Contacts of the helix formed by residues 1190 - 1207 (chain F) in PDB entry 3F5P
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 THR1190 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1132F VAL* 3.2 16.7 - - - +
1164F ASP 3.4 22.9 - - - +
1165F PTR 3.6 10.3 - - + -
1182F GLU* 4.6 6.1 + - - +
1188F VAL* 4.4 10.2 - - + +
1189F PHE* 1.3 79.3 - - - +
1191F THR* 1.3 64.0 + - - +
1192F TYR* 2.9 39.9 - - + +
1193F SER* 2.8 25.6 + - - -
1194F ASP 3.2 2.9 + - - -
1253F PRO* 5.1 1.2 - - - +
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Residues in contact with THR1191 (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 ASN* 2.9 43.8 - - + +
1130F LYS* 6.5 0.2 - - + -
1132F VAL* 3.5 5.1 - - + +
1160F ILE* 3.9 24.9 - - + +
1164F ASP* 5.1 3.6 + - + +
1190F THR* 1.3 75.1 - - - +
1192F TYR* 1.3 77.6 + - - +
1194F ASP* 3.3 6.7 + - - +
1195F VAL* 3.2 26.2 + - - +
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Residues in contact with TYR1192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1190F THR* 2.9 25.1 - - + +
1191F THR* 1.3 87.2 - - - +
1193F SER* 1.3 64.4 + - - +
1195F VAL* 3.4 6.3 + - + +
1196F TRP 3.3 11.6 + - - -
1253F PRO* 3.7 44.2 - - + +
1254F LYS* 4.5 26.6 - - + +
1256F ARG* 3.0 29.1 + - + +
1257F PRO 5.6 2.9 - - - -
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Residues in contact with SER1193 (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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1134F ARG* 5.5 0.2 - - - -
1180F SER* 3.6 21.0 + - - -
1182F GLU* 3.9 9.4 - - - -
1183F SER* 3.7 12.1 - - - -
1188F VAL 4.8 0.9 - - - -
1189F PHE* 3.8 14.2 - - - +
1190F THR* 2.8 34.4 + - - -
1192F TYR* 1.3 77.5 - - - +
1194F ASP* 1.3 69.2 + - - +
1196F TRP* 2.8 15.9 + - - +
1197F SER* 3.0 16.0 + - - -
1256F ARG* 4.0 1.3 - - - +
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Residues in contact with ASP1194 (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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1123F MET* 3.2 28.3 - - + +
1127F ASN* 3.8 7.3 + - - +
1132F VAL* 3.4 9.0 - - - +
1133F HIS* 2.7 25.4 + - - +
1134F ARG* 3.0 26.6 + - - -
1136F LEU* 4.2 4.4 + - - +
1190F THR 3.2 9.1 + - - +
1191F THR* 3.5 11.4 - - - +
1192F TYR 3.3 0.2 - - - -
1193F SER* 1.3 86.6 + - - +
1195F VAL* 1.3 57.6 + - - +
1197F SER* 3.4 10.2 + - - -
1198F PHE* 2.9 27.2 + - - +
1259F PHE* 3.6 7.3 - - + -
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Residues in contact with VAL1195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191F THR* 3.2 15.2 + - - +
1192F TYR* 3.7 11.2 - - + +
1193F SER 3.1 0.8 - - - -
1194F ASP* 1.3 72.5 - - - +
1196F TRP* 1.3 68.0 + - - +
1198F PHE* 3.0 6.3 + - - +
1199F GLY 3.0 17.2 + - - -
1248F CYS* 3.6 33.9 - - + +
1256F ARG* 4.2 8.1 - - + -
1257F PRO* 3.4 29.4 - - + +
1258F SER* 4.6 1.6 - - - -
1259F PHE* 3.6 33.2 - - + +
1262F ILE* 4.3 5.8 - - + -
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Residues in contact with TRP1196 (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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1177F ARG 5.1 1.0 + - - -
1178F TRP 3.4 18.0 + - - -
1179F MET 3.4 11.5 + - - -
1180F SER* 3.5 24.9 - - - -
1181F PRO* 3.6 27.8 - - + -
1192F TYR 3.3 6.8 + - - +
