Contacts of the helix formed by residues 274 - 285 (chain A) in PDB entry 2WNW
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 HIS 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A LYS* 3.8 21.7 - - + +
243A ASP* 3.6 27.7 - - + +
271A THR* 3.6 27.4 + - - -
272A GLY 4.2 4.7 - - - -
273A ASP* 1.3 70.9 - - - +
275A PHE* 1.3 65.1 + - - +
276A SER 3.2 3.1 - - - -
277A GLN* 3.2 17.6 + - - +
278A ILE* 4.0 3.1 + - - +
1448A GOL 3.5 4.7 - - - -
33B LEU* 3.2 29.3 + - + +
35B SER* 3.7 18.8 + - - -
387B SER* 2.8 28.2 + - - +
388B SER 2.8 17.9 + - - -
389B TYR* 3.6 13.5 - - - +
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Residues in contact with PHE 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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242A LYS* 3.5 10.1 - - - -
273A ASP* 3.0 38.1 + - + -
274A HIS* 1.3 77.3 - - - +
276A SER* 1.3 63.2 + - - +
278A ILE* 3.0 20.7 + - - +
279A GLN* 3.2 9.2 + - - +
315A HIS* 3.6 32.8 - + - -
316A ASP* 3.8 6.7 - - - -
319A GLY* 3.6 25.6 - - - -
320A ASN* 3.4 29.8 - - - -
323A SER* 3.4 19.1 - - - +
1448A GOL 3.1 26.2 + - - +
391B ASN* 4.2 6.3 - - - -
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 1.3 78.6 - - - +
277A GLN* 1.3 56.4 + - - +
279A GLN* 3.4 10.5 + - - +
280A TYR* 2.9 28.9 + - - +
1448A GOL 2.9 20.0 + - - -
322B LYS* 2.9 25.2 + - - -
385B LEU* 4.1 9.2 - - - +
386B SER 3.1 23.6 - - - -
387B SER* 3.9 1.3 - - - -
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Residues in contact with GLN 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LYS 3.4 13.5 + - - +
243A ASP* 2.9 27.9 + - - +
244A GLY 4.0 0.2 - - - -
245A LEU* 3.3 17.3 + - + -
246A VAL* 2.9 44.1 + - + +
247A ASP* 4.7 1.0 + - - +
274A HIS 3.2 7.9 + - - +
275A PHE 3.1 1.2 + - - -
276A SER* 1.3 73.8 - - - +
278A ILE* 1.3 65.1 + - - +
280A TYR* 4.5 0.9 - - - -
281A LEU* 3.3 29.1 + - - +
35B SER* 3.9 11.5 - - - -
37B LEU* 5.0 9.3 - - + +
385B LEU* 5.3 5.8 - - + -
386B SER 5.7 0.2 - - - -
387B SER* 3.0 29.1 + - - +
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Residues in contact with ILE 278 (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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242A LYS* 3.6 17.9 - - + -
245A LEU* 3.9 19.5 - - + -
267A PHE* 3.7 12.8 - - + -
274A HIS 4.4 2.7 - - - +
275A PHE* 3.0 15.6 + - - +
277A GLN* 1.3 78.7 - - - +
279A GLN* 1.3 57.1 + - - +
281A LEU 3.2 2.4 + - - -
282A ALA* 2.9 24.8 + - - +
290A LEU* 3.3 28.1 - - + +
320A ASN* 3.2 37.9 - - - +
323A SER* 3.4 20.9 - - - +
325A CYS* 4.0 12.3 - - - +
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Residues in contact with GLN 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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275A PHE 3.2 9.1 + - - +
276A SER* 3.7 12.8 + - - +
277A GLN 3.3 0.2 - - - -
278A ILE* 1.3 80.5 - - - +
280A TYR* 1.3 62.1 + - - +
282A ALA* 3.2 3.0 + - + +
283A GLN* 3.1 45.7 + - + +
322A LYS 4.1 17.6 + - - -
323A SER* 3.1 22.0 + - - +
279B GLN* 3.8 33.6 - - - +
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Residues in contact with TYR 280 (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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246A VAL* 4.0 18.6 - - + -
276A SER 2.9 18.0 + - - +
277A GLN 3.9 5.2 - - - +
278A ILE 3.3 0.2 - - - -
279A GLN* 1.3 76.9 - - - +
281A LEU* 1.3 62.8 + - + +
283A GLN* 3.2 15.9 + - - +
284A CYS* 2.9 57.1 + - + -
40B HIS* 3.1 40.7 + + + +
41B ALA 5.6 1.1 + - - -
42B LEU* 4.1 25.6 - - + -
385B LEU* 3.6 37.5 - - + -
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Residues in contact with LEU 281 (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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245A LEU* 3.7 33.0 - - + +
246A VAL* 4.2 18.6 - - + +
249A ALA* 3.7 33.4 - - + -
250A GLU 5.5 0.4 - - - +
265A LEU* 4.4 4.3 - - + -
277A GLN 3.3 13.4 + - - +
278A ILE 3.2 4.8 + - - +
280A TYR* 1.3 85.2 - - + +
282A ALA* 1.3 61.0 + - - +
284A CYS* 4.3 5.6 - - + +
285A LEU* 2.7 47.1 + - + +
290A LEU* 3.9 24.9 - - + +
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Residues in contact with ALA 282 (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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43A GLN* 6.3 1.3 - - + -
278A ILE 2.9 16.8 + - - +
279A GLN* 3.2 7.2 + - + +
281A LEU* 1.3 77.3 - - - +
283A GLN* 1.3 62.3 + - + +
285A LEU 4.7 2.7 - - - -
286A PRO* 3.5 23.3 - - - +
290A LEU* 3.6 13.6 - - + +
323A SER 3.8 14.1 - - - +
324A GLY* 4.1 12.1 - - - +
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Residues in contact with GLN 283 (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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279A GLN* 3.1 30.4 + - + +
280A TYR* 3.7 18.0 - - - +
281A LEU 3.1 0.2 - - - -
282A ALA* 1.3 81.4 - - + +
284A CYS* 1.3 63.0 + - - +
286A PRO* 3.6 11.2 - - - +
42B LEU* 5.8 2.1 - - - +
279B GLN* 3.3 21.5 + - - +
283B GLN* 2.8 55.9 + - - +
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Residues in contact with CYS 284 (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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280A TYR* 2.9 57.5 + - + +
281A LEU* 4.2 7.6 - - + +
283A GLN* 1.3 80.4 - - - +
285A LEU* 1.3 71.4 + - + +
286A PRO* 3.3 9.0 - - - +
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Residues in contact with LEU 285 (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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249A ALA* 4.5 3.4 - - + -
253A PHE* 3.6 38.1 - - + -
259A TYR* 3.9 31.9 - - + -
265A LEU* 4.7 5.8 - - + -
281A LEU* 2.7 42.9 + - + +
282A ALA* 4.0 2.6 - - - +
284A CYS* 1.3 87.0 - - + +
286A PRO* 1.3 64.2 - - - +
287A ASP 3.1 2.7 - - - -
288A LYS* 3.0 31.3 + - + +
290A LEU* 5.8 3.3 - - + +
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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