Contacts of the helix formed by residues 272 - 289 (chain B) in PDB entry 4WB7
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 LYS 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B HIS* 3.5 51.5 + - + +
217B LEU 5.4 0.4 - - - +
218B ILE* 3.8 21.3 - - + +
271B ASN* 1.3 82.3 - - + +
273B ALA* 1.3 64.1 + - - +
274B VAL 3.1 0.7 - - - -
275B ASP* 3.0 21.4 + - - +
276B TRP* 3.8 4.0 + - - +
337B GLY 3.7 22.9 + - - -
338B ASN* 4.1 14.8 - - - +
342B GLY* 5.2 6.9 - - - -
343B VAL 5.9 0.2 - - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLU* 4.3 1.1 - - - +
271B ASN* 3.0 17.6 + - - +
272B LYS* 1.3 80.5 - - - +
274B VAL* 1.3 61.0 + - - +
276B TRP* 3.2 13.7 + - - +
277B TRP 3.0 13.3 + - - -
332B LEU* 4.1 9.0 - - + -
335B ARG* 3.0 32.6 + - - +
338B ASN* 3.7 30.3 - - + +
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Residues in contact with VAL 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ILE* 4.1 15.9 - - + -
220B ARG* 4.5 7.4 - - + -
259B TYR 5.1 1.2 - - - +
261B ALA* 3.9 14.7 + - + +
263B GLU* 3.4 18.8 - - - +
264B ILE* 3.8 28.3 - - + -
270B TYR* 3.5 38.1 - - + -
271B ASN 3.1 13.7 + - - +
272B LYS 3.1 2.2 - - - -
273B ALA* 1.3 77.2 - - - +
275B ASP* 1.3 63.2 + - - +
277B TRP* 3.5 2.9 + - - +
278B ALA* 3.0 27.0 + - - +
335B ARG* 4.1 0.4 - - - +
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 3.3 30.0 - - + -
213B HIS* 2.8 28.9 + - + +
218B ILE* 3.3 9.5 - - - +
219B TYR* 2.9 30.5 + - - +
220B ARG* 2.8 29.5 + - - -
221B ASP 4.8 0.2 + - - -
222B LEU* 5.6 0.9 + - - +
272B LYS 3.0 9.5 + - - +
274B VAL* 1.3 84.5 - - - +
276B TRP* 1.3 58.5 + - - +
278B ALA* 3.3 7.3 + - - +
279B LEU 2.9 22.5 + - - -
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Residues in contact with TRP 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 3.8 15.7 - - + -
209B PHE* 3.5 36.3 - + + -
210B GLU* 4.4 4.7 - - - -
213B HIS* 3.5 22.2 + + - -
272B LYS* 3.9 18.8 - - + +
273B ALA* 3.2 13.3 + - - +
275B ASP* 1.3 74.9 - - - +
277B TRP* 1.3 64.9 + - - +
279B LEU* 3.2 25.5 + - + +
280B GLY 3.1 17.0 + - - -
327B LEU* 3.9 11.6 - - + +
335B ARG* 4.4 5.2 - - - -
336B PHE 3.4 19.1 - - - +
337B GLY* 3.4 32.6 + - - -
343B VAL* 3.8 33.0 - - + -
346B ILE* 3.4 22.7 - - + -
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Residues in contact with TRP 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLU 5.1 0.8 + - - -
259B TYR 3.7 12.7 - - - -
260B LEU 3.4 11.5 + - - -
261B ALA* 3.6 16.8 - - + -
262B PRO* 3.7 29.8 - - + -
273B ALA 3.0 6.9 + - - -
274B VAL 3.6 7.2 - - - +
276B TRP* 1.3 75.7 - - - +
278B ALA* 1.3 65.8 + - - +
280B GLY* 3.0 12.8 + - - -
281B VAL* 3.1 24.3 + - + +
293B PHE* 3.6 32.3 - + - -
305B ILE* 3.7 18.6 - - + +
308B GLY* 5.1 0.2 - - - -
327B LEU 3.7 11.2 - - - -
328B LEU* 3.4 46.2 - - + +
329B GLN 3.6 21.1 - - - -
330B VAL* 4.0 8.7 - - + -
335B ARG* 3.7 21.0 - - - +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ARG 6.5 0.2 - - - -
222B LEU* 3.7 25.9 - - + +
259B TYR* 3.7 24.0 - - + +
274B VAL 3.0 17.2 + - - +
275B ASP* 3.6 8.3 - - - +
276B TRP 3.2 0.2 - - - -
277B TRP* 1.3 82.8 - - - +
279B LEU* 1.3 62.7 + - - +
281B VAL* 3.1 7.4 + - - +
282B LEU* 2.9 22.5 + - - +
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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
----------------------------------------------------------
202B ALA* 4.5 7.4 - - - +
205B ILE* 3.9 28.3 - - + -
206B VAL* 3.7 25.4 - - + -
209B PHE* 4.4 4.5 - - + -
222B LEU* 3.6 10.2 - - + +
275B ASP 2.9 13.9 + - - +
276B TRP* 3.2 28.2 + - + +
278B ALA* 1.3 77.7 - - - +
280B GLY* 1.3 56.4 + - - +
282B LEU* 4.5 9.0 - - + -
283B ILE* 2.9 51.2 + - + +
327B LEU* 4.1 16.6 - - + -
346B ILE* 4.6 4.7 - - + -
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Residues in contact with GLY 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B TRP 3.1 7.3 + - - -
277B TRP 3.0 8.6 + - - -
279B LEU* 1.3 77.2 - - - +
