Contacts of the helix formed by residues 266 - 279 (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 GLY 266 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260F ALA 3.3 26.0 - - - -
261F MET* 3.4 17.4 - - - -
263F GLU 2.9 12.4 + - - -
265F ASN* 1.3 72.4 - - - +
267F LEU* 1.3 65.0 + - - +
268F LYS 3.1 2.5 - - - -
269F TYR* 2.9 19.4 + - - +
270F ILE* 3.1 10.1 + - - +
333F LYS 3.1 3.0 + - - -
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Residues in contact with LEU 267 (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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265F ASN* 3.1 1.5 - - - +
266F GLY* 1.3 77.1 - - - +
268F LYS* 1.3 62.2 + - - +
270F ILE* 3.2 19.6 + - + -
271F GLU* 3.0 49.1 + - + +
325F ILE* 4.3 26.5 - - + -
329F VAL* 4.3 4.7 - - + +
330F GLY* 4.3 13.2 - - - +
333F LYS* 3.0 47.3 + - + +
334F LYS* 4.0 0.8 - - - +
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Residues in contact with LYS 268 (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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265F ASN* 3.4 16.5 + - + +
266F GLY 3.1 0.4 - - - -
267F LEU* 1.3 78.3 - - - +
269F TYR* 1.3 85.8 + - + +
271F GLU* 3.6 10.4 + - - +
272F GLU* 3.0 53.6 + - + +
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Residues in contact with TYR 269 (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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258F THR* 5.3 0.2 - - - +
260F ALA* 3.7 36.3 - - + -
261F MET* 3.8 20.5 - - + +
264F GLU 5.9 0.9 - - - -
265F ASN 4.4 5.8 - - - -
266F GLY* 2.9 14.2 + - - +
268F LYS* 1.3 101.5 + - + +
270F ILE* 1.3 60.9 + - - +
271F GLU 3.3 0.2 - - - -
272F GLU* 3.3 25.9 + - - +
273F ALA* 2.9 27.9 + - - +
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Residues in contact with ILE 270 (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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261F MET* 3.9 24.6 - - + +
266F GLY 3.1 8.3 + - - +
267F LEU* 3.2 19.3 + - + +
269F TYR* 1.3 75.4 - - - +
271F GLU* 1.3 51.3 + - - +
273F ALA* 2.8 8.2 + - - +
274F ILE* 2.7 41.5 + - + +
325F ILE* 4.4 10.8 - - + -
329F VAL* 3.6 30.7 - - + -
335F GLY 4.0 7.6 - - - +
336F TYR 3.8 19.3 - - - +
337F PHE* 3.5 32.3 - - + -
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Residues in contact with GLU 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F LEU* 3.0 42.9 + - + +
268F LYS* 3.8 9.0 - - - +
270F ILE* 1.3 78.9 - - - +
272F GLU* 1.3 58.1 + - + +
274F ILE* 3.9 9.9 - - + +
275F GLU* 3.1 26.9 + - - +
325F ILE* 4.7 12.6 - - + +
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Residues in contact with GLU 272 (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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268F LYS* 3.0 45.6 + - + +
269F TYR* 3.5 30.0 - - - +
270F ILE 3.1 0.6 - - - -
271F GLU* 1.3 72.9 - - - +
273F ALA* 1.3 63.5 + - - +
275F GLU* 3.3 8.6 - - - +
276F LYS* 3.2 39.7 + - - +
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Residues in contact with ALA 273 (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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261F MET* 3.7 22.2 - - + -
269F TYR 2.9 12.5 + - - +
270F ILE 2.8 13.2 + - - +
272F GLU* 1.3 69.6 - - - +
274F ILE* 1.3 63.4 + - - +
276F LYS* 3.2 9.1 + - - +
277F LEU* 3.0 28.9 + - - +
337F PHE* 3.7 14.4 - - + -
359F CYS* 4.0 21.9 - - + +
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Residues in contact with ILE 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F ILE* 2.7 29.1 + - + +
271F GLU* 3.9 9.4 - - + +
273F ALA* 1.3 71.2 - - - +
275F GLU* 1.3 58.6 + - - +
277F LEU* 3.2 8.2 + - - +
278F SER* 2.9 27.9 + - - -
312F PHE* 3.7 12.2 - - + -
314F ALA* 3.6 26.7 - - + -
323F ILE* 3.4 33.7 - - + -
325F ILE* 3.8 30.3 - - + -
337F PHE* 4.4 7.2 - - + -
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Residues in contact with GLU 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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271F GLU 3.1 16.4 + - - +
272F GLU* 3.3 12.8 - - - +
274F ILE* 1.3 78.0 - - - +
276F LYS* 1.3 65.0 + - + +
278F SER* 2.5 28.9 + - - -
279F LYS* 3.6 31.6 + - - +
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Residues in contact with LYS 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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272F GLU* 3.2 27.2 + - - +
273F ALA* 3.2 8.5 + - - +
275F GLU* 1.3 80.7 - - + +
277F LEU* 1.3 60.4 + - - +
279F LYS* 3.8 14.7 + - - +
280F ARG* 4.1 6.1 + - - +
358F THR* 3.2 36.4 - - + +
359F CYS* 3.8 17.4 + - - +
362F ASN* 2.7 38.2 + - - +
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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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273F ALA 3.0 18.2 + - - +
274F ILE* 3.6 7.6 - - - +
275F GLU 3.2 0.2 - - - -
276F LYS* 1.3 73.7 - - - +
278F SER* 1.3 64.3 + - - +
279F LYS 3.1 2.2 - - - -
280F ARG 3.1 22.7 + - - +
281F HIS* 3.5 1.9 + - - -
284F HIS* 3.1 43.1 - - + +
312F PHE* 3.6 19.2 - - + -
323F ILE* 4.8 6.5 - - + -
337F PHE* 3.6 37.9 - - + -
341F ARG* 3.9 10.8 + - - +
355F LEU* 4.0 8.1 - - + -
358F THR* 3.9 8.1 - - + -
359F CYS* 3.7 14.4 - - - -
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Residues in contact with SER 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F ILE* 2.9 9.3 + - - -
275F GLU* 2.5 33.6 + - - -
277F LEU* 1.3 75.5 - - - +
279F LYS* 1.3 63.3 + - - +
280F ARG 3.7 0.2 + - - -
281F HIS* 4.2 7.2 + - - +
312F PHE* 3.4 43.3 - - - +
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Residues in contact with LYS 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 GLU* 3.6 39.1 + - - +
276F LYS* 3.8 9.6 + - - +
277F LEU 3.1 1.6 - - - -
278F SER* 1.3 79.8 - - - +
280F ARG* 1.3 64.0 + - + +
281F HIS 3.7 1.3 - - - -
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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