Contacts of the helix formed by residues 274 - 283 (chain F) in PDB entry 4R8A
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 ASP 274 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269F CYS* 2.9 25.2 + - + +
270F GLU 4.4 0.2 + - - -
272F GLN* 3.1 6.9 + - + +
273F ARG* 1.3 76.2 - - - +
275F PHE* 1.3 62.2 + - - +
276F ASP* 3.8 7.8 + - - +
277F LEU* 3.2 39.9 + - - +
278F ALA* 3.2 15.8 + - - +
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Residues in contact with PHE 275 (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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270F GLU* 3.3 37.9 - - + -
273F ARG* 3.4 54.5 + - + -
274F ASP* 1.3 71.0 - - - +
276F ASP* 1.3 61.5 + - - +
278F ALA* 3.7 5.1 - - - +
279F GLN* 2.9 30.8 + - - +
297F SER* 3.5 24.2 - - - +
300F ARG* 3.5 61.9 - - + -
301F GLY* 4.2 8.3 - - - +
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Residues in contact with ASP 276 (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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274F ASP* 3.3 7.5 + - - +
275F PHE* 1.3 80.5 - - - +
277F LEU* 1.3 59.6 + - - +
279F GLN* 3.2 20.7 - - - +
280F ARG* 3.5 8.7 + - - +
301F GLY* 4.7 9.4 - - - +
303F ARG* 3.3 41.4 + - - +
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Residues in contact with LEU 277 (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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237F LEU* 5.3 6.5 - - + -
241F LEU* 4.7 10.5 - - + -
269F CYS* 3.8 18.6 - - - -
274F ASP* 3.2 28.8 + - - +
275F PHE 3.3 0.2 - - - -
276F ASP* 1.3 76.8 - - - +
278F ALA* 1.3 66.9 + - - +
279F GLN 3.2 0.4 - - - -
280F ARG* 3.2 15.9 + - + +
281F LEU* 2.9 45.4 + - + +
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Residues in contact with ALA 278 (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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266F ALA* 3.4 27.5 - - - +
269F CYS* 3.8 8.0 - - + +
270F GLU* 3.7 18.8 - - + +
274F ASP 3.2 15.7 + - - +
275F PHE* 3.7 7.0 - - - +
276F ASP 3.4 0.2 - - - -
277F LEU* 1.3 80.3 - - - +
279F GLN* 1.3 56.7 + - - +
281F LEU* 3.3 0.9 + - - -
282F TYR* 2.9 38.3 + - + -
297F SER* 4.1 6.1 - - - +
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Residues in contact with GLN 279 (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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275F PHE 2.9 19.0 + - - +
276F ASP* 3.2 12.1 - - - +
278F ALA* 1.3 75.8 - - - +
280F ARG* 1.3 82.8 + - - +
281F LEU 3.1 1.4 + - - -
282F TYR* 3.1 14.5 + - - +
283F ARG* 3.1 57.2 + - + +
294F ALA 4.1 5.8 - - - +
297F SER* 4.1 14.7 - - - -
298F LEU* 3.5 38.4 - - + +
303F ARG* 3.5 16.7 + - - +
306F GLU* 5.7 0.4 + - - -
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Residues in contact with ARG 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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276F ASP 3.5 11.7 + - - +
277F LEU* 3.2 18.9 + - + +
279F GLN* 1.3 92.7 + - - +
281F LEU* 1.3 61.2 + - + +
283F ARG* 3.8 5.4 + - - +
284F GLN* 3.3 36.4 + - - +
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Residues in contact with LEU 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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237F LEU* 4.2 4.7 - - + -
241F LEU* 3.7 23.8 - - + -
262F LEU* 3.9 31.1 - - + +
265F PHE* 3.9 25.4 - - + -
266F ALA* 3.6 17.0 - - + +
269F CYS* 3.9 17.9 - - - -
277F LEU* 2.9 35.2 + - + +
280F ARG* 1.3 75.8 - - + +
282F TYR* 1.3 64.8 + - - +
283F ARG 3.1 2.0 - - - -
284F GLN* 3.0 28.2 + - - +
285F SER* 3.4 10.7 + - - -
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Residues in contact with TYR 282 (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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262F LEU 5.6 0.2 - - - -
263F PHE* 3.7 35.7 - + - -
266F ALA* 3.5 26.7 - - + +
267F GLN* 3.3 23.7 - - - +
270F GLU* 2.6 29.3 + - - -
278F ALA* 2.9 26.4 + - + +
279F GLN 3.1 4.7 + - - +
281F LEU* 1.3 76.2 - - - +
283F ARG* 1.3 57.7 + - - +
285F SER* 3.2 24.5 + - - +
290F ALA* 3.4 29.4 - - - +
291F ARG* 4.5 1.0 + - - -
293F ARG* 3.4 36.5 + - + +
294F ALA* 3.7 7.9 - - + -
297F SER* 3.5 10.5 - - - -
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Residues in contact with ARG 283 (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 GLN* 3.1 44.3 - - - +
280F ARG* 4.1 6.1 - - - +
281F LEU 3.1 1.0 - - - -
282F TYR* 1.3 73.1 - - - +
284F GLN* 1.3 60.3 + - - +
285F SER 3.1 10.0 - - - +
291F ARG* 6.0 1.6 - - - +
294F ALA* 3.7 11.0 - - + -
298F LEU* 4.9 6.3 - - - +
306F GLU* 5.8 3.2 + - - +
310F LEU* 3.7 45.8 - - - +
313F GLU* 5.6 0.2 + - - -
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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