Contacts of the helix formed by residues 274 - 285 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.3 29.2 + - + +
35A SER* 3.8 16.6 - - - -
387A SER* 2.7 35.2 + - - +
388A SER 2.8 18.0 + - - +
389A TYR* 3.7 12.6 - - - +
242B LYS* 3.8 21.4 - - + +
243B ASP* 3.6 26.5 - - + +
271B THR* 3.6 29.9 + - - -
272B GLY 4.2 4.7 - - - -
273B ASP* 1.3 70.8 - - - +
275B PHE* 1.3 63.5 + - - +
276B SER 3.2 4.5 + - - -
277B GLN* 3.2 17.0 + - - +
278B ILE* 4.0 3.1 + - - +
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Residues in contact with PHE 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A ASN* 3.7 30.5 + - - -
242B LYS* 3.5 10.1 - - - -
273B ASP* 3.0 41.5 + - + +
274B HIS* 1.3 77.0 - - - +
276B SER* 1.3 63.1 + - - +
278B ILE* 3.0 19.4 + - + +
279B GLN* 3.2 9.2 + - - +
315B HIS* 3.6 26.0 - + - -
316B ASP* 3.8 7.2 - - - -
319B GLY* 3.6 25.6 - - - -
320B ASN* 3.4 30.1 - - - -
323B SER* 3.5 18.6 - - - +
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Residues in contact with SER 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A LYS* 3.0 23.1 + - - +
385A LEU* 4.1 9.2 - - - +
386A SER 3.1 22.9 - - - -
387A SER* 4.0 6.6 - - - -
274B HIS 3.2 1.0 - - - -
275B PHE* 1.3 78.8 - - - +
277B GLN* 1.3 57.8 + - - +
279B GLN* 3.3 8.5 + - - +
280B TYR* 2.9 30.1 + - - +
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Residues in contact with GLN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A SER* 4.0 10.1 - - - -
37A LEU* 4.9 9.1 - - + +
385A LEU* 5.1 6.7 - - + -
387A SER* 3.0 30.8 + - - +
242B LYS 3.4 13.2 + - - +
243B ASP* 2.9 28.3 + - - +
244B GLY 4.0 0.2 - - - -
245B LEU* 3.3 17.2 + - + -
246B VAL* 3.0 44.5 + - + +
247B ASP* 4.6 1.4 + - - +
274B HIS* 3.2 8.8 + - - +
275B PHE 3.2 1.0 - - - -
276B SER* 1.3 75.2 - - - +
278B ILE* 1.3 65.7 + - - +
280B TYR* 3.5 0.6 + - - -
281B LEU* 3.2 28.2 + - - +
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Residues in contact with ILE 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B LYS* 3.6 17.3 - - + -
245B LEU* 4.0 21.3 - - + -
267B PHE* 3.6 14.4 - - + -
274B HIS 4.4 2.7 - - - +
275B PHE* 3.0 14.7 + - - +
277B GLN* 1.3 76.2 - - - +
279B GLN* 1.3 58.3 + - - +
281B LEU* 3.2 2.6 + - - -
282B ALA* 2.8 26.9 + - - +
290B LEU* 3.5 25.3 - - + +
320B ASN* 3.3 37.5 - - - +
323B SER* 3.5 21.1 - - - +
325B CYS* 4.0 11.7 - - - +
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Residues in contact with GLN 279 (chain B).
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* 3.8 31.6 - - - +
283A GLN* 3.3 26.8 + - - +
275B PHE 3.2 8.5 + - - +
276B SER* 3.6 11.2 - - - +
278B ILE* 1.3 80.5 - - - +
280B TYR* 1.3 62.4 + - - +
282B ALA* 3.2 7.3 + - - +
283B GLN* 3.1 25.9 + - + +
322B LYS 3.6 7.6 - - - +
323B SER* 3.1 35.0 + - - +
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Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS* 3.1 41.2 + + + +
41A ALA 5.4 1.7 + - - -
42A LEU* 4.0 26.7 - - + -
385A LEU* 3.6 39.0 - - + -
246B VAL* 4.0 18.2 - - + -
276B SER 2.9 17.1 + - - +
277B GLN 3.8 4.7 - - - +
278B ILE 3.2 0.2 - - - -
279B GLN* 1.3 74.8 - - - +
281B LEU* 1.3 63.6 + - + +
283B GLN* 3.2 7.3 + - + +
284B CYS* 3.0 56.6 + - + -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B LEU* 3.5 39.0 - - + +
246B VAL* 4.1 17.3 - - + -
249B ALA* 3.8 33.0 - - + -
250B GLU 5.5 0.4 - - - +
265B LEU* 4.3 9.2 - - + -
277B GLN 3.2 9.4 + - - +
278B ILE 3.2 7.7 + - - +
280B TYR* 1.3 79.7 - - + +
282B ALA* 1.3 60.2 + - - +
283B GLN 3.0 2.0 - - - -
284B CYS* 4.3 5.4 - - + +
285B LEU* 2.6 49.8 + - + +
290B LEU* 4.0 16.4 - - + -
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLN* 6.3 1.1 - - + -
278B ILE 2.8 16.3 + - - +
279B GLN* 3.2 13.4 + - - +
281B LEU* 1.3 76.2 - - - +
283B GLN* 1.3 63.0 + - - +
285B LEU 4.8 2.7 - - - -
286B PRO* 3.5 24.0 - - - +
290B LEU* 3.6 14.5 - - + +
323B SER 3.7 15.3 - - - +
324B GLY* 4.0 10.5 - - - +
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A GLN* 2.8 58.5 + - + +
279B GLN* 3.1 18.9 + - + +
280B TYR* 3.5 11.0 - - + +
281B LEU 3.0 0.4 - - - -
282B ALA* 1.3 80.9 + - - +
284B CYS* 1.3 63.6 + - - +
286B PRO* 3.4 12.3 - - - +
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Residues in contact with CYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B TYR* 3.0 57.0 + - + +
281B LEU* 4.2 7.4 - - + +
283B GLN* 1.3 78.5 - - - +
285B LEU* 1.3 72.6 + - + +
286B PRO* 3.3 8.8 - - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ALA* 4.3 2.9 - - + +
253B PHE* 3.8 39.9 - - + -
259B TYR* 4.0 27.6 - - + -
265B LEU* 4.3 10.5 - - + -
281B LEU* 2.6 44.5 + - + +
282B ALA* 4.0 2.3 - - - +
284B CYS* 1.3 86.3 - - + +
286B PRO* 1.3 58.3 - - - +
287B ASP 3.1 2.7 - - - -
288B LYS* 2.9 37.7 + - + +
290B LEU* 5.5 3.1 - - + +
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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