Contacts of the helix formed by residues 264 - 282 (chain W) in PDB entry 5O9G
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 264 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263W THR* 1.3 81.4 - - - +
265W GLU* 1.3 68.2 + - - +
266W ASP 3.3 1.1 - - - -
267W ILE* 3.4 15.8 + - - +
268W GLU* 3.6 16.8 + - - +
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Residues in contact with GLU 265 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263W THR* 2.7 26.9 + - - +
264W ALA* 1.3 78.5 + - - +
266W ASP* 1.3 70.5 + - - +
268W GLU* 3.1 14.5 + - - +
269W ILE* 2.9 36.6 + - + +
683W ARG* 5.5 4.7 + - - -
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Residues in contact with ASP 266 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255W GLN 5.4 0.9 - - - +
261W TYR 4.9 1.2 - - - +
262W VAL* 3.8 22.3 - - + +
263W THR* 3.2 27.5 + - - +
264W ALA 3.3 0.8 - - - -
265W GLU* 1.3 88.0 - - - +
267W ILE* 1.3 57.5 + - - +
269W ILE* 4.4 6.2 - - - +
270W MET* 2.9 40.4 + - + +
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Residues in contact with ILE 267 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255W GLN 4.4 1.1 - - - +
256W VAL* 3.3 41.5 - - + +
257W ARG* 5.8 0.4 - - + -
262W VAL* 3.8 15.3 - - + -
263W THR 3.7 18.6 - - - +
264W ALA* 3.4 8.9 + - - +
265W GLU 3.2 0.4 - - - -
266W ASP* 1.3 78.0 - - - +
268W GLU* 1.3 59.3 + - + +
270W MET* 4.9 2.2 - - + -
271W ASP* 2.9 56.3 + - - +
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Residues in contact with GLU 268 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264W ALA* 3.6 15.2 + - - +
265W GLU* 3.1 13.9 + - - +
267W ILE* 1.3 80.3 - - + +
269W ILE* 1.3 53.8 + - + +
271W ASP* 4.6 2.9 - - - +
272W MET* 2.6 37.5 + - - +
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Residues in contact with ILE 269 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265W GLU* 2.9 26.3 + - + +
266W ASP* 3.8 8.1 - - - +
268W GLU* 1.3 80.3 - - + +
270W MET* 1.3 69.4 + - + +
272W MET* 3.1 24.9 + - + +
273W GLU* 2.9 28.3 + - + +
737W ASN* 5.2 11.7 - - - +
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Residues in contact with MET 270 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252W GLU* 3.7 46.1 - - + +
255W GLN* 3.8 37.0 - - + +
256W VAL* 5.0 7.9 - - + -
266W ASP* 2.9 24.4 + - + +
267W ILE* 4.4 2.9 - - + +
269W ILE* 1.3 84.0 - - + +
271W ASP* 1.3 66.5 + - - +
273W GLU* 3.4 21.4 + - + +
274W ARG* 3.7 10.6 - - - +
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Residues in contact with ASP 271 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256W VAL* 4.9 11.2 - - - +
267W ILE* 2.9 41.5 + - - +
268W GLU* 4.6 3.1 - - - +
270W MET* 1.3 76.9 - - - +
272W MET* 1.3 62.5 + - - +
274W ARG* 3.2 33.7 + - - +
275W GLU* 2.8 26.0 - - - +
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Residues in contact with MET 272 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268W GLU 2.6 25.3 + - - +
269W ILE* 3.1 32.5 + - + +
271W ASP* 1.3 76.3 - - - +
273W GLU* 1.3 65.7 + - - +
275W GLU* 3.5 6.8 + - + +
276W ARG* 2.9 42.6 + - + +
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Residues in contact with GLU 273 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269W ILE 2.9 11.8 + - - +
270W MET* 3.6 17.0 - - + +
271W ASP 3.2 0.4 - - - -
272W MET* 1.3 82.7 - - - +
274W ARG* 1.3 57.4 + - + +
276W ARG* 3.5 14.3 - - - +
277W ARG* 2.7 72.0 + - + +
