Contacts of the helix formed by residues 280 - 288 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D LYS 4.1 3.4 - - - +
277D LEU 3.1 7.1 + - - +
279D LYS* 1.3 84.2 - - + +
281D HIS* 1.3 63.7 + - - +
282D GLN 3.4 2.5 - - - -
283D TYR* 3.1 48.3 + - + +
284D HIS* 3.2 27.3 + - + -
357D ARG* 4.4 2.2 - - - +
358D THR* 2.9 38.4 + - + -
363D GLU* 3.1 47.0 + - - +
364D THR* 3.6 9.3 + - - +
365D GLY 2.8 50.0 + - - +
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Residues in contact with HIS 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D LEU 3.6 1.9 + - - -
278D SER 4.6 4.9 - - - +
279D LYS 3.7 1.6 + - - -
280D ARG* 1.3 76.3 - - - +
282D GLN* 1.3 76.7 + - + +
284D HIS* 3.1 5.0 + - - +
285D ILE* 2.9 39.7 + - + +
307D SER* 5.9 0.4 - - - -
308D ASN 4.7 0.7 - - - -
309D ILE* 2.5 31.7 + - - -
310D ASN 4.2 11.1 - - - -
311D ASP 4.3 14.4 - - - -
312D PHE* 3.8 27.4 - - + +
322D SER* 4.4 1.1 - - - -
341D ARG* 3.1 46.1 + - + +
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Residues in contact with GLN 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D ARG 3.4 0.4 - - - -
281D HIS* 1.3 99.9 + - + +
283D TYR* 1.3 57.3 + - - +
285D ILE* 3.1 14.7 + - - +
286D ARG* 2.8 55.7 + - - +
309D ILE* 4.5 5.5 + - - +
310D ASN* 5.1 7.5 + - - +
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Residues in contact with TYR 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ARG* 3.1 49.9 + - + +
282D GLN* 1.3 79.3 - - - +
284D HIS* 1.3 74.0 + + - +
286D ARG* 3.5 30.4 + - + +
287D ALA* 3.2 23.7 + - + +
354D ALA* 4.1 23.7 - - + +
357D ARG* 3.4 26.0 + - - -
358D THR* 4.1 3.6 - - - -
363D GLU* 4.5 1.7 + - - -
365D GLY 4.3 12.8 - - - +
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Residues in contact with HIS 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D LEU* 3.3 25.8 - - + +
280D ARG* 3.2 24.0 + - + +
281D HIS 3.1 8.4 + - - +
282D GLN 3.1 0.6 - - - -
283D TYR* 1.3 89.2 - + - +
285D ILE* 1.3 65.6 + - - +
287D ALA* 3.0 13.0 + - - -
288D TYR* 2.9 49.7 + - + -
341D ARG* 3.9 20.2 - - - +
354D ALA* 3.5 29.9 + - + +
355D LEU* 3.7 4.3 - - - -
358D THR* 2.9 26.3 + - - -
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Residues in contact with ILE 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D HIS* 2.9 47.5 + - + +
282D GLN* 3.1 16.6 + - - +
284D HIS* 1.3 74.4 - - - +
286D ARG* 1.3 63.0 + - + +
288D TYR* 3.1 15.5 + - + +
289D ASP* 4.1 1.4 + - - +
292D GLY 4.6 1.3 - - - +
293D GLY* 3.8 29.3 + - - -
296D ASN* 4.8 6.0 + - + +
300D LEU* 3.7 29.8 - - + -
309D ILE* 4.0 20.6 - - + +
341D ARG* 4.3 15.7 - - + -
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Residues in contact with ARG 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D GLN* 2.8 45.8 + - - +
283D TYR* 3.8 38.0 - - + +
285D ILE* 1.3 73.5 - - + +
287D ALA* 1.3 58.4 + - - +
288D TYR 3.7 0.3 + - - -
289D ASP 3.9 4.3 - - - +
292D GLY* 3.4 38.7 - - - +
365D GLY 4.9 5.7 + - - -
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Residues in contact with ALA 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D TYR* 3.2 20.0 + - + +
284D HIS 3.0 6.9 + - - +
286D ARG* 1.3 75.7 - - - +
288D TYR* 1.3 63.3 + - + +
289D ASP* 3.5 4.0 + - - +
346D CYS* 5.1 0.9 - - - +
347D ASP 4.9 0.7 + - - +
350D SER* 2.7 36.3 + - - +
351D VAL* 4.1 4.9 - - - +
354D ALA* 4.0 25.4 - - + -
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Residues in contact with TYR 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D HIS* 2.9 52.3 + - + +
285D ILE* 3.1 11.6 + - + +
287D ALA* 1.3 84.8 - - + +
289D ASP* 1.3 60.9 + - - +
296D ASN* 4.2 8.5 - - - +
339D ASP* 2.4 30.8 + - - +
341D ARG* 3.5 22.2 - - + -
342D PRO* 3.5 36.3 - - + -
343D SER* 3.2 22.0 + - - -
346D CYS* 3.3 12.3 - - - +
351D VAL* 3.8 35.9 - - + -
354D ALA* 4.5 3.4 - - + -
355D LEU* 3.6 12.0 - - - +
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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