Contacts of the helix formed by residues 272 - 289 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A HIS* 3.5 53.3 + - + +
218A ILE* 3.6 20.3 - - + +
271A ASN* 1.3 86.3 - - + +
273A ALA* 1.3 63.6 + - - +
274A VAL 3.1 0.4 - - - -
275A ASP* 3.1 12.5 + - - +
276A TRP* 3.7 7.7 - - + +
337A GLY 3.1 25.5 + - - -
338A ASN* 4.0 14.5 - - - +
339A LEU 5.7 0.4 + - - -
342A GLY* 4.8 8.9 - - - -
343A VAL 5.5 0.6 - - - +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLU* 4.1 4.7 - - - +
271A ASN* 2.9 18.3 + - - +
272A LYS* 1.3 81.0 - - - +
274A VAL* 1.3 60.4 + - - +
276A TRP* 3.1 14.7 + - - +
277A TRP 3.1 14.0 + - - -
332A LEU* 4.2 6.1 - - + -
335A ARG* 3.0 30.0 + - - +
338A ASN* 3.7 28.9 - - + +
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Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 5.2 1.6 - - + -
220A ARG* 4.3 18.6 - - + -
259A TYR 5.3 0.5 - - - +
261A ALA* 3.9 24.8 + - + +
263A GLU* 3.5 17.5 - - + +
264A ILE* 3.9 14.8 - - + -
270A TYR* 3.4 42.6 - - + -
271A ASN 3.4 13.7 - - - +
272A LYS* 3.1 0.4 + - - -
273A ALA* 1.3 73.7 - - - +
275A ASP* 1.3 73.0 + - - +
277A TRP* 3.5 2.6 + - - +
278A ALA* 3.0 23.0 + - - +
335A ARG* 4.1 0.4 - - - +
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Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 3.4 34.6 - - + -
212A LEU* 5.7 0.2 - - - +
213A HIS* 2.8 36.6 + - + +
218A ILE* 3.5 8.3 - - - +
219A TYR* 2.9 25.0 + - - +
220A ARG* 2.9 28.8 + - - -
222A LEU 5.7 0.3 + - - -
272A LYS 3.1 4.9 + - - +
274A VAL* 1.3 84.8 - - - +
276A TRP* 1.3 56.1 + - - +
278A ALA* 3.2 7.9 + - - +
279A LEU 3.0 22.3 + - - -
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Residues in contact with TRP 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 3.8 14.8 - - + -
209A PHE* 3.5 37.5 - + + -
210A GLU* 4.4 1.3 - - - -
213A HIS* 3.5 23.1 + + - -
272A LYS* 3.7 22.6 - - + +
273A ALA* 3.1 12.7 + - + +
275A ASP* 1.3 75.7 - - - +
277A TRP* 1.3 64.3 + - - +
279A LEU* 3.2 27.8 + - + +
280A GLY 3.2 16.8 + - - -
327A LEU* 3.8 11.8 - - + +
335A ARG* 4.4 4.7 - - - -
336A PHE 3.4 19.5 - - - +
337A GLY* 3.5 31.8 + - - -
338A ASN* 5.3 0.2 - - + -
343A VAL* 3.7 32.8 - - + -
346A ILE* 3.4 22.7 - - + -
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Residues in contact with TRP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLU 5.2 0.8 + - - -
259A TYR 3.8 7.4 - - - -
260A LEU 3.4 12.5 + - - -
261A ALA* 3.5 22.9 - - + -
262A PRO* 3.5 33.7 - - + -
273A ALA 3.1 6.7 + - - -
274A VAL 3.6 7.9 - - - +
276A TRP* 1.3 75.5 - - - +
278A ALA* 1.3 65.2 + - - +
280A GLY* 3.0 13.2 + - - -
281A VAL* 3.1 25.0 + - + +
293A PHE* 3.5 35.8 - + - -
305A ILE* 3.8 11.2 - - + +
308A GLY* 5.0 0.2 - - - -
327A LEU 3.7 10.8 - - - -
328A LEU* 3.3 47.2 - - + +
329A GLN 3.7 19.7 - - - -
330A VAL* 4.0 9.2 - - + -
335A ARG* 3.7 19.1 - - - +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG 6.4 1.1 - - - -
222A LEU* 3.7 28.5 - - + +
