Contacts of the helix formed by residues 268 - 282 (chain W) in PDB entry 2Q4G
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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240W ASP* 2.6 34.4 + - - +
266W GLY 5.4 2.5 - - - +
267W ILE* 1.3 80.3 - - - +
269W ALA* 1.3 69.0 + - - +
270W LYS* 3.3 8.1 + - - +
271W GLY* 3.2 1.1 + - - -
272W CYS* 3.2 25.8 + - - -
294W GLU* 3.5 28.7 - - + +
295W LEU* 4.4 2.0 - - - +
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Residues in contact with ALA 269 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268W THR* 1.3 80.0 - - - +
270W LYS* 1.3 57.3 + - - +
272W CYS* 2.8 33.1 + - - +
273W GLY 3.2 4.7 + - - -
294W GLU 4.1 4.0 + - - -
295W LEU 4.1 13.2 + - - +
298W GLU* 4.0 29.8 - - + +
299W GLY* 4.3 2.9 - - - +
302W LEU* 3.5 9.3 - - + +
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Residues in contact with LYS 270 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240W ASP* 4.1 32.7 + - + +
241W VAL* 5.1 6.8 - - - +
244W ALA* 5.1 5.5 - - - +
268W THR* 3.3 4.6 + - - +
269W ALA* 1.3 78.6 - - - +
271W GLY* 1.3 54.6 + - - +
272W CYS 3.3 0.2 + - - -
273W GLY* 3.5 7.4 + - - +
274W ASP* 2.7 39.1 + - - +
277W ARG* 5.1 0.9 + - - -
302W LEU* 5.6 0.2 - - - -
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Residues in contact with GLY 271 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240W ASP* 3.2 31.6 + - - -
243W MET* 4.4 7.9 - - - +
267W ILE* 3.9 12.7 - - - +
268W THR 3.2 3.1 + - - -
269W ALA 3.2 1.0 - - - -
270W LYS* 1.3 75.8 - - - +
272W CYS* 1.3 59.1 + - - +
274W ASP* 3.2 13.3 - - - +
275W LEU* 3.0 24.9 + - - +
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Residues in contact with CYS 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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267W ILE* 5.2 1.8 - - - -
268W THR 3.2 22.9 + - - -
269W ALA* 2.8 13.4 + - - +
271W GLY* 1.3 74.5 - - - +
273W GLY* 1.3 66.3 + - - +
274W ASP 2.9 1.6 - - - -
275W LEU* 2.6 19.9 + - - +
276W CYS* 2.7 20.2 + - - -
290W LEU* 5.2 3.4 - - - -
295W LEU* 3.8 23.6 - - - -
299W GLY* 3.8 24.2 - - - +
302W LEU* 4.0 17.0 - - + -
303W LEU* 4.6 10.5 - - + -
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Residues in contact with GLY 273 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269W ALA 3.2 7.4 + - - -
270W LYS* 3.5 4.4 + - - -
271W GLY 3.4 0.2 - - - -
272W CYS* 1.3 77.8 - - - +
274W ASP* 1.3 60.4 + - - +
276W CYS* 3.5 8.4 + - - +
277W ARG* 3.0 42.6 + - - +
302W LEU* 3.8 16.1 - - - +
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Residues in contact with ASP 274 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240W ASP 4.8 1.6 - - - -
243W MET* 4.6 6.5 - - + -
244W ALA* 3.1 35.1 + - - +
247W CYS* 3.6 25.9 - - - -
270W LYS* 2.7 32.0 + - - +
271W GLY* 3.2 13.9 - - - +
272W CYS 2.8 1.2 + - - -
273W GLY* 1.3 76.6 - - - +
275W LEU* 1.3 61.8 + - - +
277W ARG* 3.3 45.8 + - - +
278W VAL 3.6 3.3 + - - -
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Residues in contact with LEU 275 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243W MET* 3.3 25.1 - - + +
247W CYS* 4.8 2.0 - - - -
250W LEU* 4.6 12.1 - - + -
260W LEU* 3.9 20.0 - - + -
262W ILE* 4.2 5.4 - - + -
271W GLY 3.0 12.2 + - - +