1193F SER 2.8 10.9 + - - +
1195F VAL* 1.3 77.9 - - - +
1197F SER* 1.3 68.9 + - - +
1199F GLY* 2.7 14.6 + - - -
1200F VAL* 3.2 17.4 + - + +
1213F TYR* 4.1 16.0 + - - -
1225F VAL* 3.8 22.0 - - + -
1229F GLY 4.6 3.1 - - - -
1230F LEU* 4.3 11.4 - - + -
1248F CYS 3.4 14.0 + - - +
1249F TRP* 3.4 58.0 + + + -
1250F GLN 4.6 0.2 - - - -
1251F TYR* 5.3 1.6 - + - -
1256F ARG* 4.0 12.6 - - - +
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Residues in contact with SER1197 (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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1134F ARG 5.2 5.5 + - - -
1136F LEU* 3.5 34.2 + - - +
1178F TRP* 3.1 23.3 + - - +
1179F MET* 5.2 0.5 - - - -
1180F SER 5.5 0.2 + - - -
1193F SER* 3.0 9.5 + - - -
1194F ASP* 3.6 12.8 + - - -
1196F TRP* 1.3 77.0 - - - +
1198F PHE* 1.3 64.5 + - - +
1200F VAL* 2.8 19.4 + - - +
1201F VAL* 3.0 16.2 + - - +
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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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1116F ALA* 3.6 30.3 - - + -
1119F ILE* 3.9 24.2 - - + -
1120F ALA* 3.8 15.7 - - + -
1136F LEU* 3.6 12.0 - - + +
1194F ASP 2.9 14.6 + - - +
1195F VAL 3.0 10.3 + - - +
1197F SER* 1.3 75.3 - - - +
1199F GLY* 1.3 58.6 + - - +
1201F VAL* 3.4 5.3 + - + +
1202F LEU* 3.2 52.1 + - + +
1244F LEU* 4.8 1.8 - - + -
1248F CYS* 3.6 18.8 - - - -
1259F PHE* 3.6 20.6 - + + -
1262F ILE* 3.7 30.5 - - + -
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Residues in contact with GLY1199 (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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1195F VAL 3.0 5.3 + - - -
1196F TRP 2.7 16.6 + - - -
1198F PHE* 1.3 70.7 - - - +
1200F VAL* 1.3 62.3 + - - -
1202F LEU* 3.2 11.2 + - - +
1203F TRP 3.1 17.0 + - - -
1245F MET* 3.8 4.6 - - - +
1248F CYS* 3.8 18.4 - - - -
1249F TRP* 3.4 23.7 - - - -
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Residues in contact with VAL1200 (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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1177F ARG 4.3 9.9 - - - +
1178F TRP* 3.6 29.6 - - + +
1196F TRP* 3.2 30.0 + - + +
1197F SER* 2.8 9.6 + - - +
1199F GLY* 1.3 77.2 - - - +
1201F VAL* 1.3 50.4 + - - +
1203F TRP* 3.1 6.5 + - + +
1204F GLU* 2.7 33.2 + - + +
1212F PRO* 3.8 27.1 - - + -
1213F TYR* 5.0 1.8 - - - +
1231F LEU* 4.3 10.1 - - + -
1249F TRP* 3.8 19.3 - - + +
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Residues in contact with VAL1201 (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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1087F LEU* 4.7 5.2 - - + -
1119F ILE* 4.0 30.7 - - + -
1136F LEU* 3.8 19.5 - - + +
1137F ALA* 4.1 10.1 - - - -
1138F ALA* 4.0 10.8 - - - +
1141F CYS* 5.1 1.6 - - - -
1178F TRP* 5.1 0.2 - - + -
1197F SER 3.0 19.0 + - - +
1198F PHE* 3.7 16.2 - - + +
1200F VAL* 1.3 74.3 - - + +
1202F LEU* 1.3 58.0 + - + +
1204F GLU* 3.3 20.8 - - - +
1205F ILE* 2.9 37.0 + - + +
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Residues in contact with LEU1202 (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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1112F MET* 5.5 0.7 - - + +
1116F ALA* 3.5 32.5 - - + -
1119F ILE* 6.3 0.2 - - + -
