Contacts of the strand formed by residues 283 - 286 (chain G) in PDB entry 6O81
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 LEU 283 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ASN* 3.8 35.2 - - + +
278C PHE* 5.7 0.4 - - + -
279C PRO* 5.8 0.9 - - + -
118G PHE* 3.9 22.2 - - + -
226G PHE 3.6 2.0 + - - -
227G TYR* 3.8 23.2 - - + -
228G VAL 3.2 24.5 + - - -
281G ILE* 3.9 2.6 - - - +
282G THR* 1.3 91.8 - - + +
284G LEU* 1.3 70.0 + - - +
285G PHE* 4.3 6.5 - - + -
290G VAL* 3.9 23.6 - - + +
291G LEU 3.6 23.6 - - - +
292G THR* 4.2 3.4 - - - +
293G PRO* 4.3 1.1 - - - -
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Residues in contact with LEU 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G VAL* 4.5 19.3 - - + -
204G GLY* 4.2 9.4 - - - +
206G ILE* 4.8 1.6 - - + -
228G VAL* 3.5 30.3 - - + +
230G ALA* 4.7 7.2 - - + +
235G PHE* 5.8 1.3 - - + -
281G ILE* 3.7 20.9 - - + -
283G LEU* 1.3 80.9 - - - +
285G PHE* 1.3 66.8 + - - +
286G THR* 4.8 4.9 - - - +
290G VAL* 3.5 5.4 - - - +
291G LEU* 2.9 54.0 + - + +
292G THR 4.9 0.7 - - - +
293G PRO* 3.7 23.1 - - + -
296G VAL* 4.8 11.9 - - + -
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Residues in contact with PHE 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G ILE* 3.4 12.5 - - + +
114G LEU* 5.6 2.5 - - + -
115G CYS* 3.7 31.4 - - + -
118G PHE* 3.7 28.0 - + + -
227G TYR* 3.6 47.6 - + + -
228G VAL 3.1 26.9 + - - -
229G VAL* 3.7 22.4 - - + -
230G ALA 2.9 24.4 + - - +
283G LEU* 4.3 8.7 - - + -
284G LEU* 1.3 76.0 - - - +
286G THR* 1.3 61.2 + - - +
289G GLY 3.8 3.4 - - - -
290G VAL* 3.6 33.2 - - + -
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Residues in contact with THR 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G ILE* 3.6 7.2 - - - -
114G LEU* 3.4 11.6 - - - +
230G ALA 3.4 18.0 + - - +
231G GLU* 3.6 13.5 - - - +
232G SER* 3.4 25.8 - - - +
235G PHE* 3.9 20.4 - - + -
284G LEU* 4.8 4.3 - - - +
285G PHE* 1.3 75.3 + - - +
287G ASP* 1.3 70.0 + - - +
288G LEU* 3.1 7.4 - - + +
289G GLY 2.9 24.6 + - - +
291G LEU* 3.3 22.8 - - - +
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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