Contacts of the helix formed by residues 228 - 236 (chain D) in PDB entry 1Y8R
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 228 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226D SER* 2.9 8.2 + - - +
227D GLU* 1.3 76.5 - - - +
229D ALA* 1.3 56.3 + - - +
230D LYS 3.0 4.9 - - - -
231D ALA* 3.0 26.9 + - + +
232D ALA* 3.2 13.9 + - + +
235D ARG* 6.1 1.1 - - - +
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Residues in contact with ALA 229 (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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222D VAL* 5.5 2.0 - - + -
223D ASP 3.2 26.7 - - - +
224D TRP* 3.5 23.9 - - + +
226D SER* 3.3 18.8 + - - +
228D LYS* 1.3 79.5 - - - +
230D LYS* 1.3 58.2 + - - +
231D ALA 3.2 0.2 - - - -
232D ALA* 4.1 7.6 - - - +
233D LEU* 3.1 28.6 + - - +
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Residues in contact with LYS 230 (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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224D TRP 3.2 17.7 + - - +
225D SER* 3.3 20.1 + - - +
226D SER 3.0 17.5 + - - +
227D GLU* 3.3 30.6 + - - +
228D LYS 3.0 0.6 - - - -
229D ALA* 1.3 77.7 - - - +
231D ALA* 1.3 60.4 + - - +
233D LEU* 4.2 19.2 - - + +
234D LYS* 4.0 13.7 + - - +
281D GLY 4.7 12.3 - - - -
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Residues in contact with ALA 231 (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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227D GLU* 3.7 5.1 + - - +
228D LYS* 3.0 22.9 + - + +
230D LYS* 1.3 78.2 - - - +
232D ALA* 1.3 66.3 + - - +
233D LEU 3.2 0.9 - - - -
234D LYS* 3.2 15.6 + - - +
235D ARG* 3.2 28.8 - - - +
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Residues in contact with ALA 232 (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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224D TRP* 4.8 5.4 - - + -
228D LYS* 3.2 11.0 + - + +
229D ALA* 4.4 7.0 - - - +
231D ALA* 1.3 76.7 - - - +
233D LEU* 1.3 53.5 + - - +
235D ARG* 2.6 45.1 + - - +
236D THR* 2.7 28.8 + - - +
343D LEU* 6.1 2.5 - - + -
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Residues in contact with LEU 233 (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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224D TRP* 3.3 33.6 - - + -
229D ALA 3.1 21.5 + - - +
230D LYS* 4.2 23.8 - - + +
232D ALA* 1.3 76.0 - - - +
234D LYS* 1.3 62.6 + - - +
235D ARG 3.2 1.0 + - - -
236D THR* 3.2 19.1 + - - +
241D PHE* 3.5 26.4 - - + -
282D ILE* 4.0 20.2 - - + -
286D LEU* 3.6 33.1 - - + +
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Residues in contact with LYS 234 (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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230D LYS 4.0 9.3 + - - +
231D ALA* 3.2 12.4 + - - +
232D ALA 3.1 0.4 - - - -
233D LEU* 1.3 80.9 - - - +
235D ARG* 1.3 61.7 + - + +
236D THR 4.8 1.2 - - - +
286D LEU* 5.9 1.8 - - - -
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Residues in contact with ARG 235 (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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228D LYS* 5.3 1.2 + - - +
231D ALA* 3.2 27.2 - - - +
232D ALA* 2.6 49.9 + - - +
234D LYS* 1.3 76.8 - - + +
236D THR* 1.3 58.1 + - - -
237D THR 3.8 0.5 + - - -
341D GLU* 3.5 0.9 - - - +
426E LYS* 3.0 31.5 + - - +
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Residues in contact with THR 236 (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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224D TRP* 4.2 19.9 - - + -
232D ALA* 2.7 29.8 + - - +
233D LEU* 3.2 16.8 + - - +
234D LYS 4.8 1.6 - - - +
235D ARG* 1.3 75.2 - - - +
237D THR* 1.3 76.9 + - + +
238D SER* 3.6 1.7 + - - -
240D TYR* 4.3 14.8 - - + -
241D PHE* 4.6 9.2 - - + -
286D LEU* 4.9 4.2 - - - +
341D GLU* 3.2 19.9 + - - +
343D LEU* 4.2 15.7 - - + +
426E LYS* 5.1 0.2 + - - -
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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