Contacts of the helix formed by residues 260 - 266 (chain D) in PDB entry 1Y8Q
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 LYS 260 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D THR* 3.1 33.3 + - - +
258D LEU 3.6 2.0 - - - -
259D PHE* 1.3 76.5 - - - +
261D ASP* 1.3 65.9 + - - +
262D ASP 3.0 0.9 - - - -
263D ILE* 2.9 1.9 + - - +
264D ARG* 2.6 66.2 + - + +
281D PRO* 4.0 17.3 - - + -
282D LEU 3.0 27.8 - - - +
283D ASP* 2.9 31.5 + - + +
284D TRP 5.3 0.2 - - - +
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Residues in contact with ASP 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D THR* 3.0 25.4 + - - +
257D LYS* 3.6 25.1 - - + +
260D LYS* 1.3 82.2 - - - +
262D ASP* 1.3 59.2 + - - +
264D ARG* 3.9 11.6 + - - +
265D TYR* 3.3 24.9 + - - +
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Residues in contact with ASP 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D SER* 4.4 4.8 + - - -
208D PRO* 3.4 34.3 - - + +
257D LYS* 2.7 61.2 + - - +
258D LEU* 3.4 23.2 - - - +
260D LYS 3.0 0.4 - - - -
261D ASP* 1.3 76.6 - - - +
263D ILE* 1.3 64.0 + - + +
264D ARG 3.2 0.4 - - - -
265D TYR* 3.5 5.1 + - - +
266D LEU* 2.9 28.1 + - - +
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Residues in contact with ILE 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D LEU 4.2 7.0 - - - +
259D PHE* 3.6 25.4 - - - +
260D LYS 2.9 4.1 + - - +
262D ASP* 1.3 74.8 - - + +
264D ARG* 1.3 68.4 + - - +
266D LEU* 3.1 20.9 + - + +
267D LEU* 3.3 10.4 - - - +
279D PRO* 3.5 21.8 - - + +
280D VAL 3.9 0.9 - - - -
281D PRO* 3.2 36.3 - - + -
362D ARG* 5.4 7.0 - - - +
365D ILE* 3.6 31.6 - - + -
366D PHE* 4.2 15.5 - - + -
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Residues in contact with ARG 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LYS* 2.6 57.8 + - + +
261D ASP* 3.9 11.4 + - - +
263D ILE* 1.3 72.8 - - - +
265D TYR* 1.3 56.9 + - - +
267D LEU* 2.8 35.0 + - - +
268D THR* 3.9 3.6 + - - -
281D PRO* 3.8 20.9 - - + +
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Residues in contact with TYR 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D PRO* 4.0 28.7 - - + -
210D ARG* 2.7 57.1 + - + -
261D ASP 3.3 16.8 + - - +
262D ASP* 3.7 7.4 - - - +
263D ILE 3.3 0.2 - - - -
264D ARG* 1.3 78.8 - - - +
266D LEU* 1.3 58.2 + - - +
267D LEU 3.0 1.1 - - - -
268D THR* 3.3 26.8 + - + -
269D MET* 3.1 18.7 - - + +
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Residues in contact with LEU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ARG 4.3 4.9 - - - +
177D ASN* 3.2 54.1 - - + +
208D PRO* 3.5 19.3 - - + -
262D ASP 2.9 16.4 + - - +
263D ILE* 3.3 14.6 - - + +
264D ARG 3.0 0.6 - - - -
265D TYR* 1.3 77.1 - - - +
267D LEU* 1.3 52.7 + - - +
268D THR 3.3 0.9 - - - -
269D MET* 3.5 18.1 + - + +
273D TRP* 2.6 44.3 + - + -
279D PRO* 4.1 5.4 - - + -
362D ARG* 5.1 2.2 - - - +
366D PHE* 3.7 23.6 - - + -
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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