Contacts of the helix formed by residues 260 - 267 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256B THR* 2.8 33.9 + - + +
258B LEU 3.7 0.6 - - - -
259B PHE* 1.3 78.7 - - - +
261B ASP* 1.3 72.0 - - - +
262B ASP 3.5 0.7 - - - -
263B ILE 3.6 1.3 + - - -
264B ARG* 2.9 51.6 + - - +
281B PRO* 3.9 15.1 - - + +
282B LEU 3.2 18.6 - - - +
283B ASP* 2.7 36.3 + - - +
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Residues in contact with ASP 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR* 2.8 28.9 + - - +
257B LYS* 3.6 24.5 + - + +
260B LYS* 1.3 79.4 - - - +
262B ASP* 1.3 55.4 + - - +
264B ARG* 3.0 9.0 + - - +
265B TYR* 2.6 38.6 + - - +
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Residues in contact with ASP 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL 5.1 0.9 - - - +
207B SER* 4.2 5.9 - - - -
208B PRO* 3.8 31.3 - - + +
257B LYS* 2.9 57.6 + - - +
258B LEU* 4.0 19.1 - - - +
260B LYS 3.5 0.2 - - - -
261B ASP* 1.3 75.0 - - - +
263B ILE* 1.3 56.7 + - + +
265B TYR* 3.5 9.9 - - - +
266B LEU* 2.7 36.3 + - - +
362B ARG* 6.2 1.3 - - - +
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Residues in contact with ILE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B LEU 2.8 30.1 - - - +
259B PHE* 3.6 14.6 - - - +
260B LYS 3.6 5.8 + - - +
261B ASP 3.3 0.6 - - - -
262B ASP* 1.3 78.6 - - + +
264B ARG* 1.3 60.7 + - - +
266B LEU* 3.3 12.2 - - + +
267B LEU* 3.2 20.8 + - - +
279B PRO* 3.7 27.8 - - + +
280B VAL 4.1 1.1 - - - -
281B PRO* 3.5 28.7 - - + -
362B ARG* 4.9 13.5 - - - +
365B ILE* 3.8 27.6 - - + -
366B PHE* 4.9 5.8 - - + -
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Residues in contact with ARG 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LYS* 2.9 45.1 + - - +
261B ASP* 3.3 6.3 - - - +
263B ILE* 1.3 75.3 - - - +
265B TYR* 1.3 57.4 + - - +
266B LEU 2.9 4.3 - - - -
267B LEU* 2.8 39.7 + - + +
268B THR* 3.6 4.3 + - - -
281B PRO* 4.4 19.9 - - + +
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Residues in contact with TYR 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B PRO* 3.4 39.5 - - + -
210B ARG* 3.1 37.8 + - + +
217B TRP* 3.5 29.9 - + - -
261B ASP 2.6 20.4 + - - +
262B ASP* 3.6 9.4 - - - +
264B ARG* 1.3 72.6 - - - +
266B LEU* 1.3 58.9 + - - +
268B THR* 3.0 30.1 + - + -
269B MET* 3.7 9.7 - - + +
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B ARG 4.1 2.9 - - - +
177B ASN* 3.2 55.6 - - + +
208B PRO* 3.4 15.9 - - + -
262B ASP 2.7 16.5 + - - +
263B ILE* 3.3 11.4 - - + +
265B TYR* 1.3 75.7 - - - +
267B LEU* 1.3 58.0 + - - +
268B THR 3.0 10.1 + - - -
269B MET* 3.2 31.5 + - + +
272B LEU* 3.9 10.4 - - + +
273B TRP* 4.7 5.3 + - - +
279B PRO* 4.1 13.9 - - + -
362B ARG* 5.7 2.7 - - - +
366B PHE* 4.1 21.3 - - + -
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ILE 3.2 15.3 - - - +
264B ARG* 2.8 24.4 + - + +
266B LEU* 1.3 75.6 - - - +
268B THR* 1.3 62.6 + - - +
269B MET 3.3 2.8 + - - -
270B ASP* 3.9 11.3 + - - +
273B TRP* 4.4 8.3 - - + -
278B PRO* 4.3 12.1 - - + -
279B PRO* 3.9 40.8 - - + +
281B PRO* 4.3 13.0 - - + -
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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