Contacts of the helix formed by residues 1165 - 1179 (chain u) in PDB entry 6FF7
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 TYR1165 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1161u MET 5.3 2.2 - - - +
1162u GLY* 3.6 13.4 + - - +
1163u LYS 3.6 0.4 - - - -
1164u ASP* 1.3 76.9 - - - +
1166u ILE* 1.3 64.3 + - - +
1167u TYR 3.4 2.2 - - - -
1168u ALA* 3.5 12.1 + - + +
1169u VAL* 3.3 23.2 + - - +
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Residues in contact with ILE1166 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1162u GLY 3.6 15.5 + - - +
1163u LYS 5.0 5.2 - - - +
1164u ASP 3.6 1.2 - - - -
1165u TYR* 1.3 77.7 - - - +
1167u TYR* 1.3 57.6 + - - +
1169u VAL* 3.5 1.6 + - - -
1170u THR* 3.0 32.6 + - - -
1195u MET* 6.2 4.0 - - + -
1204u CYS* 5.2 13.0 - - + +
1207u SER* 4.9 14.0 - - - -
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Residues in contact with TYR1167 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5808 THR 4.6 16.3 - - - +
5818 LYS* 5.4 2.5 - - - -
5828 PRO* 4.3 24.1 - - + +
1163u LYS 5.9 0.2 + - - -
1164u ASP 4.8 6.1 + - - +
1165u TYR* 3.4 0.6 - - - +
1166u ILE* 1.3 78.1 - - - +
1168u ALA* 1.3 60.0 + - - +
1170u THR* 4.2 9.7 + - - -
1171u PRO* 4.7 3.1 - - - +
1207u SER* 5.4 4.9 - - - -
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Residues in contact with ALA1168 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5258 PRO* 6.0 1.9 - - - +
5758 PHE* 6.5 0.9 - - + -
1164u ASP 5.0 2.8 + - - +
1165u TYR* 3.5 18.0 + - + +
1166u ILE 3.2 0.8 - - - -
1167u TYR* 1.3 79.2 - - - +
1169u VAL* 1.3 59.3 + - + +
1170u THR 3.5 0.2 - - - -
1171u PRO* 4.4 8.5 - - - +
1172u LEU* 4.7 3.6 + - - +
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Residues in contact with VAL1169 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151u LEU* 6.1 5.6 - - + -
1165u TYR 3.3 13.0 + - - +
1166u ILE* 4.6 1.3 - - - +
1168u ALA* 1.3 77.5 - - + +
1170u THR* 1.3 60.1 + - - +
1171u PRO 3.4 1.6 - - - -
1172u LEU* 3.1 13.4 + - + +
1173u LEU* 2.8 29.3 + - - +
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Residues in contact with THR1170 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1166u ILE 3.0 20.2 + - - -
1167u TYR* 4.4 9.2 - - - -
1168u ALA 3.5 0.4 - - - -
1169u VAL* 1.3 76.8 - - - +
1171u PRO* 1.4 57.0 - - - +
1173u LEU* 3.8 6.3 - - - +
1174u GLU* 2.9 30.8 + - - +
1207u SER* 4.6 18.2 - - - -
1210u HIS* 6.3 1.8 - - - -
1211u LEU* 6.4 2.7 - - - -
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Residues in contact with PRO1171 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5238 GLU 5.6 4.9 - - - +
5258 PRO* 6.0 5.8 - - + -
1167u TYR 4.7 4.5 - - - +
1168u ALA 4.4 8.3 - - - +
1169u VAL 3.4 0.6 - - - -
1170u THR* 1.4 75.7 - - - +
1172u LEU* 1.3 60.0 + - - +
1174u GLU* 4.1 6.1 - - + +
1175u ASP* 3.8 17.2 + - - +
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Residues in contact with LEU1172 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133u MET* 6.2 6.3 - - + -
1168u ALA 4.7 1.9 + - - +
1169u VAL* 3.1 20.2 + - + +
1171u PRO* 1.3 76.2 - - - +
1173u LEU* 1.3 60.6 + - - +
1174u GLU 3.3 0.2 - - - -
1175u ASP* 3.2 7.1 + - - +
1176u ALA* 2.9 26.8 + - - +
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Residues in contact with LEU1173 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1169u VAL* 2.8 16.1 + - + +
1170u THR* 3.9 7.4 - - - +
1172u LEU* 1.3 74.2 - - - +
1174u GLU* 1.3 60.9 + - - +
1176u ALA* 3.6 9.0 - - - +
1177u LEU* 2.9 31.2 + - - +
1188u ALA* 4.6 12.2 - - + +
1191u VAL* 6.0 4.3 - - + -
1192u VAL* 6.4 1.8 - - + -
1211u LEU* 5.5 10.8 - - + -
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Residues in contact with GLU1174 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1170u THR 2.9 16.7 + - - +
1171u PRO* 4.4 6.5 - - + +
1173u LEU* 1.3 76.7 - - - +
1175u ASP* 1.3 58.2 + - - +
1177u LEU* 4.3 4.1 - - - +
1178u MET* 2.9 30.4 + - - +
1214u TYR* 5.7 3.6 - - - -
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Residues in contact with ASP1175 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5218 PRO 5.4 7.4 - - - +
5228 PHE* 6.0 5.4 - - + -
1171u PRO 3.8 11.9 + - - +
1172u LEU* 3.2 11.0 + - - +
1174u GLU* 1.3 76.4 - - - +
1176u ALA* 1.3 60.3 + - - +
1178u MET* 3.6 7.1 - - - +
1179u ASP* 3.0 28.1 + - - +
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Residues in contact with ALA1176 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148u LEU* 5.6 7.6 - - + -
1172u LEU 2.9 15.7 + - - +
1173u LEU* 3.3 8.2 + - - +
1175u ASP* 1.3 77.7 - - - +
1177u LEU* 1.3 60.0 + - - +
1179u ASP* 3.3 21.3 + - - +
1184u HIS* 3.6 27.1 - - + +
1185u ARG* 4.0 1.6 + - - -
1188u ALA* 3.8 19.5 - - + -
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Residues in contact with LEU1177 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1173u LEU 2.9 16.5 + - - +
1174u GLU* 4.3 1.6 - - - +
1176u ALA* 1.3 75.0 - - - +
1178u MET* 1.3 61.2 + - - +
1179u ASP 3.3 5.5 + - - +
1185u ARG* 4.7 16.4 - - + +
1188u ALA* 4.6 6.9 - - + +
1211u LEU 5.7 0.4 - - - +
1214u TYR* 3.8 37.7 - - + +
1215u VAL* 5.2 1.3 - - - +
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Residues in contact with MET1178 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5118 LEU* 6.1 0.3 - - - +
1174u GLU 2.9 21.0 + - - +
1175u ASP* 3.7 9.9 - - - +
1176u ALA 3.2 0.2 - - - -
1177u LEU* 1.3 77.0 - - - +
1179u ASP* 1.3 63.3 + - - +
1180u ARG* 3.8 0.9 + - - -
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Residues in contact with ASP1179 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5118 LEU* 5.2 2.9 - - - +
1175u ASP 3.0 13.2 + - - +
1176u ALA* 3.4 16.9 - - - +
1177u LEU 3.3 7.3 - - - +
1178u MET* 1.3 80.6 - - - +
1180u ARG* 1.3 65.2 + - - +
1181u ASP* 3.4 8.9 + - + +
1184u HIS* 4.1 15.3 - - + -
1185u ARG* 5.6 1.7 - - - +
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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
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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