Contacts of the helix formed by residues 280 - 288 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276E LYS 4.2 2.7 - - - +
277E LEU 3.1 6.7 + - - +
279E LYS* 1.3 84.5 - - + +
281E HIS* 1.3 63.5 + - - +
282E GLN 3.5 2.0 - - - -
283E TYR* 3.1 57.0 + - + +
284E HIS* 3.1 26.4 + - + -
357E ARG* 4.5 2.8 - - - +
358E THR* 2.7 41.3 + - + +
363E GLU* 3.2 51.1 + - - +
364E THR* 3.6 32.0 + - - +
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Residues in contact with HIS 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E LEU 3.5 2.3 + - - +
278E SER 4.8 4.9 - - - +
279E LYS 3.6 1.8 - - - -
280E ARG* 1.3 75.6 - - - +
282E GLN* 1.3 75.0 + - + +
284E HIS* 3.1 5.9 + - - +
285E ILE* 2.8 36.2 + - + +
307E SER* 5.8 0.4 - - - -
308E ASN 5.0 1.8 - - - -
309E ILE* 2.8 30.3 + - - -
310E ASN 4.1 13.6 - - - -
311E ASP 4.4 2.5 - - - -
312E PHE* 3.7 36.6 - - + -
322E SER* 4.5 2.0 - - - -
341E ARG* 3.1 46.3 + - + +
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Residues in contact with GLN 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E ARG 3.5 0.6 - - - -
281E HIS* 1.3 97.7 - - + +
283E TYR* 1.3 57.8 + - - +
285E ILE* 3.2 13.1 + - - +
286E ARG* 2.9 52.3 + - + +
309E ILE* 4.4 7.9 + - - +
310E ASN* 5.2 7.1 + - - +
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Residues in contact with TYR 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E ARG* 3.1 54.3 + - + +
282E GLN* 1.3 78.3 - - - +
284E HIS* 1.3 72.9 + + - +
286E ARG* 3.4 29.8 + - - +
287E ALA* 3.1 26.6 + - + +
353E GLU* 5.5 0.2 + - - -
354E ALA* 4.0 23.6 - - + +
357E ARG* 3.6 23.7 + - - -
358E THR* 4.4 2.9 - - - -
363E GLU* 4.5 1.4 + - - -
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Residues in contact with HIS 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277E LEU* 3.3 25.7 - - + +
280E ARG* 3.1 24.9 + - + +
281E HIS 3.1 8.7 + - - +
283E TYR* 1.3 85.8 - + - +
285E ILE* 1.3 66.3 + - - +
287E ALA* 2.9 15.1 + - - -
288E TYR* 2.8 55.2 + - + -
341E ARG* 3.9 15.5 + - - +
354E ALA* 3.6 29.6 + - + +
355E LEU* 3.8 3.1 - - - -
358E THR* 2.8 29.7 + - - -
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Residues in contact with ILE 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281E HIS* 2.8 50.3 + - + +
282E GLN* 3.2 16.4 + - - +
284E HIS* 1.3 71.1 - - - +
286E ARG* 1.3 62.2 + - + +
288E TYR* 3.3 17.4 + - + +
289E ASP* 4.0 0.9 + - - +
292E GLY 4.7 1.1 - - - +
293E GLY* 3.8 23.1 + - - -
296E ASN* 5.1 4.5 + - + +
300E LEU* 3.8 28.7 - - + -
309E ILE* 3.9 30.5 - - + +
341E ARG* 4.2 15.3 - - + -
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Residues in contact with ARG 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282E GLN* 2.9 40.3 + - + +
283E TYR* 3.5 39.6 - - - +
285E ILE* 1.3 75.0 - - + +
287E ALA* 1.3 58.7 + - - +
288E TYR 3.6 0.3 + - - -
289E ASP 3.8 4.3 - - - +
292E GLY* 3.4 38.0 - - - +
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Residues in contact with ALA 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E TYR* 3.1 16.3 + - + +
284E HIS* 2.9 10.3 + - - +
286E ARG* 1.3 75.8 - - - +
288E TYR* 1.3 64.1 + - + +
289E ASP 3.6 4.6 + - - +
346E CYS* 5.2 0.7 - - - +
347E ASP 4.9 1.0 + - - +
350E SER* 2.5 36.0 + - - +
351E VAL* 4.2 4.2 + - - +
354E ALA* 3.9 26.9 - - + -
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Residues in contact with TYR 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E HIS* 2.8 51.4 + + + +
285E ILE* 3.3 11.4 + - + +
287E ALA* 1.3 86.5 - - + +
289E ASP* 1.3 60.7 + - - +
296E ASN* 3.8 7.4 + - - +
339E ASP* 2.4 41.8 + - - -
341E ARG* 3.6 20.0 - - + -
342E PRO* 3.5 32.5 - - + -
343E SER* 3.2 22.5 + - - -
346E CYS* 3.4 12.2 - - - +
351E VAL* 3.9 33.3 - - + +
354E ALA* 4.5 0.4 - - + -
355E 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
------------------------------------------------------------
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