1198F PHE* 3.2 42.6 + - + +
1199F GLY* 3.2 10.8 - - - +
1200F VAL 3.1 0.2 - - - -
1201F VAL* 1.3 75.2 - - + +
1203F TRP* 1.3 60.9 + - - +
1205F ILE* 2.8 31.1 + - + +
1206F ALA* 2.9 13.5 + - - +
1241F LEU* 4.2 16.7 - - + +
1244F LEU* 3.8 25.8 - - + -
1245F MET* 3.6 27.4 - - + +
1248F CYS* 5.1 0.2 - - - -
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Residues in contact with TRP1203 (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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1199F GLY 3.1 8.3 + - - +
1200F VAL* 3.1 11.9 + - - +
1202F LEU* 1.3 78.1 - - - +
1204F GLU* 1.3 69.0 + - - +
1206F ALA* 2.9 11.5 + - - -
1207F THR* 3.0 35.8 + - + +
1210F GLU* 3.5 39.9 - - + -
1211F GLN 3.7 15.0 - - - -
1212F PRO* 3.7 21.3 - - + -
1213F TYR 4.7 0.7 - - - -
1214F GLN* 5.8 1.3 - - + -
1231F LEU* 3.6 37.7 - - + +
1232F ASP 3.1 24.7 + - - -
1234F PRO* 3.8 20.4 - - + +
1242F PHE* 5.4 0.4 - + - -
1245F MET* 3.4 15.7 - - - +
1249F TRP* 3.9 13.0 - + + -
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Residues in contact with GLU1204 (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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1088F LYS* 4.8 12.5 + - - +
1091F LEU* 3.5 4.5 - - + +
1137F ALA* 5.3 0.2 - - - +
1138F ALA* 3.0 42.2 + - + +
1139F ARG* 4.8 1.0 + - - +
1178F TRP* 2.8 41.8 + - + +
1200F VAL* 2.7 21.6 + - + +
1201F VAL* 3.3 15.4 - - - +
1203F TRP* 1.3 80.5 - - + +
1205F ILE* 1.3 61.8 + - - +
1207F THR* 3.5 3.1 + - - -
1208F LEU 3.2 2.4 + - - -
1209F ALA* 2.7 35.2 + - - +
1210F GLU 4.6 11.3 - - - +
1212F PRO* 4.7 0.4 - - + -
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Residues in contact with ILE1205 (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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1087F LEU* 4.4 14.4 - - + -
1091F LEU* 3.7 26.6 - - + +
1107F PRO* 3.9 13.0 - - + +
1112F MET* 3.3 35.5 - - + +
1115F MET* 3.8 38.4 - - + -
1116F ALA 4.9 0.9 - - - +
1119F ILE* 4.4 8.7 - - + -
1201F VAL* 2.9 21.3 + - + +
1202F LEU* 2.8 27.1 + - + +
1204F GLU* 1.3 72.2 - - - +
1206F ALA* 1.3 63.1 + - - +
1208F LEU* 3.3 12.3 + - - +
1241F LEU* 5.5 0.7 - - + -
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Residues in contact with ALA1206 (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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1104F LEU 5.6 0.9 - - - +
1106F PRO* 3.3 22.4 - - + +
1112F MET* 2.9 21.5 - - + -
1202F LEU 2.9 10.4 + - - +
1203F TRP 2.9 7.6 + - - +
1205F ILE* 1.3 79.4 - - - +
1207F THR* 1.3 59.1 + - - +
1208F LEU* 3.4 0.9 - - - +
1234F PRO* 4.0 24.6 - - + +
1235F ASP 5.2 2.9 - - - +
1236F ASN* 5.5 0.5 - - - +
1237F CYS* 4.0 18.2 - - + +
1245F MET* 4.1 6.3 - - + -
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Residues in contact with THR1207 (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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1095F ARG* 4.0 5.9 + - - -
1104F LEU* 4.6 3.9 - - - +
1203F TRP* 3.0 41.6 + - + +
1204F GLU* 3.7 0.9 + - - -
1206F ALA* 1.3 76.2 - - - +
1208F LEU* 1.3 69.7 + - - +
1209F ALA 3.7 1.4 + - - -
1210F GLU* 3.0 53.9 + - - +
1234F PRO* 3.7 29.6 - - + -
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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