Contacts of the helix formed by residues 279 - 287 (chain B) in PDB entry 4QGC
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 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B ARG 3.6 20.0 - - - +
247B LYS* 3.8 22.6 - - - +
275B GLU* 3.0 35.0 + - + +
276B GLY 3.7 3.8 - - - -
278B ARG* 1.3 81.7 - - + +
280B PHE* 1.3 63.7 + - - +
281B ASP 3.3 2.5 - - - -
282B GLU* 3.2 44.7 + - + +
283B ILE* 3.1 16.9 - - - +
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Residues in contact with PHE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ILE* 4.2 12.3 - - + -
276B GLY 3.2 10.4 + - - +
277B VAL* 3.3 18.8 - - - +
278B ARG 3.3 3.4 + - - -
279B ARG* 1.3 77.7 - - - +
281B ASP* 1.3 61.6 + - - +
283B ILE* 3.2 4.5 + - + +
284B LEU* 2.8 41.7 + - + +
290B ILE* 3.8 32.3 - - + -
312B MET* 4.3 4.0 - - + -
313B MET* 3.6 48.7 - - + -
316B ARG* 3.7 45.1 - - + +
317B CYS* 3.9 13.5 - - - -
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Residues in contact with ASP 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ARG 5.1 0.6 + - - -
279B ARG* 3.3 1.4 - - - +
280B PHE* 1.3 82.1 - - - +
282B GLU* 1.3 57.7 + - - +
284B LEU* 3.6 7.5 + - - +
285B GLU* 3.2 26.2 + - - +
316B ARG* 3.1 40.8 + - - +
319B ARG* 5.7 1.6 + - - -
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B LYS* 3.5 2.3 - - - +
248B ALA* 3.0 38.8 + - + +
279B ARG* 3.2 54.7 + - + +
281B ASP* 1.3 76.5 - - - +
283B ILE* 1.3 68.2 + - - +
285B GLU* 3.6 6.5 + - - +
286B ALA* 3.2 23.6 + - - +
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ILE* 3.8 28.7 - - + +
246B ARG 3.8 16.2 - - - +
247B LYS* 3.8 21.1 - - - +
248B ALA* 4.1 5.6 - - - +
251B VAL* 4.3 1.3 - - + +
269B SER* 3.7 27.8 - - - +
271B ILE* 3.9 12.3 - - + -
276B GLY* 3.6 19.5 - - - +
279B ARG 3.1 15.9 - - - +
280B PHE* 3.2 7.6 + - - +
282B GLU* 1.3 77.9 - - - +
284B LEU* 1.3 56.4 + - - +
286B ALA* 3.3 2.6 + - - +
287B SER* 2.6 36.8 + - - +
290B ILE* 4.1 4.9 - - + -
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B PHE* 2.8 40.1 + - + +
281B ASP* 3.8 8.7 - - - +
283B ILE* 1.3 78.2 - - - +
285B GLU* 1.3 59.8 + - - +
287B SER* 3.3 10.0 + - - +
289B GLY 5.4 0.7 - - - -
290B ILE* 3.7 28.7 - - + +
316B ARG* 3.6 27.4 - - + +
317B CYS* 3.9 11.4 - - - -
320B ALA* 4.0 10.3 - - + -
322B LYS* 2.8 44.0 + - + -
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B HIS* 5.6 1.7 + - - -
281B ASP 3.2 15.1 + - - +
282B GLU* 4.0 7.8 - - - +
283B ILE 3.4 0.2 - - - -
284B LEU* 1.3 80.4 - - - +
286B ALA* 1.3 65.1 + - - +
322B LYS* 3.2 16.9 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ALA* 4.3 6.7 - - + +
251B VAL* 3.5 22.6 - - + +
252B HIS* 3.7 29.1 - - + +
255B ARG* 2.9 22.7 + - - -
282B GLU 3.2 16.1 + - - +
283B ILE 3.3 3.6 + - - +
284B LEU 3.2 0.2 - - - -
285B GLU* 1.3 83.4 - - - +
287B SER* 1.3 59.2 + - - +
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B VAL* 3.7 9.8 - - - +
255B ARG* 4.2 1.3 - - - +
267B ILE 3.8 4.5 - - - -
269B SER* 2.5 28.9 + - - -
283B ILE 2.6 21.7 + - - -
284B LEU* 3.3 5.2 + - - +
285B GLU 4.1 0.2 - - - +
286B ALA* 1.3 81.2 - - - +
288B ASP* 1.3 64.2 + - - +
289B GLY 3.4 22.0 - - - -
290B ILE* 4.5 2.0 - - - -
322B LYS* 2.8 26.9 + - - -
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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