Contacts of the helix formed by residues 164 - 170 (chain F) in PDB entry 1OP8
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 ASP 164 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F PRO* 3.9 32.5 - - + +
162F ILE 3.9 2.6 + - - -
163F ILE* 1.3 74.1 - - - +
165F ARG* 1.3 62.3 + - - +
166F LYS* 2.7 50.5 + - - +
167F VAL* 2.8 37.9 + - + +
168F CYS* 2.9 9.7 + - - +
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Residues in contact with ARG 165 (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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173E PHE* 4.7 7.4 - - + +
175E VAL* 4.4 11.7 - - - -
129F ASP* 2.9 39.4 + - - -
132F PRO* 5.2 0.6 - - - +
163F ILE 3.1 5.2 + - - -
164F ASP* 1.3 74.0 + - - +
166F LYS* 1.3 62.0 + - + +
168F CYS* 3.3 15.4 + - - +
169F ASN* 3.0 27.7 + - - +
176F ILE* 3.8 21.3 - - + +
177F GLY 3.1 27.2 + - - -
178F MET* 3.3 29.0 + - - +
180F MET 2.5 25.4 + - - +
181F VAL* 4.0 5.8 - - - +
182F CYS* 5.1 3.1 - - - +
230F LEU* 4.2 0.4 - - - +
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Residues in contact with LYS 166 (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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173E PHE* 3.0 85.8 + - + +
164F ASP* 2.7 28.6 + - - +
165F ARG* 1.3 69.9 - - + +
167F VAL* 1.3 66.2 + - + +
169F ASN* 3.2 6.2 + - - +
170F ASP* 3.1 19.4 + - - +
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Residues in contact with VAL 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F ILE* 3.8 15.3 - - + -
164F ASP* 2.8 23.9 + - + +
166F LYS* 1.3 76.7 - - + +
168F CYS* 1.3 59.7 + - - +
169F ASN 3.0 1.6 - - - -
170F ASP* 2.8 49.6 + - - +
171F HIS* 3.1 25.2 + - + -
186F LEU* 4.7 9.4 - - + -
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Residues in contact with CYS 168 (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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163F ILE* 4.4 1.3 - - - +
164F ASP 2.9 8.0 + - - +
165F ARG* 3.3 15.3 - - - +
167F VAL* 1.3 78.8 - - - +
169F ASN* 1.3 57.5 + - - +
170F ASP 3.5 0.2 - - - -
171F HIS* 3.9 6.5 - - - -
172F TYR* 3.4 43.5 + - - +
176F ILE* 3.6 27.4 - - + +
182F CYS* 2.0 53.2 - - + -
227F VAL* 4.9 1.1 - - - -
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Residues in contact with ASN 169 (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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173E PHE* 3.1 39.4 + - - +
165F ARG* 3.0 20.2 + - - +
166F LYS 3.2 2.7 + - - +
167F VAL 3.0 0.4 - - - -
168F CYS* 1.3 75.9 - - - +
170F ASP* 1.3 69.1 + - - +
172F TYR* 5.2 0.2 - - - +
173F ASN* 3.0 43.1 + - - +
174F PRO 4.2 1.4 - - - +
175F VAL* 3.5 12.1 - - - +
176F ILE* 2.8 52.8 + - - +
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Residues in contact with ASP 170 (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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166F LYS 3.1 11.0 + - - +
167F VAL* 2.8 41.0 + - - +
169F ASN* 1.3 84.0 - - - +
170F ARG* 1.3 74.4 + - - +
171F HIS* 2.7 42.6 + - - -
173F ASN* 3.3 9.4 + - - -
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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