Contacts of the helix formed by residues 281 - 290 (chain C) in PDB entry 6Q2N
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 ASN 281 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C ASN* 4.8 9.4 - - - +
277C CYS* 6.4 0.2 - - - -
278C LEU* 3.3 40.4 - - + +
279C LYS 3.6 2.2 - - - +
280C GLU* 1.3 81.0 + - - +
282C TYR* 1.3 54.5 + - - +
283C ALA 3.4 2.0 - - - +
284C ASP* 3.5 26.8 + - + +
285C CYS* 2.8 32.8 + - - +
116E PHE* 4.9 4.2 - - - -
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Residues in contact with TYR 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C SER* 2.8 25.6 + - - -
277C CYS* 3.5 32.3 - - + -
279C LYS* 3.4 37.1 - - + +
280C GLU 3.3 1.6 - - - -
281C ASN* 1.3 76.2 - - - +
283C ALA* 1.3 55.2 + - - +
285C CYS* 2.9 9.0 - - + +
286C LEU* 2.4 44.3 + - + +
337C CYS* 5.2 0.4 - - - -
340C ASN* 3.7 13.6 + - - +
341C ALA* 3.7 28.4 - - + +
344C ALA* 3.7 27.4 - - + +
349C SER* 5.3 5.8 - - - -
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Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C TYR* 5.3 1.6 - - + -
280C GLU 4.8 5.5 + - - +
281C ASN* 3.4 0.6 - - - +
282C TYR* 1.3 76.8 - - - +
284C ASP* 1.3 53.8 + - - +
286C LEU* 2.9 16.6 + - + +
287C LEU* 2.5 39.9 + - - +
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Residues in contact with ASP 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ASN* 3.0 35.4 + - + +
280C GLU 5.4 0.6 + - - +
281C ASN* 3.5 31.8 + - + +
282C TYR 3.3 0.2 - - - -
283C ALA* 1.3 74.6 - - - +
285C CYS* 1.3 60.7 + - - +
287C LEU* 3.7 14.4 - - - +
288C ALA 2.9 21.5 + - - -
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Residues in contact with CYS 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C ASN* 3.8 6.2 - - - +
267C CYS* 2.0 60.1 - - + -
281C ASN 2.8 19.8 + - - +
282C TYR* 2.9 18.6 + - + +
284C ASP* 1.3 71.7 - - - +
286C LEU* 1.3 60.5 + - - +
288C ALA* 3.0 17.5 + - - +
289C TYR* 3.2 6.9 + - - +
337C CYS* 4.7 5.2 - - - -
338C LEU* 3.7 21.1 - - - -
341C ALA* 4.1 13.9 - - + -
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C TYR* 3.9 17.9 - - + -
213C PHE* 4.0 34.1 - - + -
282C TYR* 2.4 36.1 + - + +
283C ALA* 2.9 17.0 + - + +
285C CYS* 1.3 67.2 - - - +
287C LEU* 1.3 54.6 + - - +
288C ALA 3.0 5.4 + - - -
289C TYR* 3.0 12.8 + - - +
290C SER* 2.4 25.9 + - - +
338C LEU* 5.6 4.7 - - + -
341C ALA* 4.9 16.2 - - + +
342C ILE* 5.6 1.1 - - + +
345C PHE* 3.5 41.3 - - + -
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C PHE 5.4 7.6 - - - +
209C TYR* 3.4 22.6 + - + +
259C ARG* 5.4 0.9 - - - -
262C ASP* 4.9 7.8 - - - +
266C ASN* 5.0 0.9 - - - -
283C ALA 2.5 20.7 + - - +
284C ASP* 3.7 14.4 - - - +
286C LEU* 1.3 70.2 - - - +
288C ALA* 1.3 61.4 + - - +
290C SER* 4.0 1.1 - - - -
291C GLY* 3.4 18.9 - - - +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ARG* 4.4 2.4 - - - +
262C ASP* 4.5 6.5 - - - -
263C PHE* 3.5 30.5 - - + +
266C ASN* 3.4 21.1 - - + +
267C CYS* 4.3 0.4 - - - -
284C ASP 2.9 14.5 + - - +
285C CYS* 3.0 11.0 + - - +
286C LEU 3.0 1.0 + - - -
287C LEU* 1.3 77.0 - - - +
289C TYR* 1.3 54.0 + - - +
291C GLY* 2.9 3.3 + - - -
292C LEU* 2.8 36.4 + - - +
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Residues in contact with TYR 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C LEU* 4.3 15.2 - - + +
213C PHE* 3.3 40.2 - + + -
263C PHE* 3.5 26.9 - + + -
285C CYS 3.2 5.2 + - - +
286C LEU* 3.0 5.9 + - - +
288C ALA* 1.3 77.0 - - - +
290C SER* 1.3 65.6 + - - +
292C LEU* 2.9 27.0 + - + +
293C ILE* 3.6 10.5 + - + +
299C PRO* 3.8 32.1 + - + +
300C ASN* 4.5 8.0 + - - -
301C TYR* 3.6 20.6 - - - -
309C VAL* 3.5 35.7 - - + +
332C PHE* 6.2 0.4 - + - -
338C LEU* 4.4 19.7 - - + -
342C ILE* 6.0 2.7 - - + -
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Residues in contact with SER 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C PHE* 3.9 19.7 - - - +
209C TYR* 3.2 37.5 + - - -
212C LEU* 3.6 21.8 - - - -
213C PHE* 4.1 4.3 - - - -
286C LEU* 2.4 23.9 + - - -
287C LEU* 5.9 0.4 - - - -
289C TYR* 1.3 76.2 - - - +
291C GLY* 1.3 62.7 + - - +
293C ILE* 3.6 23.7 + - - +
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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