Contacts of the helix formed by residues 282 - 289 (chain C) in PDB entry 6R7H
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 HIS 282 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258C ASN* 5.2 4.9 - - - -
259C ALA* 3.8 43.4 + - + +
262C GLU* 4.7 16.0 + - - +
263C LEU* 6.1 1.6 - - + -
278C LEU* 3.2 43.6 + - + +
279C VAL 3.7 3.4 - - - -
281C LYS* 1.3 109.8 + - + +
283C SER* 1.3 62.6 + - - +
284C GLU 3.3 2.5 - - - -
285C THR* 3.5 9.7 + - - +
286C PHE* 3.2 41.5 + + + -
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Residues in contact with SER 283 (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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279C VAL* 3.3 16.2 + - - -
280C ASN* 3.2 17.5 + - - -
281C LYS 3.2 2.5 + - - -
282C HIS* 1.3 77.4 - - - +
284C GLU* 1.3 61.3 + - - +
286C PHE* 3.7 6.4 + - - +
287C THR* 3.0 31.7 + - - +
292C MET* 5.4 0.8 - - - +
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Residues in contact with GLU 284 (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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281C LYS 4.5 4.6 + - - +
282C HIS* 3.3 1.0 - - - +
283C SER* 1.3 83.5 + - - +
285C THR* 1.3 60.7 + - - +
287C THR* 3.0 17.6 + - - +
288C ARG* 3.3 34.7 + - - +
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Residues in contact with THR 285 (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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225C LYS* 6.4 0.2 - - - -
256C LEU 5.9 2.7 - - - +
259C ALA* 4.2 27.7 - - + +
260C TYR* 4.7 8.9 + - + -
282C HIS* 3.5 14.5 + - - -
283C SER 3.3 0.4 - - - -
284C GLU* 1.3 79.3 - - - +
286C PHE* 1.3 67.0 + - - +
287C THR 3.2 1.0 + - - -
288C ARG* 3.5 38.8 + - - +
289C ASP* 2.9 35.5 + - - +
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Residues in contact with PHE 286 (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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259C ALA* 4.8 11.7 - - + -
260C TYR* 3.3 49.4 - + - -
263C LEU* 5.3 7.2 - - + -
278C LEU 4.8 5.8 - - - -
279C VAL* 4.8 9.6 - - + -
282C HIS* 3.2 38.6 + + + +
283C SER* 4.2 7.9 - - - +
284C GLU 3.4 0.2 - - - -
285C THR* 1.3 79.1 - - - +
287C THR* 1.3 58.9 + - - +
289C ASP 4.2 0.7 - - - -
291C ASN* 3.1 34.8 + - + +
292C MET* 3.7 22.0 + - - +
295C VAL* 3.7 44.0 - - + -
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Residues in contact with THR 287 (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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283C SER* 3.0 16.3 + - - +
284C GLU* 3.0 22.3 + - - +
286C PHE* 1.3 73.6 - - - +
288C ARG* 1.3 60.4 + - - +
289C ASP 3.2 2.5 + - - -
290C ASN* 3.6 9.5 + - - -
292C MET* 3.9 33.0 - - + -
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Residues in contact with ARG 288 (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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256C LEU 5.9 0.4 + - - -
284C GLU* 3.3 30.6 + - - +
285C THR* 3.5 41.2 + - - +
287C THR* 1.3 79.4 + - - +
289C ASP* 1.3 70.3 + - - +
290C ASN* 3.5 3.4 + - - -
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Residues in contact with ASP 289 (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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218C HIS* 6.4 0.2 - - - -
222C GLU* 3.0 21.6 - - - +
225C LYS* 2.9 29.2 + - - +
260C TYR* 4.6 1.3 + - - +
285C THR* 2.9 33.1 + - - +
287C THR 3.2 0.8 - - - -
288C ARG* 1.3 93.0 + - - +
290C ASN* 1.3 77.8 + - - +
291C ASN* 2.9 22.3 + - - +
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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