281B VAL* 1.3 61.2 + - - +
284B TYR* 3.0 22.7 + - - +
324B LEU* 3.4 13.8 - - - +
327B LEU* 3.8 27.8 - - - +
328B LEU* 3.8 11.2 - - - -
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B GLU 3.6 22.0 - - - +
259B TYR* 3.4 31.4 - - + +
277B TRP* 3.1 39.5 + - + +
278B ALA* 3.1 7.6 + - - +
280B GLY* 1.3 75.4 - - - +
282B LEU* 1.3 56.8 + - - +
284B TYR* 3.5 1.6 + - - +
285B GLU* 2.8 28.2 + - - +
291B PRO* 4.6 3.8 - - + -
292B PRO* 3.8 28.1 - - + +
293B PHE* 4.9 1.3 - - + -
328B LEU* 3.7 8.9 - - + +
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Residues in contact with LEU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B MET* 4.3 2.2 - - + -
201B TYR 5.9 0.2 - - - -
202B ALA* 5.6 0.4 - - - -
205B ILE* 4.0 21.1 - - + -
222B LEU* 4.0 14.6 - - + -
223B LYS* 4.5 2.0 - - - -
224B PRO* 3.8 36.6 - - + -
227B LEU* 3.8 27.8 - - + -
259B TYR* 3.4 12.5 - - + +
278B ALA 2.9 13.1 + - - +
279B LEU* 3.6 12.3 - - + +
281B VAL* 1.3 76.1 - - - +
283B ILE* 1.3 57.5 + - - +
285B GLU* 3.2 1.6 + - + +
286B MET* 2.8 60.7 + - + +
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ALA* 4.9 0.8 - - + +
202B ALA* 3.8 30.1 - - + -
279B LEU* 2.9 40.9 + - + +
280B GLY 3.9 3.6 - - - +
282B LEU* 1.3 71.8 - - - +
284B TYR* 1.3 67.4 + - - +
286B MET* 3.3 12.3 + - + +
287B ALA* 3.0 24.5 + - + +
320B LEU* 3.6 30.3 - - + -
323B LEU* 4.1 22.0 - - + -
324B LEU* 4.0 5.8 - - + -
327B LEU* 4.1 8.1 - - + -
351B TRP* 4.0 15.3 - - + -
352B PHE* 4.7 2.2 - - + -
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Residues in contact with TYR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B GLY 3.0 18.8 + - - +
281B VAL 3.6 3.6 - - - +
283B ILE* 1.3 76.9 - - - +
285B GLU* 1.3 57.6 + - - +
287B ALA 3.1 1.4 + - - -
288B ALA* 2.8 39.9 + - + +
290B TYR* 3.3 38.7 + + - -
291B PRO 3.7 0.9 - - - -
292B PRO* 3.5 40.0 + - + +
310B VAL* 3.8 9.4 - - + -
311B ARG 2.6 28.8 + - - -
312B PHE* 3.6 29.8 - + - -
313B PRO* 3.7 10.7 - - + +
316B PHE* 3.8 9.3 - + - -
324B LEU* 4.0 13.1 - - + +
328B LEU* 4.6 3.6 - - + -
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 3.9 14.0 - - + +
188B ARG* 2.6 40.4 + - - +
224B PRO* 4.3 5.6 - - + +
259B TYR* 2.6 30.5 + - - +
281B VAL 2.8 19.5 + - - +
282B LEU 3.2 2.0 + - - +
284B TYR* 1.3 74.1 - - - +
286B MET* 1.3 57.8 + - - +
289B GLY* 2.8 28.2 + - - -
290B TYR 3.4 20.0 - - - +
291B PRO* 3.8 16.0 - - + +
19J ARG* 3.1 24.4 + - - -
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Residues in contact with MET 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B MET* 3.7 41.7 - - - +
187B LEU* 3.7 12.7 - - + +
192B ARG* 3.7 3.6 - - - -
193B PHE* 2.9 41.0 + - + +
198B ALA* 3.5 28.5 - - + +
201B TYR* 3.9 16.6 - - - -
202B ALA* 4.2 8.5 - - + +
282B LEU* 2.8 37.5 + - + +
283B ILE* 3.7 28.0 - - + +
285B GLU* 1.3 73.8 - - + +
287B ALA* 1.3 61.2 + - - +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ARG* 3.6 11.0 - - - +
193B PHE 3.8 12.5 - - - +
195B GLU* 4.7 8.1 - - + -
198B ALA* 4.6 10.5 - - + -
283B ILE* 3.0 17.2 + - + +
286B MET* 1.3 78.3 - - - +
288B ALA* 1.3 60.7 + - - +
315B HIS* 3.3 20.5 - - + -
316B PHE* 3.6 20.0 - - + -
320B LEU* 3.9 17.5 - - + -
351B TRP* 5.9 0.2 - - + -
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ARG* 3.2 25.0 + - - -
284B TYR* 2.8 31.3 + - + +
287B ALA* 1.3 77.9 - - - +
289B GLY* 1.3 59.8 + - - +
290B TYR* 3.3 22.3 + - + +
313B PRO* 3.7 17.7 - - + -
315B HIS* 4.5 3.7 + - - -
316B PHE* 3.7 16.8 - - + -
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Residues in contact with GLY 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU* 4.7 2.2 - - - -
188B ARG* 3.7 19.9 + - - -
191B GLY 3.0 28.0 - - - +
192B ARG* 3.7 3.9 - - - +
285B GLU 2.8 16.7 + - - -
287B ALA 3.6 1.2 - - - -
288B ALA* 1.3 77.9 - - - +
290B TYR* 1.3 61.4 + - - +
7J TYR* 4.1 9.3 - - - -
10J PHE* 3.9 8.1 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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