Contacts of the helix formed by residues 266 - 276 (chain D) in PDB entry 2BKU
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 ALA 266 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227D GLN* 5.5 4.5 - - - +
230D CYS* 4.6 13.2 - - + -
262D TYR* 2.9 12.0 + - + +
264D GLU 3.5 2.4 + - - -
265D GLN* 1.3 81.8 - - + +
267D LEU* 1.3 66.4 + - - +
268D TYR 3.3 1.8 - - - -
269D ALA* 3.0 13.4 + - - +
270D LEU* 3.0 36.8 + - + +
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Residues in contact with LEU 267 (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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226D MET* 5.5 2.2 - - - -
230D CYS* 3.6 31.4 - - + -
233D THR* 5.0 2.9 - - + -
248D LEU* 3.4 46.2 - - + -
259D MET* 5.3 8.1 - - - -
262D TYR* 2.8 31.2 + - + +
263D MET* 3.7 25.4 - - + -
266D ALA* 1.3 69.2 - - - +
268D TYR* 1.3 60.1 + - - +
270D LEU* 4.4 8.7 - - + +
271D THR* 2.8 48.5 + - + +
289D PHE* 4.4 4.7 - - + -
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Residues in contact with TYR 268 (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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263D MET* 2.7 41.8 + - + +
264D GLU* 4.6 11.4 - - + +
267D LEU* 1.3 78.9 - - - +
269D ALA* 1.3 63.0 + - + +
271D THR* 3.1 9.0 + - - -
272D ILE* 3.1 28.9 - - + +
290D TRP* 5.0 3.9 - + - -
317D PHE* 5.0 2.7 - + - -
320D SER* 3.0 30.9 + - - -
321D SER* 3.0 27.4 - - - -
324D ASP* 2.9 32.9 + - + -
325D VAL* 6.2 0.2 - - + -
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Residues in contact with ALA 269 (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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264D GLU 5.8 0.9 + - - +
265D GLN 6.1 0.7 - - - -
266D ALA* 3.0 12.6 + - - +
268D TYR* 1.3 82.0 - - + +
270D LEU* 1.3 65.5 + - + +
272D ILE* 3.8 5.7 + - - +
273D ALA* 3.4 20.8 + - - +
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Residues in contact with LEU 270 (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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230D CYS* 3.7 42.0 - - + +
231D GLU* 5.6 0.4 - - - -
233D THR* 4.2 3.8 - - - +
234D GLN* 3.4 36.4 + - + +
245D PHE* 6.1 0.2 - - - -
266D ALA* 3.0 28.7 + - + +
267D LEU* 4.1 8.5 - - + +
269D ALA* 1.3 78.5 - - + +
271D THR* 1.3 60.2 + - + +
273D ALA* 3.5 6.0 - - - +
274D THR* 3.1 24.3 + - - -
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Residues in contact with THR 271 (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 THR* 6.5 0.2 - - - -
245D PHE* 4.3 15.3 - - + -
267D LEU* 2.8 34.8 + - + +
268D TYR* 3.1 6.9 + - - -
270D LEU* 1.3 77.4 - - + +
272D ILE* 1.3 63.3 + - - +
273D ALA 3.2 0.4 - - - -
274D THR* 3.3 7.1 + - - -
275D MET* 2.9 31.0 + - - +
286D THR* 3.4 6.8 + - - -
289D PHE* 3.8 30.7 - - + -
290D TRP* 3.3 27.9 + - - -
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Residues in contact with ILE 272 (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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268D TYR* 3.1 26.1 + - + +
269D ALA* 4.0 7.6 - - - +
271D THR* 1.3 82.1 + - - +
273D ALA* 1.3 63.0 + - - +
275D MET* 3.4 9.0 + - + +
276D LYS* 3.1 50.6 + - - +
290D TRP* 5.5 0.2 - - + -
324D ASP* 3.4 37.5 - - + +
325D VAL* 3.4 30.1 - - + +
328D ASN* 4.2 8.4 - - - +
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Residues in contact with ALA 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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234D GLN* 5.1 5.8 - - - +
269D ALA 3.4 11.5 + - - +
270D LEU* 3.5 12.8 - - + +
271D THR 3.2 0.2 - - - -
272D ILE* 1.3 80.4 - - - +
274D THR* 1.3 59.3 + - + +
276D LYS* 3.1 27.2 + - - +
277D SER* 3.5 5.2 + - - -
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Residues in contact with THR 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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233D THR 4.3 9.4 - - - +
234D GLN* 3.4 35.2 - - - +
241D GLN* 4.6 3.1 - - - +
245D PHE* 3.9 7.8 - - + -
270D LEU 3.1 9.3 + - - +
271D THR* 3.3 10.4 + - - -
273D ALA* 1.3 75.6 - - + +
275D MET* 1.3 64.9 + - - +
276D LYS 3.1 2.0 - - - -
277D SER* 3.2 20.3 + - - +
282D VAL* 3.6 23.0 - - + +
283D ALA* 3.6 3.5 - - - -
286D THR* 3.2 26.2 - - - +
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Residues in contact with MET 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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271D THR 2.9 17.4 + - - +
272D ILE* 3.7 8.7 - - + +
274D THR* 1.3 78.1 + - - +
276D LYS* 1.3 61.0 + - - +
277D SER 3.6 0.3 + - - -
283D ALA* 3.7 15.3 - - - +
286D THR* 3.7 17.7 - - - +
287D VAL* 4.6 8.5 - - + -
290D TRP* 3.5 36.1 - - + +
325D VAL* 3.9 27.6 - - + +
328D ASN* 3.7 29.9 - - + +
329D LEU* 4.1 16.8 - - + -
332D LEU* 3.8 30.2 - - + +
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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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272D ILE* 3.1 31.3 - - - +
273D ALA* 3.3 11.5 - - - +
274D THR 3.1 0.8 - - - -
275D MET* 1.3 77.5 - - - +
277D SER* 1.3 65.6 + - - +
278D PRO* 3.4 3.5 - - - +
328D ASN* 3.0 35.4 - - - +
335D ARG* 3.6 8.8 + - - +
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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