Contacts of the helix formed by residues 1181 - 1199 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125F ILE* 3.8 15.1 - - - +
1153F LEU* 4.2 8.3 - - - -
1159F PHE* 4.7 1.3 - - - -
1179F TYR* 3.5 20.2 - - - +
1180F ARG* 1.3 79.6 - - - +
1182F PRO* 1.4 64.9 - - - +
1183F GLU* 3.5 3.4 + - - -
1184F LEU* 3.4 7.6 + - - +
1185F GLU* 3.2 21.1 + - - +
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Residues in contact with PRO1182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120F ARG* 3.5 39.8 + - - +
1125F ILE* 4.1 0.9 - - + -
1153F LEU* 4.2 19.5 - - + -
1180F ARG* 3.4 38.6 - - + +
1181F GLY* 1.4 88.7 - - - +
1183F GLU* 1.3 68.2 + - + +
1185F GLU* 3.4 3.1 + - - +
1186F MET* 3.1 30.3 + - + +
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Residues in contact with GLU1183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1172F GLU* 4.4 2.0 - - - +
1179F TYR* 6.6 0.4 - - + -
1180F ARG* 3.0 39.5 + - - +
1181F GLY 3.5 1.1 + - - -
1182F PRO* 1.3 81.1 - - + +
1184F LEU* 1.3 66.5 + - - +
1186F MET* 3.3 6.1 + - - -
1187F TRP 3.3 12.5 + - - -
1236F PRO* 3.7 33.6 - - + +
1237F GLU* 5.9 1.0 - - - -
1239F ARG* 2.8 34.4 + - + +
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Residues in contact with LEU1184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127F ARG* 6.0 5.8 - - + +
1162F PHE* 4.1 21.1 - - + -
1168F TYR 4.3 3.4 - - - +
1169F CYS* 4.1 9.4 - - - -
1170F ALA* 3.4 40.8 - - + +
1172F GLU* 4.6 1.7 + - - +
1173F VAL* 4.3 9.6 - - + -
1179F TYR* 3.6 53.9 - - + +
1181F GLY 3.4 8.4 + - - +
1183F GLU* 1.3 78.3 - - - +
1185F GLU* 1.3 56.7 + - - +
1187F TRP* 3.6 2.1 + - - +
1188F SER* 3.2 25.2 + - - -
1239F ARG* 4.1 0.2 - - - +
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Residues in contact with GLU1185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116F VAL* 3.3 24.4 - - - +
1119F LEU* 6.0 1.2 - - - +
1120F ARG* 2.7 28.8 + - - +
1124F ILE 5.2 1.7 - - - +
1125F ILE* 3.4 22.0 - - + +
1126F HIS* 3.9 15.1 + - - +
1127F ARG* 4.7 2.7 + - - +
1129F ILE* 3.4 26.8 - - + +
1181F GLY 3.2 13.6 + - - +
1182F PRO 3.6 8.1 - - - +
1183F GLU 3.3 0.4 - - - -
1184F LEU* 1.3 75.0 - - - +
1186F MET* 1.3 59.5 + - - +
1188F SER* 2.9 20.0 + - - +
1189F LEU* 3.0 22.5 + - + +
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Residues in contact with MET1186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120F ARG* 4.2 12.3 - - - +
1182F PRO* 3.1 20.2 + - + +
1183F GLU* 3.3 7.2 + - - +
1185F GLU* 1.3 73.2 - - - +
1187F TRP* 1.3 61.3 + - - +
1189F LEU* 3.3 13.1 + - + +
1190F GLY 3.0 22.2 + - - -
1231F LEU* 3.3 20.3 - - + +
1239F ARG* 4.2 5.8 - - - -
1240F THR 3.4 22.9 - - - +
1241F THR* 3.6 9.9 - - - +
1242F LEU* 3.5 43.5 - - + +
1245F LEU* 3.5 29.4 - - + -
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Residues in contact with TRP1187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167F GLU 4.9 1.6 + - - -
1168F TYR 3.3 22.0 + - - -
1169F CYS 3.3 14.6 + - - -
1170F ALA* 3.5 12.6 - - + -
1171F PRO* 3.6 23.1 - - + -
1183F GLU 3.3 10.7 + - - +
1184F LEU 3.6 8.1 - - - +
1186F MET* 1.3 79.2 - - - +