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Residues in contact with ARG 274 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185W HIS* 3.5 30.0 + - + -
249W PHE* 4.4 11.1 - - - -
252W GLU* 3.0 36.1 + - - +
253W ASP* 4.6 3.6 + - - -
256W VAL* 4.4 12.5 - - - +
270W MET 3.7 9.8 + - - +
271W ASP* 3.4 32.0 + - - +
272W MET 3.2 0.2 - - - -
273W GLU* 1.3 77.6 - - + +
275W GLU* 1.3 64.8 + - - +
277W ARG* 3.2 4.8 + - - +
278W LEU* 2.9 36.2 + - + +
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Residues in contact with GLU 275 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271W ASP* 2.8 18.9 - - - +
272W MET* 3.5 7.6 + - + +
274W ARG* 1.3 81.2 - - - +
276W ARG* 1.3 56.9 + - - +
278W LEU* 3.7 19.4 - - + +
279W ASP* 2.9 41.7 + - - +
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Residues in contact with ARG 276 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272W MET* 2.9 32.9 + - - +
273W GLU* 3.5 23.6 - - - +
274W ARG 3.1 0.2 - - - -
275W GLU* 1.3 74.9 - - - +
277W ARG* 1.3 61.0 + - - +
279W ASP* 3.2 30.6 + - - +
280W GLU* 2.9 51.3 + - - +
749W GLN* 6.0 3.6 - - - +
752W ILE* 3.4 36.8 - - - +
756W HIS* 4.5 22.0 - - - +
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Residues in contact with ARG 277 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183W ILE 5.6 0.9 - - - +
245W TYR* 5.9 7.0 - - + +
273W GLU* 2.7 48.3 + - + +
274W ARG* 3.8 4.0 - - - +
276W ARG* 1.3 76.7 - - - +
278W LEU* 1.3 58.3 + - + +
280W GLU* 3.1 29.0 + - - +
281W PHE* 2.9 61.7 + - + -
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Residues in contact with LEU 278 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183W ILE* 5.4 3.8 - - + +
184W ASN* 4.3 28.3 - - + +
274W ARG* 2.9 25.0 + - + +
275W GLU* 3.7 25.8 - - + +
277W ARG* 1.3 78.6 - - + +
279W ASP* 1.3 58.9 + - - +
281W PHE* 4.4 9.6 - - + +
282W GLU* 2.9 52.2 + - + +
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Residues in contact with ASP 279 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275W GLU* 2.9 28.6 + - - +
276W ARG* 3.2 30.3 + - - +
278W LEU* 1.3 78.7 - - - +
280W GLU* 1.3 60.6 + - - +
281W PHE 3.6 0.3 + - - -
282W GLU* 4.7 10.5 - - - +
283W GLU* 3.4 27.0 + - - +
752W ILE* 5.7 1.3 - - - +
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Residues in contact with GLU 280 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276W ARG* 2.9 42.2 + - - +
277W ARG* 3.1 36.6 + - - +
279W ASP* 1.3 77.0 - - - +
281W PHE* 1.3 65.8 + - + +
283W GLU* 4.7 4.6 + - - +
284W PHE* 3.3 29.1 - - - -
749W GLN* 3.9 18.6 + - - +
752W ILE* 3.8 27.5 - - + +
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Residues in contact with PHE 281 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181W ILE* 4.8 8.7 - - + -
182W VAL 3.5 18.6 - - - -
183W ILE* 3.2 57.8 - - + +
222W HIS* 5.5 0.9 - - - -
245W TYR* 5.7 3.6 - + - -
277W ARG* 2.9 42.1 + - + +
278W LEU* 3.2 9.2 + - + +
280W GLU* 1.3 92.0 - - + +
282W GLU* 1.3 64.8 + - + +
283W GLU 3.2 2.4 + - - -
284W PHE* 3.4 28.5 + + - +
285W HIS* 3.2 18.3 + - - +
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Residues in contact with GLU 282 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278W LEU* 2.9 38.5 + - + +
279W ASP* 4.7 10.7 - - - +
281W PHE* 1.3 77.6 - - + +
283W GLU* 1.3 62.7 + - + +
284W PHE 3.2 1.1 + - - -
285W HIS* 3.5 26.1 + - + +
286W VAL* 4.4 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
------------------------------------------------------------
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