Contacts of the helix formed by residues 223 - 233 (chain R) 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 ARG 223 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219R MET 3.5 5.8 + - - +
220R GLU* 3.1 22.1 + - - +
221R PRO 3.4 0.4 - - - -
222R PHE* 1.3 78.7 - - - +
224R PRO* 1.3 63.3 - - - +
226R ILE* 3.0 23.0 + - - +
227R ASP* 3.6 3.9 + - - +
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Residues in contact with PRO 224 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113R LYS 5.4 1.3 - - - +
116R ASN* 4.5 31.6 - - + +
117R GLN* 4.6 9.2 - - + +
120R TYR* 5.0 7.6 - - + -
220R GLU 4.8 0.8 - - - -
221R PRO 4.8 1.5 - - - +
222R PHE 3.4 1.2 - - - -
223R ARG* 1.3 77.2 - - - +
225R ILE* 1.3 63.0 + - - +
227R ASP* 3.0 12.9 + - + +
228R ARG* 2.9 23.4 + - - +
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Residues in contact with ILE 225 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222R PHE* 3.5 16.0 + - + +
223R ARG 3.1 0.8 + - - -
224R PRO* 1.3 78.0 - - - +
226R ILE* 1.3 60.8 + - - +
228R ARG* 3.7 12.4 + - - +
229R ILE* 3.8 10.4 + - - +
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Residues in contact with ILE 226 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177R LEU* 5.8 5.2 - - - +
180R GLY* 4.7 22.9 - - - -
181R TYR 5.4 0.4 - - - +
222R PHE 4.3 1.7 + - - +
223R ARG* 3.0 12.9 + - - +
225R ILE* 1.3 78.1 - - - +
227R ASP* 1.3 59.1 + - - +
228R ARG 3.2 0.3 + - - -
229R ILE* 3.3 6.5 + - - +
230R VAL* 2.9 29.2 + - - +
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Residues in contact with ASP 227 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160R LEU* 5.4 2.3 - - - +
223R ARG 3.6 3.3 + - - +
224R PRO* 3.0 16.8 + - + +
226R ILE* 1.3 78.2 - - - +
228R ARG* 1.3 58.5 + - - +
230R VAL* 3.8 8.9 - - - +
231R TYR* 2.9 28.6 + - - +
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Residues in contact with ARG 228 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120R TYR* 6.1 5.2 - - + -
224R PRO 2.9 11.2 + - - +
225R ILE* 3.8 12.6 - - - +
226R ILE 3.1 0.4 - - - -
227R ASP* 1.3 73.8 - - - +
229R ILE* 1.3 60.8 + - - +
231R TYR* 3.0 8.6 + - - +
232R GLN* 2.9 27.6 + - - +
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Residues in contact with ILE 229 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225R ILE 3.8 8.3 + - - +
226R ILE* 3.3 7.6 + - - +
228R ARG* 1.3 79.7 - - - +
230R VAL* 1.3 57.3 + - - +
232R GLN* 3.3 6.9 + - - +
233R ASN* 2.9 33.6 + - - +
244R GLU* 5.4 16.2 - - + +
245R LEU* 5.8 4.3 - - + +
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Residues in contact with VAL 230 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173R ILE* 5.4 8.3 - - + +
176R ALA* 5.0 16.8 - - + -
177R LEU* 5.5 6.1 - - + +
226R ILE 2.9 17.7 + - - +
227R ASP* 3.9 8.5 - - - +
229R ILE* 1.3 77.3 - - - +
231R TYR* 1.3 57.0 + - - +
233R ASN* 3.9 2.2 - - - -
234R ARG* 3.0 30.2 + - - +
241R ILE* 6.3 2.9 - - - -
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Residues in contact with TYR 231 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160R LEU* 4.7 23.8 - - + +
227R ASP 2.9 20.1 + - - +
228R ARG* 3.0 7.4 + - - +
230R VAL* 1.3 78.0 - - - +
232R GLN* 1.3 65.1 + - - +
234R ARG* 3.7 13.7 + - - +
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Residues in contact with GLN 232 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228R ARG 2.9 13.4 + - - +
229R ILE* 3.3 8.0 + - - +
231R TYR* 1.3 79.4 - - - +
233R ASN* 1.3 57.8 + - + +
234R ARG 3.3 1.6 + - - -
235R HIS* 4.9 2.3 + - - +
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Residues in contact with ASN 233 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229R ILE 2.9 17.1 + - - +
230R VAL* 3.9 2.9 - - - +
232R GLN* 1.3 75.8 - - + +
234R ARG* 1.3 54.1 + - - +
235R HIS 3.1 3.4 - - - -
236R ASN* 2.8 41.3 + - + +
240R LYS 5.5 0.2 - - - +
241R ILE* 4.9 14.4 - - + +
244R GLU* 4.7 19.5 - - + -
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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