Contacts of the helix formed by residues 286 - 293 (chain C) in PDB entry 4KEU
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 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232C VAL* 3.5 16.1 - - + +
236C ASN* 2.9 22.0 + - - -
277C ARG* 2.8 40.9 + - - +
282C LEU* 2.9 16.4 + - + +
285C GLU* 1.3 81.2 - - - +
287C THR* 1.3 64.0 + - - +
288C ILE 3.6 1.3 - - - -
289C PRO* 3.4 4.5 - - - +
290C PHE* 3.0 23.2 + - - +
293C ARG* 4.8 3.8 + - - +
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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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224C TYR* 3.0 47.7 - - + +
232C VAL* 4.6 1.6 - - - +
236C ASN* 3.3 18.8 + - - +
253C ILE* 4.6 6.5 - - + -
282C LEU* 3.8 2.5 + - - +
283C ILE* 3.4 24.4 + - + -
286C ASP* 1.3 81.4 + - - +
288C ILE* 1.3 68.1 + - + +
290C PHE* 3.1 4.7 + - - +
291C LEU* 2.9 38.6 + - + +
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Residues in contact with ILE 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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18C PHE* 4.1 7.6 - - + -
283C ILE* 2.7 26.8 + - + +
284C PHE* 3.7 35.9 - - + -
287C THR* 1.3 75.6 - - + +
289C PRO* 1.4 61.7 - - + +
291C LEU* 3.1 11.5 + - + +
292C LYS* 2.9 57.1 + - + +
301C ILE* 5.0 13.0 - - + -
305C PHE* 4.1 32.3 - - + -
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Residues in contact with PRO 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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283C ILE 3.6 7.2 - - - +
284C PHE 3.4 20.4 - - - +
285C GLU 4.0 10.8 - - - +
286C ASP* 3.4 12.3 - - - +
288C ILE* 1.4 97.5 - - + +
290C PHE* 1.3 54.6 + - - +
292C LYS* 3.8 8.5 - - + +
293C ARG* 2.9 44.2 + - - +
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Residues in contact with PHE 290 (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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233C ASP 6.0 0.2 - - - -
236C ASN* 3.4 57.4 - - + +
237C GLU* 4.6 9.2 - - + -
240C LEU* 3.9 27.6 - - + -
286C ASP* 3.0 17.8 + - - +
287C THR 3.1 7.8 + - - +
289C PRO* 1.3 76.0 - - - +
291C LEU* 1.3 74.8 + - + +
293C ARG* 3.2 35.2 - - - +
294C ASN* 2.8 44.5 + - - +
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Residues in contact with LEU 291 (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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236C ASN* 4.5 1.1 - - - +
239C THR* 4.2 16.2 - - + -
240C LEU* 4.0 33.4 - - + +
243C ILE* 4.1 20.2 - - + -
253C ILE* 4.3 9.4 - - + -
287C THR* 2.9 31.3 + - + +
288C ILE* 3.5 11.4 - - + +
290C PHE* 1.3 94.3 - - + +
292C LYS* 1.3 62.3 + - + +
294C ASN* 3.0 13.2 + - - -
296C VAL* 3.1 35.1 + - + +
301C ILE* 5.8 3.8 - - + -
304C ILE* 5.3 2.5 - - + -
305C PHE* 5.9 2.2 - - + -
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Residues in contact with LYS 292 (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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288C ILE* 2.9 37.7 + - + +
289C PRO* 4.0 7.6 - - + +
291C LEU* 1.3 76.8 - - + +
293C ARG* 1.3 58.2 + - - +
294C ASN 3.0 3.4 + - - -
295C GLY* 3.7 7.8 + - - -
296C VAL 3.5 22.9 + - - +
297C ASN* 5.7 0.2 - - - -
298C GLU* 3.3 37.7 + - - +
301C ILE* 4.2 15.0 - - + +
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Residues in contact with ARG 293 (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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286C ASP* 4.8 3.6 + - - +
289C PRO* 2.9 19.9 + - - +
290C PHE* 3.2 56.8 - - - +
291C LEU 3.2 0.4 - - - -
292C LYS* 1.3 74.7 - - - +
294C ASN* 1.3 68.5 + - - +
295C GLY 3.6 0.9 - - - -
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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