Contacts of the helix formed by residues 268 - 279 (chain A) in PDB entry 6O81
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 THR 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A PHE* 6.3 4.0 - - + -
130A SER* 4.4 2.9 - - - +
131A LEU* 4.5 15.3 - - + +
132A GLY 4.8 0.2 - - - +
152A TYR* 4.7 12.8 - - - +
260A PHE* 3.4 10.6 - - - -
267A GLN* 1.3 91.7 - - + +
269A ARG* 1.3 64.2 + - - +
270A ASP* 3.6 19.2 + - - -
271A ASP* 2.8 22.1 + - - +
272A PHE* 3.3 13.9 - - - +
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Residues in contact with ARG 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 4.5 15.4 - - + +
150A LEU* 4.4 15.7 - - + -
152A TYR* 5.2 8.2 + - + +
181A MET* 5.0 7.8 - - + -
183A MET* 3.4 30.9 - - - +
215A PHE* 4.8 7.5 - - - -
217A LYS* 5.9 0.4 - - - +
246A ASP* 2.4 38.1 + - - -
248A HIS* 3.3 39.2 + - + +
250A SER* 3.8 30.0 - - - -
260A PHE* 5.0 0.9 - - - -
268A THR* 1.3 79.0 - - - +
270A ASP* 1.3 60.8 + - + +
272A PHE* 3.2 10.1 + - + +
273A VAL* 2.9 41.2 + - + +
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Residues in contact with ASP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A PHE* 3.7 30.1 - - + -
217A LYS* 3.6 25.9 - - - +
248A HIS* 6.5 1.1 - - + -
268A THR* 3.6 12.9 + - - -
269A ARG* 1.3 80.8 - - + +
271A ASP* 1.3 76.9 + - - +
273A VAL* 3.3 2.8 + - - +
274A ARG* 2.9 52.7 + - - +
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Residues in contact with ASP 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASP 4.1 4.9 - - - +
266A TYR* 3.9 11.4 - - + -
267A GLN* 3.0 31.4 + - - +
268A THR* 2.8 33.0 + - - +
270A ASP* 1.3 80.7 + - - +
272A PHE* 1.3 58.4 + - - -
274A ARG* 3.4 28.9 + - - +
275A GLY* 2.9 25.1 + - - -
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Residues in contact with PHE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A MET* 3.7 32.5 - - + -
256A VAL* 4.0 21.5 - - + -
259A LEU* 4.1 29.2 - - + -
260A PHE* 3.6 27.1 - + + -
266A TYR* 3.5 32.9 - + + -
268A THR 3.3 17.7 - - - +
269A ARG* 3.2 10.7 + - + +
271A ASP* 1.3 83.1 + - - +
273A VAL* 1.3 65.1 + - + +
275A GLY 3.4 0.7 + - - -
276A LEU* 2.9 48.1 + - + +
287A ILE* 4.9 0.7 - - + -
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A MET* 4.4 6.5 - - - -
183A MET* 4.3 21.8 - - + -
212A VAL* 5.4 1.3 - - + -
215A PHE* 3.7 26.7 - - + -
269A ARG* 2.9 28.0 + - + +
270A ASP* 3.8 4.5 - - - +
272A PHE* 1.3 88.1 - - + +
274A ARG* 1.3 57.4 + - - +
276A LEU* 3.3 0.9 + - - +
277A LEU* 2.9 46.3 + - + +
287A ILE* 3.9 26.9 - - + -
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A HIS* 6.4 0.7 - - + -
215A PHE* 3.5 28.9 - - + +
216A GLN* 5.0 9.2 - - - +
270A ASP* 2.9 45.2 + - - +
271A ASP* 3.4 22.4 - - - +
272A PHE 3.3 0.2 - - - -
273A VAL* 1.3 76.3 - - - +
275A GLY* 1.3 57.7 + - - +
277A LEU* 4.4 5.9 - - - +
278A VAL* 3.3 30.5 + - - +
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A TYR* 3.2 25.3 + - - -
271A ASP 2.9 16.4 + - - -
273A VAL 3.2 0.2 - - - -
274A ARG* 1.3 77.2 - - - +
276A LEU* 1.3 59.0 + - - +
277A LEU 3.3 0.4 - - - -
278A VAL* 3.4 9.0 - - - +
279A ASN* 3.1 30.7 + - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A VAL* 4.3 5.6 - - + -
259A LEU* 4.4 5.4 - - + -
266A TYR* 3.8 4.2 + - + +
272A PHE* 2.9 41.3 + - + +
273A VAL* 3.3 5.1 + - - +
275A GLY* 1.3 75.2 - - - +
277A LEU* 1.3 63.9 + - + +
279A ASN* 3.4 19.1 - - - +
280A GLU* 4.1 5.5 - - - +
283A LEU* 3.5 40.2 - - + +
284A GLY 3.6 8.9 - - - +
285A ASN* 3.6 29.8 - - + +
287A ILE* 3.8 23.1 - - + -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL* 3.4 31.0 - - + +
213A LEU* 3.4 25.8 - - - +
214A HIS* 3.8 5.6 - - - +
215A PHE* 3.8 26.7 - - + +
230A LEU* 5.7 3.1 - - - +
273A VAL* 2.9 38.4 + - + +
274A ARG* 4.4 6.1 - - - +
275A GLY 3.3 0.2 - - - -
276A LEU* 1.3 80.0 - - + +
278A VAL* 1.3 60.2 + - + +
280A GLU* 3.3 29.1 - - - +
286A GLN* 6.4 0.4 - - - -
287A ILE* 5.1 11.4 - - + +
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A HIS* 6.0 6.3 - - + +
274A ARG 3.3 21.3 + - - +
275A GLY* 3.4 11.7 - - - +
277A LEU* 1.3 80.4 - - + +
279A ASN* 1.3 62.1 + - + +
280A GLU* 3.4 5.9 + - - +
281A GLU* 4.2 10.4 - - - +
449T LYS* 4.9 13.7 - - + -
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Residues in contact with ASN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A TYR* 5.1 2.9 - - - +
275A GLY 3.1 19.3 + - - +
276A LEU* 3.4 12.4 - - - +
277A LEU 3.5 0.2 - - - -
278A VAL* 1.3 75.5 - - + +
280A GLU* 1.3 58.9 + - - +
281A GLU* 3.6 8.7 - - - +
282A ILE* 3.0 28.2 - - + +
283A LEU* 3.5 15.4 - - + +
449T LYS* 5.1 12.3 - - + -
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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