Contacts of the helix formed by residues 280 - 288 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276J LYS 4.3 2.2 - - - +
277J LEU 3.1 8.7 + - - +
279J LYS* 1.3 84.3 - - - +
281J HIS* 1.3 60.7 + - - +
282J GLN 3.6 1.8 - - - -
283J TYR* 3.2 55.5 + - + +
284J HIS* 3.0 30.5 + - + -
341J ARG* 4.6 0.2 + - - -
357J ARG* 4.3 3.2 - - - +
358J THR* 2.9 37.9 + - + -
363J GLU* 3.1 48.7 + - - +
364J THR* 3.7 10.0 - - - +
365J GLY* 3.4 37.5 + - - +
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Residues in contact with HIS 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J LEU 3.7 0.8 + - - -
278J SER 4.5 6.7 - - - +
279J LYS 3.8 1.2 - - - -
280J ARG* 1.3 74.6 - - - +
282J GLN* 1.3 90.8 + - - +
284J HIS* 3.1 5.4 + - - +
285J ILE* 2.9 37.8 + - + +
300J LEU* 6.1 0.2 - - + -
308J ASN 4.8 1.3 - - - -
309J ILE* 2.7 28.1 + - - -
310J ASN 4.3 10.3 - - - -
311J ASP 3.9 18.0 + - - -
312J PHE* 3.8 21.4 - - + -
322J SER* 4.3 2.0 - - - -
341J ARG* 3.1 40.6 + - + +
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Residues in contact with GLN 282 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J HIS* 1.3 100.6 + - - +
283J TYR* 1.3 65.7 + - - +
285J ILE* 3.1 13.7 + - - +
286J ARG* 2.9 46.8 + - + +
309J ILE 4.5 5.7 + - - -
310J ASN* 5.0 6.3 + - - +
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Residues in contact with TYR 283 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280J ARG* 3.2 56.4 + - + +
281J HIS 3.2 0.6 - - - -
282J GLN* 1.3 78.6 - - - +
284J HIS* 1.3 71.6 + + - +
286J ARG* 3.4 31.4 + - + +
287J ALA* 3.1 28.8 + - + +
353J GLU* 5.5 0.3 + - - -
354J ALA* 4.1 24.0 - - + +
357J ARG* 3.5 24.9 + - - -
358J THR* 4.5 1.8 - - - -
363J GLU* 4.7 0.5 + - - -
365J GLY 5.8 3.4 - - - -
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Residues in contact with HIS 284 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277J LEU* 3.2 29.7 - - + +
280J ARG* 3.0 23.6 - - + +
281J HIS 3.1 7.9 + - - +
283J TYR* 1.3 85.4 - + - +
285J ILE* 1.3 66.3 + - - +
287J ALA* 2.8 16.5 + - - +
288J TYR* 2.8 53.9 + - + -
341J ARG* 3.6 20.0 + - - +
354J ALA* 3.8 25.8 + - + +
355J LEU* 3.9 4.3 - - + -
358J THR* 3.0 24.0 + - - -
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Residues in contact with ILE 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281J HIS* 2.9 46.5 + - + +
282J GLN* 3.5 17.9 - - - +
284J HIS* 1.3 77.2 - - - +
286J ARG* 1.3 64.7 + - + +
288J TYR* 3.2 16.0 + - + +
289J ASP* 4.0 5.2 + - - +
292J GLY 4.5 1.6 - - - +
293J GLY* 3.9 26.7 + - - -
296J ASN* 5.3 4.3 + - + +
300J LEU* 3.7 29.6 - - + -
309J ILE* 4.2 21.1 - - + +
341J ARG* 4.3 14.6 - - + +
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Residues in contact with ARG 286 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282J GLN* 2.9 37.0 + - + +
283J TYR* 3.6 39.8 + - - +
285J ILE* 1.3 77.2 - - + +
287J ALA* 1.3 58.6 + - - +
288J TYR 3.6 0.3 + - - -
289J ASP 3.7 5.4 - - - +
292J GLY* 3.4 39.0 - - - +
365J GLY 6.3 0.8 - - - -
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Residues in contact with ALA 287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283J TYR* 3.1 18.8 + - + +
284J HIS 2.8 8.7 + - - +
286J ARG* 1.3 75.9 - - - +
288J TYR* 1.3 62.2 + - + +
289J ASP 3.7 3.6 - - - +
346J CYS* 5.3 0.9 - - - +
347J ASP 5.6 0.7 + - - -
350J SER* 2.5 38.2 + - - +
351J VAL* 4.1 2.3 + - - +
354J ALA* 3.9 27.1 - - + -
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Residues in contact with TYR 288 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284J HIS* 2.8 53.6 + + + +
285J ILE* 3.2 11.7 + - + +
286J ARG 3.3 0.2 - - - -
287J ALA* 1.3 81.8 - - - +
289J ASP* 1.3 60.7 + - - +
296J ASN* 3.8 7.4 + - - +
339J ASP* 2.5 29.2 + - - -
341J ARG* 3.7 21.1 - - + -
342J PRO* 3.5 35.8 - - + +
343J SER* 3.1 23.0 + - - -
346J CYS* 3.3 12.6 - - - +
351J VAL* 3.4 37.9 - - + -
354J ALA* 4.6 4.5 - - + -
355J LEU* 3.7 11.8 - - - +
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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