Contacts of the helix formed by residues 269 - 283 (chain R) in PDB entry 6QX2
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 ASN 269 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113R MET 3.7 5.1 + - - -
114R ASP 3.1 25.0 + - - +
115R GLY* 3.3 16.8 - - - -
267R GLN 3.9 2.8 + - - +
268R VAL* 1.3 73.4 - - - +
270R LYS* 1.3 57.1 + - - +
271R ALA* 3.0 7.4 + - - +
272R ARG* 3.0 58.3 + - + +
273R MET* 2.9 30.3 + - - +
4V C 4.5 8.1 + - - +
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Residues in contact with LYS 270 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113R MET* 3.1 22.0 + - + +
114R ASP* 3.4 17.7 - - - +
264R ILE* 3.9 20.6 - - + -
268R VAL 3.5 3.6 + - - -
269R ASN* 1.3 69.5 - - - +
271R ALA* 1.3 63.7 + - - +
273R MET* 3.2 10.1 + - + +
274R ILE* 3.0 37.6 + - + +
294R ASP* 3.9 10.3 - - - +
296R THR* 3.8 27.8 - - + +
302R VAL* 4.4 15.9 - - + -
304R VAL* 4.4 11.2 - - + -
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Residues in contact with ALA 271 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114R ASP* 3.0 36.3 + - + +
269R ASN* 3.0 9.0 + - - +
270R LYS* 1.3 74.1 - - - +
272R ARG* 1.3 61.0 + - - +
274R ILE* 3.5 10.0 + - - +
275R GLU* 3.2 22.1 + - - +
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Residues in contact with ARG 272 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269R ASN* 3.0 40.1 + - + +
271R ALA* 1.3 73.8 - - - +
273R MET* 1.3 59.2 + - - +
275R GLU* 3.1 9.8 + - + +
276R LYS* 2.9 40.2 + - + +
326R PRO* 6.4 0.2 - - + -
3V G 3.3 57.1 + - - +
4V C 3.2 26.3 + - - -
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Residues in contact with MET 273 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245R SER* 4.6 0.7 - - - -
261R VAL* 5.1 0.9 - - + -
264R ILE* 4.2 26.7 - - + -
268R VAL* 4.1 12.1 - - + -
269R ASN 2.9 18.3 + - - +
270R LYS* 3.5 6.5 - - + +
272R ARG* 1.3 74.9 - - - +
274R ILE* 1.3 74.3 + - + +
276R LYS* 3.4 5.7 + - - +
277R ILE* 3.3 31.6 + - + +
304R VAL* 4.8 12.8 - - + -
326R PRO* 4.1 35.1 - - + +
327R LEU* 3.5 43.1 - - + +
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Residues in contact with ILE 274 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270R LYS* 3.0 27.7 + - + +
271R ALA* 3.7 9.9 - - - +
273R MET* 1.3 78.1 - - + +
275R GLU* 1.3 62.6 + - - +
277R ILE* 3.0 11.4 + - + +
278R ALA* 2.9 27.3 + - + +
292R LEU* 3.5 21.7 - - + +
293R ARG 6.2 0.2 - - - -
294R ASP* 3.6 43.5 - - + +
304R VAL* 3.9 25.1 - - + -
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Residues in contact with GLU 275 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271R ALA 3.2 13.5 + - - +
272R ARG* 3.1 13.1 + - + +
274R ILE* 1.3 78.1 - - - +
276R LYS* 1.3 55.6 + - - +
278R ALA* 3.6 10.9 - - - +
279R GLU* 2.8 45.4 + - + +
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Residues in contact with LYS 276 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272R ARG* 2.9 28.3 + - + +
273R MET 3.6 8.7 - - - +
275R GLU* 1.3 75.1 - - - +
277R ILE* 1.3 57.0 + - - +
279R GLU* 3.4 18.4 + - - +
280R LEU* 3.0 33.2 + - + +
324R GLN 5.8 0.9 - - - +
325R THR* 4.6 5.8 - - + -
326R PRO* 3.8 34.8 - - + -
3V G 5.6 4.0 - - - +
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Residues in contact with ILE 277 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273R MET* 3.3 34.7 + - + +
274R ILE* 3.0 12.0 + - + +
276R LYS* 1.3 72.7 - - - +
278R ALA* 1.3 67.4 + - - +
280R LEU* 3.2 6.7 + - - +
281R VAL* 3.1 24.5 + - + +
289R ILE* 4.5 12.6 - - + -
292R LEU* 3.7 25.6 - - + -
304R VAL* 5.5 1.8 - - + -
306R ILE* 4.5 13.2 - - + -
321R LEU* 4.0 22.4 - - + -
325R THR* 3.7 23.6 - - + +
327R LEU* 4.4 13.5 - - + -
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Residues in contact with ALA 278 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274R ILE* 2.9 13.4 + - + +
275R GLU* 3.6 20.0 - - - +
277R ILE* 1.3 75.1 - - - +
279R GLU* 1.3 51.3 - - - +
281R VAL* 3.3 7.3 + - - +
282R ARG* 2.8 36.6 + - - +
292R LEU* 3.6 17.6 - - + +
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Residues in contact with GLU 279 (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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275R GLU* 2.8 28.8 + - + +
276R LYS* 3.5 21.0 - - - +
278R ALA* 1.3 74.0 - - - +
280R LEU* 1.3 63.6 + - - +
282R ARG* 3.8 6.7 - - + +
283R ASP* 3.0 52.9 + - - +
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Residues in contact with LEU 280 (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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276R LYS 3.0 17.1 + - - +
277R ILE* 3.2 8.9 + - - +
279R GLU* 1.3 79.0 - - + +
281R VAL* 1.3 59.1 + - - +
283R ASP* 3.6 1.7 + - + -
284R LYS 3.3 2.8 + - - -
285R LYS* 2.8 51.1 + - + -
286R ILE* 3.6 22.5 + - + -
321R LEU* 5.1 1.3 - - + -
324R GLN* 3.4 46.2 - - + +
325R THR* 3.8 18.6 - - + -
413t GLN* 5.6 8.5 - - + -
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Residues in contact with VAL 281 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277R ILE* 3.1 15.3 + - + +
278R ALA* 3.6 10.3 - - - +
280R LEU* 1.3 72.8 - - - +
282R ARG* 1.3 66.2 + - - +
284R LYS* 2.9 15.9 + - - +
286R ILE* 3.9 20.6 - - + +
289R ILE* 3.8 50.9 - - + +
292R LEU* 6.0 1.1 - - + -
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Residues in contact with ARG 282 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278R ALA 2.8 19.9 + - - +
279R GLU* 3.8 9.6 - - + +
281R VAL* 1.3 73.5 - - - +
283R ASP* 1.3 65.0 + - - +
284R LYS* 3.4 4.0 + - - +
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Residues in contact with ASP 283 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279R GLU* 3.0 38.7 + - - +
280R LEU* 4.2 2.5 - - - +
281R VAL 3.2 0.2 - - - -
282R ARG* 1.3 82.1 - - - +
284R LYS* 1.3 67.3 - - - +
285R LYS* 2.9 12.2 + - + +
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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