Contacts of the helix formed by residues 259 - 266 (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 MET 259 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216D MET* 4.7 3.6 - - + -
226D MET* 3.9 9.0 - - - +
248D LEU* 5.8 1.8 - - - +
251D ILE* 3.6 33.0 - - + -
252D MET* 3.8 33.2 - - + -
255D TYR* 3.5 24.5 - - + +
256D TYR* 2.9 14.8 + - - +
257D THR 3.4 0.8 - - - -
258D PHE* 1.3 84.3 - - + +
260D LYS* 1.3 65.6 + - - +
261D PRO* 3.4 1.8 - - - -
262D TYR* 3.3 32.5 + - + +
263D MET* 3.1 22.8 + - + +
267D LEU* 5.3 6.1 - - - -
317D PHE* 3.7 16.8 - - + -
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Residues in contact with LYS 260 (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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214B ASN* 3.1 24.4 + - - +
217B GLU* 2.5 49.1 + - + +
258B PHE* 6.1 2.0 - - + -
258D PHE 3.6 0.4 - - - -
259D MET* 1.3 75.9 - - - +
261D PRO* 1.3 70.2 - - + +
263D MET* 3.4 1.6 + - - +
264D GLU* 2.9 55.5 + - + +
315D TYR* 3.6 49.0 + - + -
317D PHE* 3.5 19.6 - - + -
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Residues in contact with PRO 261 (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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219B GLU* 6.3 3.4 - - + +
258B PHE* 6.3 3.1 - - + -
222D ARG* 6.4 0.2 - - - +
258D PHE 3.6 13.7 - - - +
259D MET 3.4 3.6 - - - -
260D LYS* 1.3 95.4 - - + +
262D TYR* 1.3 61.2 + - + +
264D GLU* 3.2 8.4 + - + +
265D GLN* 2.7 46.4 + - + +
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Residues in contact with TYR 262 (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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222D ARG* 2.9 34.1 + - - +
223D ASN* 2.5 35.1 + - - -
226D MET* 3.8 32.5 - - + -
230D CYS* 5.5 3.4 - - - -
258D PHE 3.2 27.8 - - - -
259D MET* 3.3 27.4 + - + +
261D PRO* 1.3 81.3 - - + +
263D MET* 1.3 64.9 + - - +
265D GLN* 4.5 2.0 - - - +
266D ALA* 2.9 13.6 + - + +
267D LEU* 2.8 42.3 + - + -
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Residues in contact with MET 263 (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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252D MET* 4.0 20.0 - - + -
259D MET* 3.1 21.3 + - + +
260D LYS 3.6 4.3 - - - +
262D TYR* 1.3 79.0 - - - +
264D GLU* 1.3 58.4 + - + +
265D GLN 3.4 0.2 + - - -
266D ALA 3.6 0.2 + - - -
267D LEU* 3.6 20.3 + - + -
268D TYR* 2.7 53.0 + - + +
289D PHE* 4.0 9.6 - - + -
290D TRP* 3.8 25.1 - - + -
293D ILE* 3.7 21.3 - - + -
317D PHE* 3.5 35.9 - - + -
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Residues in contact with GLU 264 (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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217B GLU 4.7 2.4 - - - +
218B ARG* 4.6 20.5 + - - +
260D LYS* 2.9 51.2 + - + +
261D PRO* 3.7 7.6 - - + +
263D MET* 1.3 80.2 - - + +
265D GLN* 1.3 73.3 + - + +
266D ALA 3.7 0.2 + - - -
268D TYR* 4.6 12.6 - - + +
269D ALA* 6.1 0.5 - - - +
317D PHE* 5.7 1.3 - - + -
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Residues in contact with GLN 265 (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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261D PRO* 2.7 26.9 + - + +
262D TYR* 4.8 2.0 - - - +
264D GLU* 1.3 87.5 - - + +
266D ALA* 1.3 60.7 + - + +
269D ALA* 6.1 0.9 - - - -
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Residues in contact with ALA 266 (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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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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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