186 (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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1120A ARG* 3.8 13.2 - - - +
1182A PRO* 3.1 20.6 + - + +
1183A GLU* 3.5 10.5 - - - +
1184A LEU 3.2 0.2 - - - -
1185A GLU* 1.3 72.4 - - - +
1187A TRP* 1.3 63.5 + - - +
1189A LEU* 3.5 13.1 + - + +
1190A GLY 3.3 15.1 + - - -
1231A LEU* 3.5 31.5 - - + +
1239A ARG* 4.3 5.8 - - - -
1240A THR 3.4 19.3 - - - +
1241A THR* 3.6 22.7 - - - +
1242A LEU* 3.7 27.1 - - + +
1245A LEU* 3.5 32.3 - - + -
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Residues in contact with TRP1187 (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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1167A GLU 5.1 0.8 + - - -
1168A TYR 3.2 20.9 + - - -
1169A CYS 3.3 10.9 + - - -
1170A ALA* 3.6 20.6 - - + -
1171A PRO* 3.5 20.6 - - + -
1183A GLU 3.1 11.3 + - - +
1184A LEU 3.3 7.4 + - - +
1186A MET* 1.3 75.1 - - - +
1188A SER* 1.3 56.8 + - - +
1190A GLY* 3.0 15.8 + - - -
1191A VAL* 3.1 24.3 + - + +
1203A PHE* 3.6 21.3 - + - -
1209A THR* 3.0 37.5 - - - -
1212A ALA* 3.9 11.2 - - + -
1231A LEU 3.6 9.2 - - - -
1232A LEU* 3.5 38.1 - - + +
1233A GLN 3.7 9.2 - - - -
1234A PRO 4.1 1.1 - - - -
1239A ARG* 3.6 25.9 - - - +
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Residues in contact with SER1188 (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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1129A ILE* 3.8 31.1 + - - +
1168A TYR* 3.5 29.3 - - - -
1184A LEU* 3.1 12.5 + - - -
1185A GLU* 2.9 18.9 + - - -
1187A TRP* 1.3 76.2 - - - +
1189A LEU* 1.3 53.8 + - - +
1191A VAL* 4.4 3.4 - - - -
1192A THR* 2.7 37.1 + - - -
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Residues in contact with LEU1189 (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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1109A PHE* 3.6 19.6 - - + -
1112A LEU* 3.6 38.1 - - + +
1113A VAL* 5.4 2.5 - - + -
1116A VAL* 4.1 30.5 - - + -
1129A ILE* 4.2 10.1 - - + -
1185A GLU* 3.1 19.3 + - + +
1186A MET* 3.6 22.0 - - + +
1187A TRP 3.2 0.4 - - - -
1188A SER* 1.3 77.4 - - - +
1190A GLY* 1.3 58.3 + - - +
1191A VAL 3.4 0.2 - - - -
1192A THR* 3.9 2.0 - - - -
1193A LEU* 2.9 30.3 + - - +
1231A LEU* 4.3 5.2 - - + -
1242A LEU* 4.9 1.1 - - + -
1245A LEU* 4.0 21.5 - - + -
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Residues in contact with GLY1190 (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 MET 3.3 4.8 + - - -
1187A TRP 3.0 8.9 + - - -
1189A LEU* 1.3 76.4 - - - +
1191A VAL* 1.3 58.7 + - - +
1193A LEU* 3.7 3.3 - - - +
1194A TYR* 2.9 30.1 + - - +
1228A VAL* 5.1 3.0 - - - +
1231A LEU* 3.8 26.6 - - - +
1232A LEU* 3.8 16.0 - - - +
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Residues in contact with VAL1191 (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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1167A GLU 3.8 20.2 - - - +
1168A TYR* 3.6 34.3 - - + -
1187A TRP* 3.1 38.3 + - + +
1188A SER* 3.9 1.8 - - - +
1189A LEU 3.4 0.2 - - - -
1190A GLY* 1.3 72.4 - - - +
1192A THR* 1.3 56.3 + - - +
1194A TYR* 3.4 6.3 + - - +
1195A THR* 2.7 40.5 + - - +
1201A ASN* 4.3 4.3 - - - +
1202A PRO* 3.9 24.0 - - + -
1203A PHE* 5.3 2.0 - - + -
1232A LEU* 3.9 8.1 - - + -
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Residues in contact with THR1192 (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 LEU* 5.3 6.1 - - + -
1109A PHE* 5.4 2.5 - - + -
1112A LEU* 4.0 15.0 - - + -
1129A ILE* 3.5 11.0 + - + +
1130A LYS* 3.7 8.2 - - - -
1131A ASP* 4.5 4.9 - - + +
1134A ILE* 3.9 27.8 - - + -
1168A TYR* 3.2 18.4 - - - -
1188A SER 2.7 22.1 + - - -
1189A LEU* 3.9 7.2 - - - -
1191A VAL* 1.3 74.0 - - - +
1193A LEU* 1.3 58.8 + - - +
1195A THR* 3.4 4.9 + - - -
1196A LEU* 3.0 29.5 + - + +
