Contacts of the strand formed by residues 180 - 186 (chain S) in PDB entry 3J7Y
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 PHE 180 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2262A C 3.8 11.7 - - - -
2263A C 3.1 44.9 - - - +
43M ARG* 3.7 17.9 - - - +
173S ARG* 3.7 22.4 - - + -
174S PHE* 3.2 15.4 - - - -
175S ARG* 3.2 75.1 + - + -
178S LYS* 3.2 9.6 - - + +
179S ASN* 1.3 76.3 - - - +
181S LYS* 1.3 61.7 + - - +
182S LYS* 3.7 29.4 - - + -
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Residues in contact with LYS 181 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2023A U 5.0 13.6 + - - +
2024A C 3.5 17.0 + - - -
2296A U 3.1 26.4 + - - +
43M ARG* 4.2 18.8 + - + +
43R VAL* 4.8 2.0 - - - +
47R ILE* 3.3 31.0 - - + +
172S MET* 4.1 17.5 - - + -
173S ARG 3.4 5.6 - - - -
174S PHE* 4.3 14.6 - - + -
179S ASN* 4.1 3.9 + - - +
180S PHE* 1.3 81.5 - - - +
182S LYS* 1.3 61.8 + - - +
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Residues in contact with LYS 182 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2024A C 3.4 7.9 - - - +
2025A C 2.8 41.6 + - - +
2026A A 3.8 14.5 + - - -
2261A C 3.8 0.6 + - - -
2262A C 2.7 41.2 + - - +
2263A C 3.9 2.7 + - - -
43M ARG* 3.8 15.9 - - - +
172S MET* 3.2 12.5 - - - +
173S ARG* 3.1 43.3 + - + +
180S PHE* 3.7 29.6 - - + -
181S LYS* 1.3 76.6 - - - +
183S LYS* 1.3 65.1 + - - +
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Residues in contact with LYS 183 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2023A U 4.9 0.8 - - - +
2024A C 2.8 31.1 + - - +
27R HIS* 5.4 5.5 + - - -
50R PHE* 3.7 24.5 - - - -
170S ILE* 4.3 4.9 - - + -
171S ILE 3.5 7.4 - - - +
172S MET* 3.7 27.1 - - + +
182S LYS* 1.3 78.4 - - - +
184S ARG* 1.3 61.0 + - - +
185S ILE* 3.5 34.8 + - + +
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Residues in contact with ARG 184 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2024A C 6.3 0.4 - - - -
2143A G 3.7 27.3 + - - -
2259A C 5.2 0.8 + - - -
2261A C 3.2 87.4 - - - +
2262A C 6.0 0.4 - - - +
169S ARG 3.8 0.5 - - - +
170S ILE* 3.8 0.5 - - - -
171S ILE* 2.8 57.5 + - + +
183S LYS* 1.3 73.9 - - - +
185S ILE* 1.3 69.1 + - - +
186S VAL* 3.5 33.8 - - + +
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Residues in contact with ILE 185 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168S PRO* 3.5 31.6 - - + -
169S ARG 3.6 5.6 - - - +
170S ILE* 4.5 13.7 - - + -
183S LYS* 3.5 36.7 + - + +
184S ARG* 1.3 81.9 + - - +
186S VAL* 1.3 66.1 + - - +
187S THR* 5.4 1.3 - - + -
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Residues in contact with VAL 186 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2143A G 4.1 10.3 - - - +
2144A A 5.7 2.5 - - - +
167S TRP 3.9 0.3 - - - +
168S PRO* 3.3 5.2 - - - +
169S ARG* 2.8 43.8 + - + +
171S ILE* 3.3 34.1 - - + -
184S ARG* 3.5 24.5 - - + +
185S ILE* 1.3 79.6 - - - +
187S THR* 1.3 72.2 + - - +
188S THR* 4.1 13.5 - - + +
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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