Contacts of the helix formed by residues 280 - 288 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LYS 3.8 10.8 - - - +
277A LEU 3.0 6.2 + - - +
279A LYS* 1.3 81.3 - - + +
281A HIS* 1.3 66.2 + - - +
282A GLN 3.4 2.2 - - - -
283A TYR* 3.0 60.3 + - + +
284A HIS* 3.2 18.3 - - + -
357A ARG* 4.5 2.4 - - - +
358A THR* 2.8 32.2 + - + +
363A GLU* 3.1 52.3 + - - +
364A THR* 3.6 18.6 + - - +
365A GLY 3.3 26.4 + - - +
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Residues in contact with HIS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU 3.3 3.0 + - - +
278A SER 4.4 5.2 - - - +
279A LYS 3.6 1.6 - - - -
280A ARG* 1.3 76.9 - - - +
282A GLN* 1.3 78.3 + - + +
284A HIS* 3.1 14.2 + - - +
285A ILE* 3.2 22.6 + - + +
307A SER* 6.1 0.2 - - - -
308A ASN 4.9 0.7 - - - -
309A ILE* 2.8 30.8 + - - -
310A ASN 4.0 15.4 - - - -
311A ASP 3.9 15.7 - - - -
312A PHE* 3.7 26.1 - - + -
322A SER* 4.7 0.2 - - - -
341A ARG* 2.9 47.8 + - + +
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ARG 3.4 0.4 - - - -
281A HIS* 1.3 91.8 + - + +
283A TYR* 1.3 63.8 + - - +
285A ILE* 3.9 12.1 - - + +
286A ARG* 3.3 41.6 + - + +
309A ILE* 4.2 10.2 - - - +
310A ASN* 5.0 8.5 + - - +
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Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ARG* 3.0 58.7 + - + +
281A HIS 3.2 0.4 - - - -
282A GLN* 1.3 78.8 - - - +
284A HIS* 1.3 74.1 + + - +
286A ARG* 3.6 30.1 + - - +
287A ALA* 3.4 20.3 + - + +
354A ALA* 4.4 21.1 - - + +
357A ARG* 3.6 21.4 + - - -
358A THR* 4.0 6.1 - - - -
363A GLU* 4.7 0.3 + - - -
365A GLY 5.2 4.5 - - - +
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Residues in contact with HIS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 3.4 24.4 - - + +
280A ARG* 3.2 23.6 - - + -
281A HIS 3.1 8.3 + - - +
283A TYR* 1.3 87.7 - + - +
285A ILE* 1.3 66.4 + - - +
286A ARG 3.1 1.6 - - - -
287A ALA* 2.8 16.7 + - - +
288A TYR* 2.8 54.5 + - + -
341A ARG* 3.9 17.1 + - - +
354A ALA* 3.5 28.8 + - + +
355A LEU* 3.9 3.1 - - + -
358A THR* 2.9 25.3 + - - -
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Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A HIS* 3.2 41.1 + - + +
282A GLN* 3.9 17.0 - - + +
284A HIS* 1.3 74.5 - - - +
286A ARG* 1.3 62.8 + - + +
288A TYR* 3.2 16.7 + - + +
289A ASP* 4.0 2.3 + - - +
292A GLY 4.5 1.1 - - - +
293A GLY* 3.9 28.6 + - - -
296A ASN* 5.0 5.3 + - + +
300A LEU* 3.7 29.4 - - + -
309A ILE* 4.0 24.9 - - + +
341A ARG* 4.3 14.4 - - + -
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A GLN* 3.3 38.8 + - + +
283A TYR* 3.6 37.3 + - - +
284A HIS 3.1 0.6 - - - -
285A ILE* 1.3 77.1 - - + +
287A ALA* 1.3 57.9 + - - +
288A TYR 3.3 1.1 + - - -
289A ASP 4.0 4.7 - - - +
292A GLY* 3.5 38.8 - - - +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A TYR* 3.4 15.0 + - + +
284A HIS 2.8 12.9 + - - +
286A ARG* 1.3 72.5 - - - +
288A TYR* 1.3 64.8 + - + +
289A ASP 3.6 3.2 + - - +
346A CYS* 5.1 0.7 - - - +
347A ASP 4.8 1.2 + - - +
350A SER* 2.9 37.5 + - - +
351A VAL* 4.0 4.9 - - - +
354A ALA* 3.9 25.6 - - + -
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Residues in contact with TYR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A HIS* 2.8 51.9 + - + +
285A ILE* 3.2 11.5 + - - +
287A ALA* 1.3 85.3 - - + +
289A ASP* 1.3 64.8 + - - +
296A ASN* 4.2 6.5 - - - +
339A ASP* 2.4 41.9 + - - +
341A ARG* 3.6 18.4 - - + -
342A PRO* 3.5 32.1 - - + -
343A SER* 3.2 19.9 + - - -
346A CYS* 3.3 10.5 - - - +
351A VAL* 3.8 35.4 - - + +
354A ALA* 4.4 3.8 - - + -
355A LEU* 3.6 12.3 - - - +
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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