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Residues in contact with LEU1193 (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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1109A PHE* 3.8 26.9 - - + -
1189A LEU 2.9 18.7 + - - +
1190A GLY 3.7 3.6 - - - +
1192A THR* 1.3 76.9 - - - +
1194A TYR* 1.3 63.6 + - - +
1196A LEU* 3.2 7.6 + - + +
1197A VAL* 3.2 36.7 + - + +
1224A LEU* 4.2 1.6 - - + -
1227A LEU* 3.6 30.5 - - + -
1228A VAL* 3.7 22.7 - - + -
1231A LEU* 3.8 17.0 - - + -
1250A TRP* 3.7 33.4 - - + -
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Residues in contact with TYR1194 (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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1190A GLY 2.9 18.0 + - - +
1191A VAL 3.7 4.3 - - - +
1193A LEU* 1.3 78.4 - - - +
1195A THR* 1.3 55.2 + - - +
1197A VAL* 5.3 0.4 - - - -
1198A PHE* 2.9 66.7 + + + +
1200A GLU* 3.1 36.5 + - + -
1201A ASN 4.0 0.9 - - - -
1202A PRO* 3.5 45.0 + - + +
1214A ILE* 4.0 25.5 - - + +
1215A HIS 3.7 9.0 + - - -
1216A PRO* 3.4 22.6 - - + +
1217A PRO* 3.7 5.7 - - - +
1228A VAL* 4.7 7.2 - - + +
1232A LEU* 4.3 11.9 - - + -
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Residues in contact with THR1195 (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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1094A ILE* 3.8 20.8 - - + +
1131A ASP* 3.9 21.3 - - - +
1168A TYR* 3.9 7.6 + - - +
1191A VAL* 2.7 24.9 + - - +
1192A THR* 3.8 4.9 - - - -
1194A TYR* 1.3 72.5 - - - +
1196A LEU* 1.3 66.5 + - - +
1199A GLU* 3.0 22.3 + - - -
1200A GLU* 3.7 23.0 + - - +
1201A ASN* 3.4 26.3 + - - +
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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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1090A LEU* 4.4 20.9 - - + -
1093A PHE* 4.9 2.5 - - + -
1094A ILE* 3.8 16.5 - - + +
1098A PRO* 5.7 0.2 - - - +
1100A LEU* 3.9 37.4 - - + +
1105A ALA* 3.4 35.2 - - + +
1108A ILE* 4.0 23.3 - - + -
1109A PHE* 4.1 19.7 - - + +
1192A THR* 3.0 18.8 + - + +
1193A LEU* 3.2 7.4 + - + +
1195A THR* 1.3 79.2 - - - +
1197A VAL* 1.3 66.6 + - + +
1199A GLU* 4.0 9.2 - - - +
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Residues in contact with VAL1197 (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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1100A LEU* 5.5 3.6 - - - +
1102A GLU* 6.0 2.2 - - + -
1105A ALA* 4.1 24.2 - - + -
1193A LEU* 3.2 31.9 + - + +
1194A TYR* 4.5 0.9 - - - +
1196A LEU* 1.3 78.7 - - + +
1198A PHE* 1.3 95.2 + - + +
1199A GLU* 3.6 5.0 + - - +
1218A TYR* 3.3 20.9 - - + -
1220A VAL* 4.4 4.5 - - + -
1224A LEU* 3.7 26.5 - - + -
1228A VAL* 6.1 0.2 - - + -
1250A TRP* 4.4 1.8 - - + -
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Residues in contact with PHE1198 (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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1194A TYR* 2.9 53.8 + + + +
1197A VAL* 1.3 91.3 - - + +
1199A GLU* 1.3 70.1 + - - +
1200A GLU* 3.3 3.8 + - + +
1216A PRO* 3.4 18.2 - - + -
1217A PRO* 3.6 37.3 - - + +
1218A TYR* 3.4 44.0 + + + -
1220A VAL* 3.6 27.4 - - + -
1224A LEU* 4.8 2.5 - - + -
1225A MET* 3.6 25.1 - - + -
1228A VAL* 5.0 4.7 - - + -
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Residues in contact with GLU1199 (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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20A MG 2.3 30.0 - - - -
1094A ILE* 4.2 26.1 - - + +
1097A HIS* 4.2 16.1 + - + +
1098A PRO* 3.0 26.8 - - + +
1100A LEU* 5.4 2.4 + - - +
1195A THR* 3.0 16.4 + - - +
1196A LEU 4.0 13.9 - - - +
1197A VAL 4.1 2.5 - - - +
1198A PHE* 1.3 77.2 - - - +
1200A GLU* 1.3 59.0 - - - +
1218A TYR* 2.5 38.2 + - - +
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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