Contacts of the helix formed by residues 272 - 283 (chain D) in PDB entry 6Q2J
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 SER 272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243D LYS 4.6 3.6 + - - -
246D GLN* 5.6 1.6 + - - -
270D SER* 3.2 13.5 - - - -
271D GLY* 1.3 82.3 - - - +
273D ASP* 1.3 63.6 + - - +
274D ASP* 3.8 17.3 + - - +
275D CYS* 3.2 23.9 + - - +
276D LYS* 3.5 6.6 + - - +
317D PHE* 4.5 0.2 - - - -
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Residues in contact with ASP 273 (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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180D PHE* 4.7 11.9 - - + -
184D GLN* 4.9 3.6 + - - -
271D GLY 4.7 2.3 - - - +
272D SER* 1.3 72.2 - - - +
274D ASP* 1.3 61.0 + - - +
275D CYS 3.3 0.2 - - - -
276D LYS* 3.3 31.5 + - + +
277D ALA* 2.9 28.1 + - - +
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Residues in contact with ASP 274 (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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243D LYS* 3.7 38.1 - - + +
272D SER* 3.2 12.0 + - - +
273D ASP* 1.3 79.0 - - - +
275D CYS* 1.3 56.9 + - - +
277D ALA* 3.4 5.4 + - - +
278D ALA* 2.9 29.8 + - - +
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Residues in contact with CYS 275 (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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240D PHE* 4.7 2.2 - - - -
243D LYS* 4.0 6.4 - - - +
244D CYS* 2.0 58.0 - - + -
269D CYS* 4.3 9.9 - - - -
270D SER 3.5 20.4 - - - +
272D SER* 3.2 14.5 + - - +
274D ASP* 1.3 76.7 - - - +
276D LYS* 1.3 59.4 + - - +
278D ALA* 3.4 0.4 + - - -
279D TYR* 3.0 29.8 + - - +
316D CYS* 4.7 2.7 - - - -
317D PHE* 4.4 11.4 - - + -
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Residues in contact with LYS 276 (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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180D PHE* 4.5 12.3 - - + -
184D GLN* 3.1 31.8 - - + +
188D PHE* 3.5 27.3 - - + -
271D GLY 5.0 2.4 + - - -
272D SER 3.9 4.0 - - - +
273D ASP* 3.3 33.0 + - - +
274D ASP 3.3 0.4 - - - -
275D CYS* 1.3 77.5 - - - +
277D ALA* 1.3 57.7 + - - +
279D TYR* 3.3 5.0 + - - +
280D ILE* 3.0 37.9 + - + +
317D PHE* 3.6 43.0 - - + -
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Residues in contact with ALA 277 (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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180D PHE* 4.2 24.2 - - + -
273D ASP 2.9 17.1 + - - +
274D ASP* 3.9 6.5 - - - +
275D CYS 3.3 0.2 - - - -
276D LYS* 1.3 76.1 - - - +
278D ALA* 1.3 58.0 + - - +
280D ILE* 3.5 2.5 + - - +
281D ASP* 2.9 40.4 + - - +
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Residues in contact with ALA 278 (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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239D THR* 4.0 21.8 - - + +
240D PHE* 3.7 32.5 - - + +
243D LYS* 4.4 3.4 - - + -
274D ASP 2.9 17.9 + - - +
275D CYS* 3.8 4.9 - - - +
277D ALA* 1.3 77.8 - - - +
279D TYR* 1.3 57.2 + - - +
281D ASP* 3.2 8.0 + - - +
282D ILE* 3.0 32.6 + - - +
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Residues in contact with TYR 279 (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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187D ALA* 4.7 5.6 - - + -
188D PHE* 3.5 40.8 - + + -
240D PHE* 3.8 23.7 - + + -
275D CYS* 3.0 19.4 + - - +
276D LYS 3.9 2.2 - - - +
278D ALA* 1.3 74.1 - - - +
280D ILE* 1.3 65.7 + - - +
282D ILE* 3.2 39.0 - - + +
283D LEU* 3.4 34.5 + - + +
287D LEU 6.1 1.1 - - - -
311D LEU 4.3 17.4 + - - -
312D HIS 5.1 3.4 - - - -
313D ARG* 3.8 26.1 - - + +
317D PHE* 6.5 0.7 - - + -
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Residues in contact with ILE 280 (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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175D TYR* 4.1 36.0 - - + +
180D PHE* 4.0 25.4 - - + -
183D ALA* 4.0 8.1 - - + -
184D GLN* 3.8 35.0 - - + +
187D ALA* 4.2 18.2 - - + -
188D PHE* 5.4 3.6 - - + -
276D LYS* 3.0 25.0 + - + +
277D ALA* 3.9 4.0 - - - +
279D TYR* 1.3 80.5 - - + +
281D ASP* 1.3 64.4 + - - +
283D LEU* 3.2 24.6 + - + +
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Residues in contact with ASP 281 (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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172D ARG* 5.7 2.9 - - - +
176D GLN* 5.4 10.2 + - - +
232D LEU* 5.8 0.7 - - - +
236D HIS* 3.4 34.8 + - + +
239D THR* 5.8 4.7 - - + +
277D ALA* 2.9 27.0 + - - +
278D ALA* 3.2 8.6 + - - +
280D ILE* 1.3 80.8 - - - +
282D ILE* 1.3 60.8 + - - +
283D LEU 3.7 4.3 + - - +
285D THR* 5.3 3.5 - - - +
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Residues in contact with ILE 282 (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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233D CYS* 6.1 0.2 - - - -
236D HIS* 3.4 37.0 - - + +
237D TYR 4.1 1.8 - - - +
240D PHE* 4.0 25.8 - - + -
278D ALA 3.0 15.2 + - - +
279D TYR* 3.2 42.2 - - + +
281D ASP* 1.3 75.3 - - - +
283D LEU* 1.3 64.1 + - + +
284D GLY 3.2 1.4 + - - -
285D THR* 2.8 26.6 + - - +
287D LEU* 4.0 38.2 - - + +
288D GLN 4.8 1.0 + - - -
311D LEU* 5.0 4.9 - - + -
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Residues in contact with LEU 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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171D ILE* 3.9 9.6 - - + +
172D ARG* 4.3 9.8 - - - +
175D TYR* 3.8 36.4 - - + +
187D ALA* 3.7 31.4 - - + +
206D HIS* 6.2 3.1 - - + -
279D TYR* 3.4 39.1 + - + +
280D ILE* 3.2 18.5 + - - +
281D ASP 4.3 3.3 - - - +
282D ILE* 1.3 75.3 - - + +
284D GLY* 1.3 56.7 + - - +
288D GLN* 3.8 34.8 - - + +
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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