Contacts of the helix formed by residues 269 - 283 (chain B) in PDB entry 2WVL
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 269 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ALA* 3.5 19.1 - - + -
267B GLY* 2.9 11.5 - - - +
268B TYR* 1.3 76.5 - - - +
270B VAL* 1.3 64.4 + - - +
271B GLU 3.4 1.6 - - - -
272B PRO* 3.5 5.6 - - - -
273B GLN* 2.9 30.0 + - - +
325B ALA* 4.0 7.8 - - + +
329B THR* 3.8 23.1 - - + -
363B PRO* 4.4 12.3 - - + -
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LYS* 5.8 1.6 - - + -
145B ALA* 3.6 26.7 - - + +
148B MET* 3.8 34.5 - - + -
252B HIS* 5.8 0.2 - - - +
264B LEU* 4.7 14.3 - - + +
265B ALA* 3.7 19.7 + - - +
267B GLY 3.2 20.9 - - - +
268B TYR* 3.3 1.8 - - - -
269B ALA* 1.3 80.8 - - - +
271B GLU* 1.3 72.8 + - - +
273B GLN* 4.0 1.2 - - - +
274B GLU* 3.1 34.2 + - - +
400B GDD 6.0 1.1 - - - +
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Residues in contact with GLU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LYS* 3.9 14.4 + - - -
148B MET* 4.3 9.0 - - - +
198B ARG* 3.3 12.9 + - - +
247B ALA 3.4 15.9 - - - +
248B ASN* 3.9 3.5 - - - +
249B ALA* 3.2 41.8 + - + +
250B GLY 3.9 0.4 - - - -
252B HIS* 4.0 15.3 - - + -
268B TYR* 4.9 3.0 + - - +
270B VAL* 1.3 83.1 - - - +
272B PRO* 1.4 69.7 - - + +
274B GLU* 3.0 25.5 + - - +
275B LEU 3.7 0.3 + - - -
400B GDD 2.9 42.0 + - - -
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Residues in contact with PRO 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ARG* 4.8 0.7 - - - +
229B LEU* 4.2 10.8 - - + +
247B ALA 3.1 15.4 - - - +
248B ASN* 4.1 8.5 - - - +
268B TYR 3.6 15.5 - - - +
269B ALA 3.4 14.6 - - - +
271B GLU* 1.4 93.2 - - + +
273B GLN* 1.3 61.2 + - - +
275B LEU* 3.1 16.5 + - - +
276B VAL* 3.2 15.9 + - - +
326B CYS* 3.8 33.4 - - + -
329B THR* 3.8 16.8 - - + +
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Residues in contact with GLN 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B PRO 4.6 3.1 - - - +
265B ALA* 3.5 22.4 - - + +
269B ALA 2.9 21.6 + - - +
270B VAL 4.0 1.6 - - - +
272B PRO* 1.3 75.9 - - - +
274B GLU* 1.3 66.0 + - - +
276B VAL* 3.8 20.1 - - - +
277B SER* 2.8 51.0 + - - +
280B GLU* 4.9 4.7 - - - +
329B THR* 3.5 30.6 + - + +
363B PRO* 4.1 7.9 - - - +
365B LEU* 3.8 30.9 - - + +
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Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 5.5 1.0 - - - +
196B MET* 3.5 17.8 - - + +
198B ARG* 3.0 22.0 + - - +
252B HIS* 2.7 37.5 + - - -
254B MET* 3.7 13.3 - - + +
262B LEU* 4.3 11.0 - - + +
263B PRO 5.3 2.5 - - - -
264B LEU* 4.3 20.4 - - + +
270B VAL* 3.1 27.7 + - - +
271B GLU* 3.0 11.6 + - - +
273B GLN* 1.3 75.3 - - - +
275B LEU* 1.3 58.3 + - - +
277B SER* 3.5 3.6 + - - -
278B LEU* 3.1 34.2 + - - +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 4.9 8.1 - - + -
196B MET* 4.4 3.1 - - - -
198B ARG* 3.7 46.4 - - - +
229B LEU* 3.3 29.2 - - + -
244B VAL* 3.9 18.4 - - + -
246B THR* 3.8 10.8 - - - +
247B ALA* 4.3 1.8 - - - +
272B PRO 3.1 8.3 + - - +
274B GLU* 1.3 76.4 - - - +
276B VAL* 1.3 64.8 + - - +
278B LEU* 3.3 5.6 - - + +
279B LEU* 3.0 34.2 + - + +
300B ILE* 3.7 30.5 - - + -
302B GLN* 5.7 0.9 - - - +
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 4.7 7.6 - - + -
232B LEU* 3.9 18.8 - - + -
272B PRO 3.2 12.8 + - - +
