Contacts of the helix formed by residues 279 - 291 (chain F) in PDB entry 6IWQ
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 GLY 279 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247F ASP* 2.7 22.4 + - - -
277F ARG* 3.3 5.3 + - - +
278F GLU* 1.3 73.7 - - - +
280F LEU* 1.3 60.0 + - - -
281F ILE 3.5 2.2 - - - -
282F GLN 4.2 0.2 - - - -
283F ALA* 2.9 31.4 + - - +
411F ILE* 3.7 28.3 - - - -
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Residues in contact with LEU 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F VAL* 4.7 20.4 - - + +
247F ASP* 4.3 0.6 + - - -
277F ARG* 5.6 1.7 - - - +
279F GLY* 1.3 69.0 - - - -
281F ILE* 1.3 66.6 + - - +
283F ALA* 3.6 5.8 + - - +
284F ARG* 3.2 55.3 + - - +
301F ASP* 5.2 6.5 - - - +
411F ILE* 3.7 17.3 - - + +
412F TRP* 4.2 26.7 - - + +
415F GLU* 4.6 8.1 - - - +
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Residues in contact with ILE 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F GLY 3.5 0.4 - - - -
280F LEU* 1.3 77.9 - - + +
282F GLN* 1.3 81.3 + - + +
284F ARG* 3.2 19.6 + - - +
285F SER* 3.3 8.5 + - - -
405F TYR* 3.7 23.5 - - + -
409F LEU* 3.5 22.4 - - + +
410F GLN 3.4 26.7 - - - +
411F ILE* 4.8 2.2 - - - +
412F TRP* 4.0 8.3 - - - +
413F GLY* 3.4 17.7 - - - +
415F GLU* 3.6 38.6 - - + +
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Residues in contact with GLN 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F ARG* 6.2 0.4 - - - +
278F GLU* 3.6 31.9 - - + +
279F GLY 3.7 1.8 + - - -
280F LEU 3.5 0.2 - - - -
281F ILE* 1.3 89.6 - - + +
283F ALA* 1.3 64.9 + - - +
285F SER* 3.2 17.6 + - - +
286F ILE* 3.1 29.8 + - + +
405F TYR 4.6 1.5 + - - +
406F ASP 3.4 21.0 + - - -
407F PRO* 3.6 22.3 - - - +
409F LEU 3.0 27.2 + - - +
410F GLN* 5.9 1.1 - - - -
411F ILE 6.3 0.2 - - - +
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Residues in contact with ALA 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214F VAL* 3.5 31.2 - - + +
245F ILE* 3.9 13.7 - - + +
247F ASP* 4.0 13.2 - - - +
274F ASN* 4.7 0.2 - - - +
278F GLU* 4.4 1.0 - - - +
279F GLY 2.9 22.4 + - - +
280F LEU 3.6 3.8 - - - +
281F ILE 3.2 0.2 - - - -
282F GLN* 1.3 78.4 - - - +
284F ARG* 1.3 60.5 + - - +
286F ILE* 3.3 14.2 + - - +
287F GLY* 3.1 18.4 + - - -
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Residues in contact with ARG 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F VAL* 4.0 16.1 - - + +
280F LEU* 3.2 44.5 + - + +
281F ILE* 3.2 11.0 + - - +
283F ALA* 1.3 80.4 - - - +
285F SER* 1.3 61.7 + - - +
287F GLY* 3.2 8.6 + - - -
288F ALA 3.2 1.9 + - - -
299F TYR* 3.0 52.8 + - + +
301F ASP* 4.6 5.7 + - - -
389F GLY 3.4 24.1 + - - -
390F GLY* 3.8 19.8 + - - -
392F PHE* 4.6 2.4 - - - -
405F TYR* 3.8 23.0 + - + -
415F GLU* 3.4 36.6 + - - +
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Residues in contact with SER 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281F ILE 3.3 3.2 + - - -
282F GLN* 3.2 25.1 + - - -
284F ARG* 1.3 76.3 - - - +
286F ILE* 1.3 65.6 + - - +
288F ALA* 3.2 13.1 + - - +
289F GLN* 3.2 24.2 + - - +
299F TYR* 5.0 0.2 - - - -
399F PHE* 5.8 0.4 - - - -
404F LEU* 4.0 17.4 - - - +
405F TYR* 3.6 36.5 + - - +
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Residues in contact with ILE 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F ILE* 5.0 4.9 - - + -
274F ASN* 3.1 38.4 - - - +
278F GLU* 3.6 22.0 - - + +
282F GLN* 3.1 16.8 + - + +
283F ALA* 3.6 7.6 - - - +
285F SER* 1.3 75.9 - - - +
287F GLY* 1.3 57.5 + - - +
289F GLN* 3.2 16.9 + - + +
290F LYS* 2.8 65.5 + - + +
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Residues in contact with GLY 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F VAL* 4.1 14.9 - - - +
243F VAL* 4.7 0.7 - - - +
245F ILE* 3.7 26.7 - - - -
283F ALA 3.1 11.2 + - - -
284F ARG* 3.2 5.1 + - - -
285F SER 3.1 0.8 - - - -
286F ILE* 1.3 78.4 - - - +
288F ALA* 1.3 60.7 + - - +
290F LYS* 3.1 9.9 + - - +
291F ALA* 3.2 19.2 + - - +
299F TYR* 4.7 0.2 - - - -
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Residues in contact with ALA 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284F ARG 3.2 4.4 + - - +
285F SER 3.2 10.2 + - - +
287F GLY* 1.3 77.2 - - - +
289F GLN* 1.3 61.3 + - - +
291F ALA 3.8 3.1 + - - +
297F LEU* 3.6 21.8 - - + -
299F TYR* 3.2 22.3 + - - +
396F ARG* 3.3 26.9 + - - -
400F PHE* 3.7 6.3 - - + -
404F LEU* 3.7 23.3 - - + -
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Residues in contact with GLN 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285F SER* 3.2 16.3 - - - +
286F ILE* 3.2 23.1 + - + +
288F ALA* 1.3 79.1 - - - +
290F LYS* 1.3 63.9 + - + +
291F ALA 3.1 2.3 + - - -
292F LYS* 3.5 23.6 - - - +
396F ARG* 4.2 2.3 + - - +
400F PHE* 4.2 19.8 - - + -
404F LEU* 4.4 13.6 - - + +
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Residues in contact with LYS 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F GLU* 4.7 1.7 - - - +
243F VAL* 4.3 7.2 - - + +
245F ILE* 5.1 1.6 - - + -
272F PHE* 3.2 59.0 - - + +
273F ARG 4.3 11.3 + - - -
274F ASN* 4.7 5.8 + - - -
286F ILE* 2.8 51.4 + - + +
287F GLY* 3.1 6.8 + - - +
289F GLN* 1.3 75.8 - - + +
291F ALA* 1.3 57.2 + - - +
292F LYS* 3.7 8.0 + - - +
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Residues in contact with ALA 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F SER* 4.0 15.4 + - - -
212F VAL* 4.1 6.7 - - + -
241F GLU* 3.2 22.6 - - - +
243F VAL* 3.5 19.5 - - + -
287F GLY 3.2 14.5 + - - +
288F ALA 3.8 1.4 + - - +
289F GLN 3.1 2.4 - - - -
290F LYS* 1.3 79.0 - - - +
292F LYS* 1.3 59.1 + - - +
297F LEU* 4.4 3.3 - - + +
396F ARG* 3.1 24.4 + - - -
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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