Contacts of the helix formed by residues 222 - 233 (chain p) in PDB entry 6QXT
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 PHE 222 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184p LEU* 5.9 7.0 - - + -
218p ILE 5.5 0.4 + - - +
219p MET* 3.4 14.6 + - + +
220p GLU 3.2 1.0 - - - -
221p PRO* 1.3 74.8 - - - +
223p ARG* 1.3 64.0 + - - +
224p PRO 3.3 2.5 - - - -
225p ILE* 3.3 22.7 + - + +
226p ILE* 3.9 3.5 + - - +
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Residues in contact with ARG 223 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219p MET 3.9 5.5 + - - +
220p GLU* 3.5 14.3 + - - +
221p PRO 3.4 1.6 - - - -
222p PHE* 1.3 77.7 - - - +
224p PRO* 1.3 58.4 - - - +
226p ILE* 2.9 25.4 + - - +
227p ASP* 2.9 12.1 + - - +
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Residues in contact with PRO 224 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113p LYS 5.7 0.7 - - - +
116p ASN* 4.4 30.1 - - + +
117p GLN* 4.8 6.1 - - + +
120p TYR* 4.7 14.0 - - + +
220p GLU 5.2 0.2 - - - -
221p PRO 4.5 3.3 - - - +
222p PHE 3.3 0.4 - - - -
223p ARG* 1.3 77.8 - - - +
225p ILE* 1.3 57.9 + - - +
227p ASP* 3.5 11.6 - - + +
228p ARG* 2.9 29.1 + - - +
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Residues in contact with ILE 225 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222p PHE* 3.3 18.0 + - + +
223p ARG 3.1 0.4 + - - -
224p PRO* 1.3 79.4 - - - +
226p ILE* 1.3 61.1 + - - +
228p ARG* 3.5 10.9 + - - +
229p ILE* 3.7 11.8 + - - +
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Residues in contact with ILE 226 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176p ALA 6.1 0.4 - - - +
177p LEU* 5.9 5.2 - - - +
180p GLY* 5.1 18.8 - - - -
181p TYR 5.7 0.4 - - - +
222p PHE 3.9 2.7 + - - +
223p ARG* 2.9 13.4 + - - +
225p ILE* 1.3 75.4 - - - +
227p ASP* 1.3 61.6 + - - +
229p ILE* 3.4 4.3 + - - +
230p VAL* 2.9 31.6 + - - +
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Residues in contact with ASP 227 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223p ARG 2.9 11.9 + - - +
224p PRO* 3.2 15.2 + - + +
226p ILE* 1.3 76.8 - - - +
228p ARG* 1.3 56.3 + - - +
230p VAL* 3.8 6.8 - - - +
231p TYR* 2.9 30.3 + - - +
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Residues in contact with ARG 228 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120p TYR* 6.4 1.8 - - + -
224p PRO 2.9 15.0 + - - +
225p ILE* 3.8 7.6 - - - +
226p ILE 3.2 0.4 - - - -
227p ASP* 1.3 74.1 - - - +
229p ILE* 1.3 61.5 + - - +
231p TYR* 3.0 7.9 + - - +
232p GLN* 2.9 28.3 + - - +
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Residues in contact with ILE 229 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225p ILE 3.7 7.8 + - - +
226p ILE* 3.4 7.0 + - - +
228p ARG* 1.3 77.6 - - - +
230p VAL* 1.3 57.4 + - - +
232p GLN* 3.9 6.4 - - - +
233p ASN* 2.9 34.5 + - - +
244p GLU* 4.9 22.0 - - + +
245p LEU* 5.5 3.4 - - - +
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Residues in contact with VAL 230 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173p ILE* 5.5 6.7 - - + +
176p ALA* 5.3 13.5 - - + -
177p LEU* 5.7 7.2 - - + +
226p ILE 2.9 19.6 + - - +
227p ASP* 3.9 7.9 - - - +
229p ILE* 1.3 75.9 - - - +
231p TYR* 1.3 58.2 + - - +
233p ASN* 3.9 1.7 - - - -
234p ARG* 3.1 30.7 + - - +
241p ILE* 6.3 2.7 - - - -
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Residues in contact with TYR 231 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160p LEU* 5.5 10.3 - - + -
227p ASP 2.9 19.0 + - - +
228p ARG* 3.0 7.8 + - - +
230p VAL* 1.3 78.5 - - - +
232p GLN* 1.3 60.8 + - - +
234p ARG* 3.9 12.4 + - - +
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Residues in contact with GLN 232 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228p ARG 2.9 14.1 + - - +
229p ILE* 3.3 7.2 + - - +
231p TYR* 1.3 80.3 - - - +
233p ASN* 1.3 59.1 + - + +
234p ARG 3.3 1.6 + - - -
235p HIS* 4.6 5.2 + - - +
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Residues in contact with ASN 233 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229p ILE 2.9 16.0 + - - +
230p VAL* 3.9 2.0 - - - +
232p GLN* 1.3 74.9 - - + +
234p ARG* 1.3 55.7 + - - +
235p HIS 3.1 3.8 - - - -
236p ASN* 2.8 42.5 + - + +
240p LYS 5.3 0.7 - - - +
241p ILE* 4.4 25.5 - - + +
244p GLU* 4.8 12.8 - - + -
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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