272W CYS* 2.6 14.8 + - - +
274W ASP* 1.3 71.3 - - - +
276W CYS* 1.3 59.4 + - - +
278W VAL* 3.0 10.7 + - + +
279W LEU* 2.8 34.0 + - + +
285W LEU* 5.4 1.1 - - + -
288W LEU* 3.3 43.5 - - + -
290W LEU* 4.1 16.2 - - + -
303W LEU* 5.0 2.9 - - + -
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Residues in contact with CYS 276 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272W CYS 2.7 28.3 + - - +
273W GLY* 3.8 7.9 - - - +
275W LEU* 1.3 71.9 - - - +
277W ARG* 1.3 63.8 + - + +
279W LEU* 3.7 8.1 - - - +
280W ARG* 2.9 29.1 + - - +
302W LEU* 3.5 39.0 - - - -
303W LEU* 3.9 17.9 - - - -
306W THR* 3.4 17.7 - - - +
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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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247W CYS* 6.1 0.9 - - - -
251W LEU* 3.5 17.7 - - + +
270W LYS 5.1 0.6 + - - -
273W GLY* 3.0 25.6 + - - +
274W ASP* 3.3 39.0 + - - +
275W LEU 3.1 0.4 - - - -
276W CYS* 1.3 78.5 - - + +
278W VAL* 1.3 60.5 + - - +
280W ARG* 4.4 3.5 - - - +
281W ALA* 3.2 24.8 + - - +
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Residues in contact with VAL 278 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247W CYS* 4.0 17.5 - - + -
250W LEU* 3.7 39.9 - - + -
251W LEU* 3.6 26.9 - - + -
274W ASP 3.6 6.7 + - - +
275W LEU* 3.0 12.6 + - + +
277W ARG* 1.3 76.7 - - - +
279W LEU* 1.3 60.1 + - - +
282W LYS* 2.7 43.0 + - + +
285W LEU* 4.1 21.1 - - + -
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Residues in contact with LEU 279 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275W LEU* 2.8 21.8 + - + +
276W CYS* 3.2 11.2 + - - +
278W VAL* 1.3 78.8 - - - +
280W ARG* 1.3 64.0 + - - +
282W LYS 3.5 15.6 + - - +
285W LEU* 3.5 28.5 - - + +
288W LEU* 4.1 16.6 - - + -
303W LEU* 4.0 29.8 - - + +
306W THR* 4.0 8.7 - - + -
307W LEU* 5.8 4.0 - - + -
312W CYS* 3.3 41.1 - - - +
314W LEU* 4.1 22.0 - - + -
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Residues in contact with ARG 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 CYS 2.9 17.0 + - - +
277W ARG* 4.5 2.9 - - - +
279W LEU* 1.3 76.5 - - - +
281W ALA* 1.3 60.6 + - - +
306W THR* 3.7 12.9 - - + +
309W GLU* 3.0 50.5 + - + +
310W PRO* 3.8 25.9 + - - +
311W GLY* 3.8 15.6 - - - -
312W CYS 3.8 9.6 + - - +
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Residues in contact with ALA 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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251W LEU* 3.8 18.6 - - + +
277W ARG 3.2 18.6 + - - +
278W VAL 3.2 1.2 + - - -
279W LEU 3.1 0.6 - - - -
280W ARG* 1.3 80.6 - - - +
282W LYS* 1.3 65.9 + - + +
283W GLU* 3.4 13.6 + - - +
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Residues in contact with LYS 282 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250W LEU 3.2 23.6 - - - +
251W LEU* 4.1 11.4 - - - +
252W HIS 2.6 27.0 + - - +
253W PRO* 3.2 15.5 + - + +
255W SER* 2.7 28.1 + - - -
256W ARG* 4.8 5.2 - - - +
278W VAL* 2.7 35.0 + - + +
279W LEU 3.5 12.5 + - - +
281W ALA* 1.3 78.5 - - + +
283W GLU* 1.3 63.0 + - - +
284W SER* 2.9 17.9 + - - +
285W LEU* 3.2 21.8 + - + +
313W GLN 5.0 1.0 + - - -
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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