1188F SER* 1.3 55.4 + - - +
1190F GLY* 3.2 2.1 + - - -
1191F VAL* 3.1 36.6 + - + +
1203F PHE* 3.7 28.3 - + - -
1209F THR* 3.6 36.5 - - + +
1212F ALA* 4.3 0.2 - - + -
1231F LEU 3.5 9.9 - - - -
1232F LEU* 3.3 49.0 - - + +
1233F GLN 3.8 8.1 - - - -
1234F PRO 4.0 0.7 - - - -
1239F ARG* 3.8 18.7 - - - +
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Residues in contact with SER1188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127F ARG 5.9 2.0 - - - -
1129F ILE* 4.0 30.3 + - - +
1168F TYR* 3.6 29.9 - - - -
1184F LEU* 3.2 12.3 + - - -
1185F GLU* 2.9 21.3 + - - -
1186F MET 3.3 0.2 - - - -
1187F TRP* 1.3 77.6 - - - +
1189F LEU* 1.3 51.9 + - - +
1191F VAL* 4.5 1.1 - - - -
1192F THR* 2.5 37.2 + - - -
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Residues in contact with LEU1189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109F PHE* 3.6 20.8 - - + -
1112F LEU* 3.7 36.6 - - + +
1113F VAL* 5.1 1.8 - - + -
1116F VAL* 4.1 23.8 - - + -
1129F ILE* 4.3 11.2 - - + -
1185F GLU* 3.0 28.5 + - + +
1186F MET* 3.6 34.1 - - + +
1187F TRP 3.2 0.4 - - - -
1188F SER* 1.3 76.7 - - - +
1190F GLY* 1.3 57.2 + - - +
1192F THR* 3.8 3.1 - - - -
1193F LEU* 3.0 29.8 + - - +
1231F LEU* 4.6 2.7 - - + -
1242F LEU* 4.8 0.9 - - + -
1245F LEU* 4.2 10.8 - - + -
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Residues in contact with GLY1190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186F MET 3.0 10.1 + - - -
1187F TRP 3.2 4.2 + - - -
1189F LEU* 1.3 75.7 - - - +
1191F VAL* 1.3 58.4 + - - +
1193F LEU* 3.8 4.1 + - - +
1194F TYR* 3.0 28.9 + - - +
1228F VAL* 4.8 3.8 - - - +
1231F LEU* 3.6 29.1 - - - +
1232F LEU* 3.8 14.5 - - - +
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Residues in contact with VAL1191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167F GLU 3.8 10.3 - - - +
1168F TYR* 3.4 30.7 - - + -
1187F TRP* 3.1 41.1 + - + +
1188F SER 3.9 0.4 - - - +
1190F GLY* 1.3 72.7 - - - +
1192F THR* 1.3 54.4 + - - +
1194F TYR* 3.2 6.3 + - - +
1195F THR* 2.8 39.5 + - - +
1201F ASN* 3.5 26.2 - - - +
1202F PRO* 3.9 13.7 - - + -
1203F PHE* 5.6 0.7 - - + -
1232F LEU* 3.7 9.6 - - + -
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Residues in contact with THR1192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090F LEU* 5.1 6.7 - - + +
1109F PHE* 5.7 0.7 - - + -
1112F LEU* 3.8 26.2 - - + -
1129F ILE* 3.3 20.5 + - + +
1130F LYS* 4.4 1.1 - - - -
1131F ASP* 4.3 15.7 - - + +
1134F ILE* 4.1 15.3 - - + -
1168F TYR* 3.8 8.7 - - - -
1188F SER 2.5 25.0 + - - -
1189F LEU* 3.8 7.9 - - - -
1191F VAL* 1.3 76.4 - - - +
1193F LEU* 1.3 56.9 + - - +
1195F THR* 3.4 5.2 + - - -
1196F LEU* 3.0 27.9 + - + +
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Residues in contact with LEU1193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109F PHE* 3.8 32.9 - - + -
1189F LEU 3.0 18.4 + - - +
1190F GLY 3.9 2.9 - - - +
1192F THR* 1.3 74.3 - - - +
1194F TYR* 1.3 64.1 + - - +
1196F LEU* 3.3 7.1 + - + +
1197F VAL* 3.2 33.5 + - + +
1224F LEU* 4.2 3.4 - - + -
1227F LEU* 3.6 35.4 - - + -
1228F VAL* 3.8 20.9 - - + -
