Contacts of the helix formed by residues 282 - 287 (chain C) in PDB entry 4PEI
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 THR 282 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C MET* 3.4 19.5 - - - +
278C ASN 2.8 23.4 + - - +
279C LEU* 3.3 7.3 + - - +
280C ILE 3.2 0.2 - - - -
281C MET* 1.3 77.4 - - - +
283C TRP* 1.3 65.8 + - - +
284C PRO* 3.2 4.5 - - - -
285C ALA* 2.8 15.3 + - - +
286C PHE* 3.3 23.5 - - - -
299C ILE* 3.9 25.1 - - + -
302C LEU* 4.0 15.3 - - + -
303C LEU* 3.7 20.4 - - + -
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Residues in contact with TRP 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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101C TYR* 5.3 0.2 - - - -
279C LEU 3.5 5.2 + - - -
280C ILE 3.0 16.2 + - - +
282C THR* 1.3 76.1 - - - +
284C PRO* 1.3 63.7 - - + +
286C PHE* 2.6 39.8 + - + +
287C SER* 3.0 35.1 + - - -
341C ARG* 3.5 57.7 - - + -
344C ILE* 3.6 25.8 - - + -
345C GLU* 3.5 48.4 + - + +
348C TYR* 3.8 31.9 - + + -
349C ASN* 5.0 2.4 + - - -
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Residues in contact with PRO 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 MET 3.5 10.8 - - - +
282C THR* 3.2 5.6 - - - -
283C TRP* 1.3 99.4 - - + +
285C ALA* 1.3 57.6 + - - +
287C SER* 3.2 22.3 + - - -
294C ASP* 5.3 0.9 - - - +
297C TYR* 3.2 43.6 + - + +
302C LEU* 4.2 13.0 - - + -
348C TYR* 3.4 36.1 - - + +
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Residues in contact with ALA 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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282C THR 2.8 12.0 + - - +
283C TRP 2.8 0.2 + - - -
284C PRO* 1.3 79.9 - - - +
286C PHE* 1.3 63.4 + - + +
287C SER 3.6 0.4 - - - -
288C ASN 5.5 0.2 + - - -
291C GLN 5.4 0.2 - - - +
292C PHE* 4.3 0.5 - - - +
293C PRO* 3.2 6.8 - - + +
294C ASP* 2.8 35.1 + - - +
297C TYR* 3.8 19.3 - - + -
299C ILE* 4.0 23.1 - - + -
302C LEU* 3.8 17.9 - - + -
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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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101C TYR* 4.0 18.8 - + - +
160C TYR* 3.6 37.5 - + - -
164C MET* 4.2 14.8 - - + -
279C LEU* 5.7 5.2 - - + -
282C THR* 3.3 37.2 - - - -
283C TRP* 2.6 25.4 + - + +
285C ALA* 1.3 77.2 - - + +
287C SER* 1.3 49.9 + - - +
288C ASN 3.2 6.7 + - - +
292C PHE* 3.7 33.7 - + + +
293C PRO* 3.8 20.4 - - + -
299C ILE* 4.5 2.0 - - + -
341C ARG* 2.8 43.7 + - - +
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Residues in contact with SER 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 TRP* 3.0 38.1 + - - -
284C PRO* 3.2 18.8 + - - +
285C ALA 3.6 1.0 - - - -
286C PHE* 1.3 77.7 - - - +
288C ASN* 1.3 60.8 + - - +
289C LYS 3.6 2.4 + - - -
297C TYR* 5.1 2.6 + - - -
341C ARG* 3.7 5.4 + - - -
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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