Contacts of the strand formed by residues 158 - 165 (chain F) in PDB entry 5OF4
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 LYS 158 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F GLU* 3.4 26.6 + - - +
8F LEU 3.2 6.7 + - - -
9F ASN* 3.1 15.5 - - - +
10F LEU* 3.0 25.8 + - - +
157F MET* 1.3 79.6 - - - +
159F SER* 1.3 62.7 + - - +
160F ARG* 3.0 41.3 + - + +
188F ASN 5.8 3.8 - - - +
190F LEU* 3.7 21.2 - - - +
236F ASP 5.3 3.2 + - - -
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Residues in contact with SER 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F LEU* 4.3 11.9 - - - -
12F VAL* 6.3 0.2 - - - -
144F ILE* 3.6 34.6 - - - +
148F ASN* 4.3 6.9 + - - +
157F MET* 3.7 22.9 - - - +
158F LYS* 1.3 75.4 - - - +
160F ARG* 1.3 59.8 + - - +
161F ILE* 4.6 1.1 - - - -
187F GLN* 6.1 0.2 - - - +
188F ASN 5.2 3.9 + - - -
189F ILE* 3.4 40.3 - - - +
190F LEU 3.9 0.6 + - - -
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Residues in contact with ARG 160 (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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9F ASN* 4.6 9.0 + - - +
10F LEU 3.3 10.0 + - - +
11F LEU* 3.3 19.5 - - + -
12F VAL* 3.2 19.1 + - - +
158F LYS* 3.0 39.2 + - + +
159F SER* 1.3 75.7 - - - +
161F ILE* 1.3 70.3 + - - +
190F LEU* 3.5 38.8 - - + +
192F ASP* 3.7 18.1 + - - +
234F ASP 2.6 21.9 + - - -
235F GLN* 2.8 48.7 + - - +
236F ASP 4.5 3.8 + - - -
238F ARG* 5.0 6.9 - - - +
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Residues in contact with ILE 161 (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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11F LEU* 4.9 0.9 - - - -
12F VAL* 3.4 21.3 - - + +
14F VAL* 5.7 0.4 - - + -
137F LEU* 3.9 20.2 - - + -
140F ALA* 6.0 0.2 - - + -
141F LEU* 5.8 1.1 - - + -
144F ILE* 3.6 31.0 - - + -
159F SER 4.2 1.8 - - - +
160F ARG* 1.3 86.0 - - - +
162F LEU* 1.3 60.5 + - - +
163F VAL* 3.6 29.2 - - + -
189F ILE* 3.8 11.0 - - + -
190F LEU 3.0 19.7 + - - +
191F ILE* 3.6 24.9 - - + -
192F ASP* 3.0 24.6 + - - +
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Residues in contact with LEU 162 (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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11F LEU* 4.8 13.6 - - + +
12F VAL 2.5 23.7 + - - +
13F ILE* 3.6 16.5 - - + -
14F VAL* 3.5 14.0 + - - +
44F LEU* 4.8 18.6 - - + -
161F ILE* 1.3 75.8 - - - +
163F VAL* 1.3 84.6 + - - +
164F ILE* 4.9 6.3 - - + -
192F ASP* 3.6 29.6 - - + +
193F ALA* 4.2 4.9 - - - +
194F CYS* 5.2 0.2 - - + -
227F LEU* 4.6 20.2 - - + +
230F VAL* 4.1 24.5 - - + -
231F PHE* 5.5 4.0 - - + +
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Residues in contact with VAL 163 (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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14F VAL* 4.1 17.9 - - + -
137F LEU* 4.6 11.4 - - + -
161F ILE* 3.6 20.6 - - + -
162F LEU* 1.3 84.3 - - - +
164F ILE* 1.3 67.8 + - - +
165F LYS* 3.7 39.0 - - + +
191F ILE* 4.1 8.1 - - + -
192F ASP 2.9 14.6 + - - +
193F ALA* 3.3 7.2 - - + -
194F CYS* 2.9 27.0 + - - +
203F LEU* 4.5 9.9 - - + -
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Residues in contact with ILE 164 (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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13F ILE* 4.5 9.9 - - + -
14F VAL* 2.9 28.1 + - - +
15F VAL* 4.8 10.3 - - + -
16F ASP* 3.8 10.5 + - + +
37F CYS* 5.2 7.2 - - - -
41F VAL* 4.2 22.4 - - + -
44F LEU* 4.4 7.0 - - + -
162F LEU* 4.9 5.4 - - + -
163F VAL* 1.3 76.3 - - - +
165F LYS* 1.3 68.6 + - - +
166F ALA* 4.7 1.6 - - + +
194F CYS* 3.6 15.5 - - + +
196F LEU* 4.1 31.9 - - + -
227F LEU* 3.8 33.0 - - + -
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Residues in contact with LYS 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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14F VAL* 5.0 4.5 - - + -
16F ASP* 4.7 4.3 - - + -
133F LEU* 3.3 49.2 + - + +
137F LEU* 5.9 5.7 - - - +
163F VAL* 3.7 23.0 - - + +
164F ILE* 1.3 79.3 - - - +
166F ALA* 1.3 62.5 + - - +
167F ALA 3.6 8.7 - - - +
169F ASP* 3.1 25.6 + - + +
177F PHE* 4.1 7.3 - - - -
194F CYS 3.0 7.7 + - - +
195F VAL* 3.3 26.7 - - - +
196F LEU* 3.3 3.5 + - - -
203F LEU* 3.4 41.6 - - + +
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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