Contacts of the helix formed by residues 222 - 233 (chain z) 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 z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184z LEU* 5.9 6.5 - - + -
219z MET* 3.4 15.0 + - + +
220z GLU 3.2 1.2 - - - -
221z PRO* 1.3 76.0 - - + +
223z ARG* 1.3 62.6 + - - +
224z PRO 3.3 2.9 - - - -
225z ILE* 3.3 23.4 + - + +
226z ILE* 3.9 3.3 + - - +
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Residues in contact with ARG 223 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219z MET 3.9 5.4 + - - +
220z GLU* 3.5 14.6 + - - +
221z PRO 3.4 1.8 - - - -
222z PHE* 1.3 76.8 - - - +
224z PRO* 1.3 58.7 - - - +
226z ILE* 2.9 25.5 + - - +
227z ASP* 2.9 11.8 + - - +
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Residues in contact with PRO 224 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113z LYS 5.7 0.2 - - - +
116z ASN* 4.4 30.3 - - + +
117z GLN* 4.8 6.3 - - + +
120z TYR* 4.7 14.0 - - + +
220z GLU 5.2 0.2 - - - -
221z PRO 4.5 3.0 - - - +
222z PHE 3.3 0.8 - - - -
223z ARG* 1.3 77.4 - - - +
225z ILE* 1.3 57.0 + - - +
227z ASP* 3.5 11.7 - - + +
228z ARG* 2.9 29.1 + - - +
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Residues in contact with ILE 225 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221z PRO 5.5 0.2 + - - -
222z PHE* 3.3 16.9 + - + +
223z ARG 3.1 1.0 - - - -
224z PRO* 1.3 78.6 - - - +
226z ILE* 1.3 62.8 + - - +
228z ARG* 3.5 10.8 + - - +
229z ILE* 3.7 12.0 + - - +
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Residues in contact with ILE 226 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176z ALA 6.1 0.4 - - - +
177z LEU* 5.9 4.7 - - - +
180z GLY* 5.1 18.6 - - - -
181z TYR 5.7 0.2 - - - +
222z PHE 3.9 1.9 + - - +
223z ARG* 2.9 13.1 + - - +
225z ILE* 1.3 77.1 - - - +
227z ASP* 1.3 60.7 + - - +
229z ILE* 3.4 4.6 + - - +
230z VAL* 2.9 31.6 + - - +
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Residues in contact with ASP 227 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223z ARG 2.9 13.1 + - - +
224z PRO* 3.2 14.6 + - + +
226z ILE* 1.3 76.4 - - - +
228z ARG* 1.3 56.1 + - - +
230z VAL* 3.8 6.5 - - - +
231z TYR* 2.9 29.8 + - - +
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Residues in contact with ARG 228 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120z TYR* 6.4 1.6 - - + -
224z PRO 2.9 15.4 + - - +
225z ILE* 3.8 8.7 - - - +
226z ILE 3.2 0.4 - - - -
227z ASP* 1.3 73.9 - - - +
229z ILE* 1.3 60.2 + - - +
231z TYR* 3.0 7.0 + - - +
232z GLN* 2.9 28.5 + - - +
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Residues in contact with ILE 229 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225z ILE 3.7 8.3 + - - +
226z ILE* 3.4 6.3 + - - +
228z ARG* 1.3 78.4 - - - +
230z VAL* 1.3 57.7 + - - +
232z GLN* 3.9 6.2 - - - +
233z ASN* 2.9 34.5 + - - +
244z GLU* 4.9 22.0 - - + +
245z LEU* 5.5 2.7 - - - +
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Residues in contact with VAL 230 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173z ILE* 5.5 7.2 - - + +
176z ALA* 5.3 13.2 - - + -
177z LEU* 5.7 6.7 - - + +
226z ILE 2.9 19.5 + - - +
227z ASP* 3.9 8.3 - - - +
229z ILE* 1.3 77.3 - - - +
231z TYR* 1.3 57.6 + - - +
233z ASN* 5.2 1.3 - - - -
234z ARG* 3.1 30.8 + - - +
241z ILE* 6.3 2.5 - - - -
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Residues in contact with TYR 231 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160z LEU* 5.5 10.1 - - + -
227z ASP 2.9 19.2 + - - +
228z ARG* 3.0 7.2 + - - +
230z VAL* 1.3 77.9 - - - +
232z GLN* 1.3 62.7 + - - +
234z ARG* 3.9 12.6 + - - +
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Residues in contact with GLN 232 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228z ARG 2.9 14.6 + - - +
229z ILE* 3.3 6.9 + - - +
231z TYR* 1.3 80.9 - - - +
233z ASN* 1.3 59.0 + - + +
234z ARG 3.3 1.1 + - - -
235z HIS* 4.6 5.0 + - - +
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Residues in contact with ASN 233 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229z ILE 2.9 16.6 + - - +
230z VAL* 3.9 1.8 - - - -
232z GLN* 1.3 74.5 - - + +
234z ARG* 1.3 56.3 + - - +
235z HIS 3.1 4.0 - - - -
236z ASN* 2.8 43.0 + - + +
240z LYS 5.3 0.4 - - - +
241z ILE* 4.4 25.5 - - + +
244z GLU* 4.8 12.1 - - + -
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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