Contacts of the helix formed by residues 281 - 286 (chain A) 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 THR 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.0 33.7 + - - +
56A ALA* 3.7 31.9 - - - +
59A PHE* 3.8 22.7 - - + -
255A HIS* 4.2 0.2 - - - -
279A SER* 3.1 2.0 + - - -
280A ILE* 1.3 85.7 - - + +
282A LEU* 1.3 64.6 + - - +
283A ILE 3.2 2.9 - - - -
284A PHE* 3.2 20.8 + - + +
285A GLU* 2.7 36.9 + - - +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A TYR* 4.0 5.4 - - + -
225A GLY* 3.4 37.9 - - - +
232A VAL* 3.9 17.7 - - + -
255A HIS* 3.3 14.0 + - + -
277A ARG* 3.7 44.4 - - + +
279A SER* 3.5 8.6 + - - +
281A THR* 1.3 78.0 - - - +
283A ILE* 1.3 57.3 + - - +
285A GLU* 3.1 16.6 + - + +
286A ASP* 2.9 44.9 + - + +
287A THR* 5.4 1.6 - - - +
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.8 22.2 - - + -
224A TYR* 4.1 9.4 - - + -
253A ILE* 3.8 24.9 - - + +
254A SER 4.8 0.4 - - - +
255A HIS* 2.9 34.4 + - + +
282A LEU* 1.3 75.5 - - - +
284A PHE* 1.3 77.8 + - + +
287A THR* 3.4 23.2 + - - +
288A ILE* 2.8 38.2 + - + +
305A PHE* 3.3 35.0 - - + -
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Residues in contact with PHE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 3.5 42.4 - + - -
20A LEU* 4.9 1.3 - - + -
56A ALA 4.8 0.2 - - - -
59A PHE* 3.6 60.3 - + + -
61A VAL* 3.7 24.7 - - + -
280A ILE 4.9 3.1 - - - -
281A THR* 3.2 23.2 + - + +
283A ILE* 1.3 92.1 - - + +
285A GLU* 1.3 59.2 + - - +
286A ASP 3.3 0.2 - - - -
288A ILE* 4.2 13.7 - - + -
289A PRO* 3.3 22.4 - - - +
58B GLN* 4.8 1.6 - - - -
59B PHE* 4.4 12.8 - + + -
285B GLU* 3.6 12.6 - - - +
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ARG* 4.9 3.5 - - - -
59A PHE* 4.5 11.5 - - + -
277A ARG* 5.5 0.9 - - - +
279A SER* 4.3 5.2 + - - -
281A THR* 2.7 38.7 + - - +
282A LEU* 3.1 19.4 + - + +
284A PHE* 1.3 81.1 - - - +
286A ASP* 1.3 58.8 + - + +
289A PRO* 4.1 4.1 - - - +
277B ARG* 5.2 6.6 + - - -
285B GLU* 3.3 34.9 - - - +
289B PRO* 4.0 27.8 - - + +
293B ARG* 4.5 8.7 + - - -
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Residues in contact with ASP 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A VAL* 3.5 23.4 - - - +
236A ASN* 3.0 18.4 + - - -
277A ARG* 5.0 7.5 + - - -
282A LEU* 2.9 27.1 + - + +
284A PHE 3.3 0.8 - - - -
285A GLU* 1.3 81.6 - - - +
287A THR* 1.3 68.1 + - - +
288A ILE 3.5 1.1 - - - -
289A PRO* 3.3 5.8 - - - +
290A PHE* 2.9 22.7 + - - +
293A ARG* 4.5 4.9 + - - +
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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