Contacts of the helix formed by residues 280 - 288 (chain F) in PDB entry 2QC8
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 280 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276F LYS 4.1 2.7 + - - +
277F LEU 3.1 9.9 + - - +
279F LYS* 1.3 83.6 - - - +
281F HIS* 1.3 65.6 + - - +
282F GLN 3.3 2.2 - - - +
283F TYR* 3.3 55.7 - - + +
284F HIS* 3.2 30.8 + - + -
357F ARG* 4.3 3.6 - - - +
358F THR* 3.1 31.0 + - + -
363F GLU* 3.1 50.0 + - - +
364F THR* 3.7 10.9 + - - +
365F GLY* 3.6 30.5 + - - +
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Residues in contact with HIS 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F LEU 3.5 2.7 + - - -
278F SER 4.5 4.3 - - - +
279F LYS 3.7 2.0 - - - -
280F ARG* 1.3 80.4 - - - +
282F GLN* 1.3 74.5 + - + +
284F HIS* 3.2 3.5 + - - +
285F ILE* 3.0 35.3 + - + +
300F LEU* 6.1 0.2 - - + -
307F SER* 5.8 0.7 - - - -
308F ASN 4.7 1.6 - - - -
309F ILE* 2.8 31.7 + - - -
310F ASN* 4.2 13.0 - - - -
311F ASP 3.9 18.2 + - - -
312F PHE* 3.7 25.2 - - + -
322F SER* 4.7 0.4 - - - -
341F ARG* 2.9 47.8 + - + +
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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
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280F ARG* 3.3 0.8 - - - +
281F HIS* 1.3 87.0 - - + +
283F TYR* 1.3 65.3 + - - +
285F ILE* 3.4 24.5 + - - +
286F ARG* 3.2 42.7 + - - +
309F ILE* 4.6 5.1 + - - +
310F ASN* 5.8 3.2 + - - +
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Residues in contact with TYR 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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280F ARG* 3.3 57.0 + - + +
281F HIS 3.3 1.0 - - - -
282F GLN* 1.3 78.5 - - - +
284F HIS* 1.3 73.3 + + - +
286F ARG* 3.5 29.0 + - - +
287F ALA* 3.2 25.3 + - + +
354F ALA* 4.1 23.5 - - + -
357F ARG* 3.7 21.2 + - - -
358F THR* 4.7 0.4 - - - -
363F GLU* 4.8 1.1 + - - -
365F GLY 5.7 4.0 - - - +
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Residues in contact with HIS 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F LEU* 3.1 27.8 - - + +
280F ARG* 3.2 21.8 - - + +
281F HIS 3.2 8.7 + - - +
282F GLN 3.2 0.4 - - - -
283F TYR* 1.3 85.6 - + - +
285F ILE* 1.3 66.8 + - - +
286F ARG 3.1 1.3 - - - -
287F ALA* 2.9 14.3 + - - +
288F TYR* 2.8 56.3 + - + -
341F ARG* 3.8 13.0 + - - +
354F ALA* 3.6 28.3 + - + +
355F LEU* 3.9 4.3 - - + -
358F THR* 2.7 25.6 + - - -
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Residues in contact with ILE 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 HIS* 3.0 48.7 + - + +
282F GLN* 3.7 18.8 - - - +
284F HIS* 1.3 74.9 - - - +
286F ARG* 1.3 63.9 + - + +
288F TYR* 3.2 19.5 + - + +
289F ASP* 4.0 2.1 + - - +
292F GLY 4.7 1.1 - - - +
293F GLY* 3.9 28.2 - - - -
296F ASN* 5.1 4.0 + - + +
300F LEU* 4.1 25.6 - - + -
309F ILE* 4.2 22.7 - - + +
341F ARG* 4.2 14.8 - - + +
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Residues in contact with ARG 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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282F GLN* 3.2 31.7 + - - +
283F TYR* 3.6 37.5 + - - +
284F HIS 3.1 1.0 - - - -
285F ILE* 1.3 79.1 - - + +
287F ALA* 1.3 60.4 + - - +
288F TYR 3.4 0.9 + - - -
289F ASP 3.5 14.6 - - - +
292F GLY* 3.5 32.6 - - - +
365F GLY 5.6 3.8 + - - -
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Residues in contact with ALA 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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283F TYR* 3.2 15.7 + - + +
284F HIS 2.9 8.3 + - - +
286F ARG* 1.3 77.8 - - - +
288F TYR* 1.3 63.6 + - + +
289F ASP* 3.5 3.1 + - - -
346F CYS* 5.2 0.7 - - - +
347F ASP 4.9 0.7 + - - +
350F SER* 2.7 39.1 + - - +
351F VAL* 4.0 5.2 + - - +
354F ALA* 4.1 25.1 - - + -
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Residues in contact with TYR 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 HIS* 2.8 55.5 + + + +
285F ILE* 3.2 14.7 + - + +
287F ALA* 1.3 85.5 - - + +
289F ASP* 1.3 60.2 + - - +
296F ASN* 3.6 7.1 + - - +
339F ASP* 2.5 29.5 + - - -
341F ARG* 3.6 22.0 - - + -
342F PRO* 3.6 34.5 - - + -
343F SER* 3.1 23.9 + - - -
346F CYS* 3.3 11.0 - - - +
351F VAL* 3.8 35.2 - - + -
354F ALA* 4.5 3.4 - - + -
355F LEU* 3.8 10.2 - - - +
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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