Contacts of the helix formed by residues 1168 - 1180 (chain C) in PDB entry 5O9Z
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 PRO1168 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1034 A 5.4 9.4 - - - +
1158C HIS* 3.7 17.9 - - + +
1159C ASN* 4.5 21.1 - - + +
1162C GLY* 4.4 2.5 - - - +
1166C ARG* 3.8 6.3 - - - +
1167C MET* 1.3 87.4 - - - +
1169C LYS* 1.3 57.6 + - - +
1171C GLY* 3.3 1.0 + - - -
1172C LYS* 2.9 28.9 + - - +
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Residues in contact with LYS1169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934 G 4.6 2.1 - - - +
944 A 3.6 28.2 + - - +
1167C MET* 3.2 1.0 - - - -
1168C PRO* 1.3 81.6 - - - +
1170C MET* 1.3 57.1 + - - +
1172C LYS* 3.1 6.1 + - - +
1173C THR* 2.9 29.5 + - - -
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Residues in contact with MET1170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944 A 5.1 0.7 - - - -
1136C PRO* 6.5 0.9 - - + -
1139C VAL* 5.3 13.2 - - + -
1167C MET* 3.2 24.1 + - + +
1169C LYS* 1.3 79.1 - - - +
1171C GLY* 1.3 57.2 + - - +
1173C THR* 4.1 5.3 - - - -
1174C ILE* 2.9 30.1 + - - +
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Residues in contact with GLY1171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1157C ASN 4.4 2.4 - - - +
1158C HIS* 3.6 24.6 - - - -
1161C ILE* 4.9 6.5 - - - +
1162C GLY* 4.2 10.1 - - - -
1167C MET 2.8 12.7 + - - -
1168C PRO 3.3 1.1 + - - -
1169C LYS 3.2 0.2 - - - -
1170C MET* 1.3 75.7 - - - +
1172C LYS* 1.3 58.1 + - - +
1174C ILE* 3.7 5.9 - - - +
1175C HIS* 2.9 26.3 + - - +
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Residues in contact with LYS1172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924 C 4.6 1.3 - - - +
934 G 3.1 37.6 - - - +
1158C HIS* 3.6 17.2 - - + +
1168C PRO 2.9 16.1 + - - +
1169C LYS* 3.1 5.3 + - - +
1171C GLY* 1.3 75.2 - - - +
1173C THR* 1.3 59.5 + - - +
1175C HIS* 3.0 6.7 + - - +
1176C LYS* 2.9 27.5 + - - +
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Residues in contact with THR1173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934 G 4.1 22.5 - - - -
944 A 4.1 5.8 - - - -
1169C LYS 2.9 16.3 + - - -
1170C MET* 4.1 6.5 - - - -
1172C LYS* 1.3 76.0 - - - +
1174C ILE* 1.3 57.2 + - - +
1176C LYS* 3.3 6.3 + - - +
1177C TYR* 2.9 30.7 + - - +
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Residues in contact with ILE1174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135C LEU* 6.0 6.3 - - + -
1139C VAL* 6.4 2.7 - - + -
1161C ILE* 6.3 1.6 - - + -
1170C MET 2.9 21.8 + - - +
1171C GLY* 3.7 5.8 - - - +
1173C THR* 1.3 75.3 - - - +
1175C HIS* 1.3 51.6 + - - +
1177C TYR* 4.5 5.8 - - - +
1178C VAL* 2.7 39.3 + - + +
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Residues in contact with HIS1175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156C LEU 5.2 5.8 - - - +
1157C ASN* 5.2 3.1 - - - -
1158C HIS* 5.0 9.0 - - + +
1171C GLY 2.9 19.6 + - - +
1172C LYS* 3.0 10.7 + - - +
1174C ILE* 1.3 77.0 - - - +
1176C LYS* 1.3 59.9 + - - +
1178C VAL* 4.2 2.6 - - - +
1179C HIS* 2.9 28.4 + - - +
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Residues in contact with LYS1176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924 C 5.3 9.0 - - - +
934 G 5.8 4.3 - - - -
1172C LYS 2.9 14.5 + - - +
1173C THR* 3.9 6.1 - - - +
1175C HIS* 1.3 75.6 - - - +
1177C TYR* 1.3 61.0 + - - +
1179C HIS* 3.1 7.5 + - - +
1180C LEU* 2.9 28.1 + - - +
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Residues in contact with TYR1177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129C LEU* 5.9 7.0 - - + -
1134C LYS* 4.6 23.6 - - + +
1135C LEU* 6.5 0.2 - - + -
1173C THR 2.9 17.7 + - - +
1174C ILE* 4.5 4.5 - - - +
1176C LYS* 1.3 76.9 - - - +
1178C VAL* 1.3 61.3 + - - +
1180C LEU* 3.3 16.8 + - - +
1181C PHE* 3.6 8.7 + - - +
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Residues in contact with VAL1178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1129C LEU* 6.4 1.3 - - - -
1153C LEU* 5.4 13.0 - - + -
1174C ILE 2.7 24.4 + - - +
1175C HIS* 4.2 4.3 - - - +
1177C TYR* 1.3 76.7 - - - +
1179C HIS* 1.3 61.8 + - - +
1181C PHE* 3.2 22.6 + - - +
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Residues in contact with HIS1179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175C HIS 2.9 22.1 + - - +
1176C LYS* 3.1 9.6 + - - +
1178C VAL* 1.3 77.9 - - - +
1180C LEU* 1.3 57.2 + - - +
1181C PHE 3.2 4.1 + - - +
1208C PHE* 4.8 2.3 - - - -
1209C GLN* 3.8 17.3 + - + +
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Residues in contact with LEU1180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1176C LYS 2.9 15.0 + - - +
1177C TYR* 3.6 11.7 - - - +
1178C VAL 3.2 0.8 - - - -
1179C HIS* 1.3 75.8 - - - +
1181C PHE* 1.3 62.8 + - - +
1182C PRO* 3.6 5.0 - - - +
1209C GLN* 2.9 34.7 - - + +
1211C ASP* 5.5 9.5 + - + +
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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