1231F LEU* 4.2 6.5 - - + -
1250F TRP* 3.6 32.1 - - + -
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Residues in contact with TYR1194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190F GLY 3.0 21.1 + - - +
1191F VAL* 3.2 5.6 + - - +
1193F LEU* 1.3 76.5 - - - +
1195F THR* 1.3 56.9 + - - +
1197F VAL* 4.7 0.7 - - - -
1198F PHE* 2.9 75.8 + + + +
1200F GLU* 3.3 22.0 - - + -
1201F ASN 3.9 2.6 + - - -
1202F PRO* 3.5 38.7 + - + +
1214F ILE* 3.9 25.8 - - + -
1215F HIS 3.7 10.0 + - - -
1216F PRO* 3.4 25.9 - - + +
1217F PRO* 4.1 3.8 - - + +
1228F VAL* 4.4 11.4 - - + +
1232F LEU* 4.1 9.9 - - + -
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Residues in contact with THR1195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094F ILE* 3.4 13.1 - - + +
1131F ASP* 3.3 29.4 - - + +
1168F TYR* 4.1 12.2 + - - +
1191F VAL* 2.8 27.3 + - - +
1192F THR* 3.7 5.2 - - - -
1194F TYR* 1.3 73.4 - - - +
1196F LEU* 1.3 62.3 + - - +
1199F GLU* 2.9 28.9 + - - -
1200F GLU* 4.0 22.4 + - - +
1201F ASN* 4.3 8.7 + - - -
1202F PRO* 4.4 0.2 - - - +
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Residues in contact with LEU1196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090F LEU* 3.9 30.7 - - + -
1093F PHE* 4.3 13.2 - - + -
1094F ILE* 3.6 19.4 - - + +
1098F PRO* 6.0 0.2 - - - +
1100F LEU* 3.8 25.7 - - + +
1105F ALA* 3.6 28.7 - - + +
1108F ILE* 3.9 22.4 - - + -
1109F PHE* 4.5 11.2 - - + +
1192F THR* 3.0 17.5 + - + +
1193F LEU* 3.7 8.5 - - + +
1194F TYR 3.3 0.2 - - - -
1195F THR* 1.3 79.1 - - - +
1197F VAL* 1.3 65.2 + - + +
1199F GLU* 4.1 5.5 - - - +
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Residues in contact with VAL1197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100F LEU* 4.9 6.1 - - - +
1102F GLU* 6.3 1.3 - - + -
1105F ALA* 4.1 22.2 - - + -
1193F LEU* 3.2 33.8 + - + +
1194F TYR* 4.7 0.4 - - - -
1196F LEU* 1.3 79.4 - - + +
1198F PHE* 1.3 100.2 + - + +
1199F GLU* 3.6 7.2 - - - +
1218F TYR* 2.7 30.6 + - - +
1224F LEU* 4.1 25.4 - - + -
1228F VAL* 5.9 0.7 - - + -
1250F TRP* 4.5 0.7 - - + -
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Residues in contact with PHE1198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1194F TYR* 2.9 60.8 + + + +
1197F VAL* 1.3 95.0 - - + +
1199F GLU* 1.3 71.1 + - - +
1200F GLU* 3.2 2.0 + - - +
1216F PRO* 3.6 17.7 - - + -
1217F PRO* 3.6 37.5 - - + +
1218F TYR* 3.4 39.7 - + - -
1220F VAL* 3.7 34.3 - - + -
1224F LEU* 5.1 0.4 - - + -
1225F MET* 4.0 7.6 - - - -
1228F VAL* 5.1 7.6 - - + -
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Residues in contact with GLU1199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094F ILE* 3.7 32.7 - - + +
1097F HIS* 2.9 30.0 + - + +
1098F PRO* 3.2 33.6 - - - +
1100F LEU* 5.8 1.4 - - - +
1195F THR* 2.9 23.4 + - - +
1196F LEU 4.1 11.0 - - - +
1197F VAL 4.2 4.9 - - - +
1198F PHE* 1.3 79.8 - - - +
1200F GLU* 1.3 59.1 + - - +
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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
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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