273B GLN* 3.8 17.9 - - - +
275B LEU* 1.3 77.1 - - - +
277B SER* 1.3 58.1 + - - +
279B LEU* 3.3 9.8 + - - +
280B GLU* 2.9 50.1 + - - +
329B THR* 4.0 25.8 - - - +
330B VAL* 4.4 7.6 - - + -
333B SER* 3.7 17.7 - - - +
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Residues in contact with SER 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU* 4.0 10.1 - - - -
263B PRO* 3.7 33.0 + - - +
273B GLN* 2.8 37.8 + - - +
274B GLU 4.0 3.1 - - - -
276B VAL* 1.3 73.6 - - - +
278B LEU* 1.3 61.7 + - - +
280B GLU* 4.3 9.9 + - - +
281B LEU* 2.8 39.4 + - - +
365B LEU* 4.5 1.2 - - - +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 3.8 8.3 - - + +
196B MET* 4.2 17.3 - - + -
258B LEU* 3.8 28.9 - - + -
262B LEU* 4.2 9.8 - - + +
274B GLU 3.1 16.3 + - - +
275B LEU* 3.3 11.9 - - - +
277B SER* 1.3 76.5 - - - +
279B LEU* 1.3 59.2 + - + +
282B TYR* 2.9 55.0 + - + +
298B VAL* 4.2 11.7 - - + -
300B ILE* 3.3 37.2 - - + -
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.6 40.0 - - + -
15B VAL* 4.4 9.4 - - + -
17B LEU* 4.1 24.0 - - + -
229B LEU* 5.2 5.2 - - + +
232B LEU* 4.4 13.7 - - + -
233B ILE* 3.9 28.5 - - + -
275B LEU* 3.0 25.0 + - + +
276B VAL* 3.6 10.5 - - + +
278B LEU* 1.3 80.8 - - + +
280B GLU* 1.3 57.2 + - - +
283B GLY* 3.0 27.8 + - - +
285B VAL* 5.5 0.7 - - - +
300B ILE* 5.8 1.3 - - + -
335B LEU* 3.7 12.0 - - + +
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Residues in contact with GLU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLN* 4.9 3.8 - - - +
276B VAL* 2.9 36.7 + - - +
277B SER* 3.9 9.3 + - - +
278B LEU 3.3 0.2 - - - -
279B LEU* 1.3 74.6 - - - +
281B LEU* 1.3 64.5 + - + +
283B GLY 4.4 1.7 + - - -
284B GLY 5.5 0.5 + - - -
285B VAL* 5.7 1.0 + - - +
286B PHE* 3.6 31.5 + - + +
333B SER* 2.7 32.5 + - - +
334B LYS* 3.3 28.7 + - + +
335B LEU* 3.9 18.6 - - + -
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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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261B ARG 4.0 10.5 - - - +
262B LEU* 4.2 8.1 - - + -
263B PRO* 3.9 30.7 - - + -
277B SER* 2.8 22.4 + - - +
280B GLU* 1.3 82.9 - - + +
282B TYR* 1.3 89.2 + - + +
283B GLY 3.7 0.4 + - - -
284B GLY 5.2 0.3 + - - -
286B PHE* 5.1 1.9 - - - +
287B PRO 4.9 1.6 - - - +
288B LEU* 3.6 21.3 - - - +
368B PRO* 5.8 0.7 - - + -
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Residues in contact with TYR 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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12B PHE 3.6 2.4 - - - +
13B GLY* 3.4 0.7 - - - -
14B VAL* 2.9 38.8 + - + +
15B VAL* 3.7 11.1 + - + -
258B LEU* 4.5 8.1 - - + -
261B ARG* 3.4 37.1 + - - +
262B LEU* 4.9 1.8 - - + -
278B LEU* 2.9 41.5 + - + +
281B LEU* 1.3 99.2 - - + +
283B GLY* 1.3 59.6 + - - +
284B GLY 3.4 2.9 + - - -
288B LEU* 3.2 33.3 - - + +
290B ASP* 4.7 5.2 + - + -
293B VAL* 3.5 26.9 - - + -
298B VAL* 3.9 9.9 - - + -
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.5 26.1 - - - -
13B GLY* 3.2 19.5 + - - -
236B VAL* 5.8 0.2 - - - +
279B LEU 3.0 22.8 + - - -
280B GLU 4.4 1.4 + - - -
281B LEU 3.7 1.4 - - - -
282B TYR* 1.3 75.5 - - - +
284B GLY* 1.3 60.2 + - - +
285B VAL* 3.2 13.2 + - - +
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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