259A TYR* 3.7 22.9 - - + +
274A VAL 3.0 14.4 + - - +
275A ASP* 3.2 12.5 + - - +
277A TRP* 1.3 82.0 - - - +
279A LEU* 1.3 57.0 + - - +
281A VAL* 3.2 7.0 + - - +
282A LEU* 2.9 28.4 + - - +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ALA* 4.4 9.2 - - - +
205A ILE* 3.9 26.9 - - + -
206A VAL* 3.8 22.2 - - + +
209A PHE* 4.5 4.5 - - + -
222A LEU* 3.7 12.3 - - + +
275A ASP 3.0 12.7 + - - +
276A TRP* 3.4 33.7 - - + +
277A TRP 3.2 0.2 - - - -
278A ALA* 1.3 72.7 - - - +
280A GLY* 1.3 61.6 + - - +
282A LEU* 3.2 5.7 + - + +
283A ILE* 2.9 53.4 + - + +
327A LEU* 4.2 15.7 - - + -
346A ILE* 4.8 4.0 - - + -
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Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TRP 3.2 7.7 + - - -
277A TRP 3.0 8.6 + - - -
279A LEU* 1.3 77.4 - - - +
281A VAL* 1.3 61.8 + - - +
284A TYR* 2.9 25.3 + - - +
324A LEU* 3.4 11.3 - - - +
327A LEU* 3.8 27.9 - - - +
328A LEU* 3.8 10.8 - - - -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLU 3.6 22.0 - - - +
259A TYR* 3.4 30.3 - - + -
277A TRP* 3.1 38.8 + - + +
278A ALA* 3.2 8.5 + - - +
280A GLY* 1.3 74.4 - - - +
282A LEU* 1.3 57.2 + - - +
284A TYR* 3.3 2.6 + - - +
285A GLU* 2.8 27.7 + - - +
291A PRO* 4.7 3.4 - - + -
292A PRO* 3.7 29.1 - - + +
293A PHE* 4.8 1.3 - - + -
328A LEU* 3.8 8.5 - - + -
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A MET* 4.3 7.2 - - + -
201A TYR* 5.9 0.2 - - + -
205A ILE* 4.1 15.7 - - + -
222A LEU* 3.9 19.7 - - + -
223A LYS* 4.3 2.9 - - - -
224A PRO* 3.7 40.2 - - + -
227A LEU* 3.8 26.9 - - + -
259A TYR* 3.5 11.8 - - + +
278A ALA 2.9 15.9 + - - +
279A LEU* 3.2 9.6 + - + +
281A VAL* 1.3 74.9 - - - +
283A ILE* 1.3 59.9 + - - +
285A GLU* 3.2 1.4 + - - +
286A MET* 2.8 55.3 + - + +
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Residues in contact with ILE 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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198A ALA* 5.0 1.5 - - + +
202A ALA* 3.8 28.9 - - + -
279A LEU* 2.9 46.0 + - + +
280A GLY 3.9 2.7 - - - +
282A LEU* 1.3 72.9 - - - +
284A TYR* 1.3 64.9 + - - +
286A MET* 3.7 10.8 - - + +
287A ALA* 3.0 24.2 + - + +
320A LEU* 3.7 30.5 - - + -
323A LEU* 4.2 13.2 - - + -
324A LEU* 4.0 5.8 - - + -
327A LEU* 4.0 16.4 - - + -
351A TRP* 4.0 15.3 - - + -
352A PHE* 4.6 2.9 - - + -
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Residues in contact with TYR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLY 2.9 17.9 + - - +
281A VAL 3.5 4.0 - - - +
283A ILE* 1.3 79.1 - - - +
285A GLU* 1.3 57.4 + - - +
287A ALA 3.8 0.3 - - - -
288A ALA* 2.8 38.3 + - + +
290A TYR* 3.3 40.9 + + - -
291A PRO 3.7 1.1 - - - -
292A PRO* 3.4 44.9 + - + +
310A VAL* 3.9 4.9 - - + -
311A ARG 2.6 29.3 + - - -
312A PHE* 3.7 17.5 - + - -
313A PRO* 3.8 9.9 - - + +
316A PHE* 3.8 16.2 - + - -
324A LEU* 4.0 18.6 - - + +
328A LEU* 4.5 3.6 - - + -
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 3.9 11.5 - - + +
188A ARG* 2.6 40.2 + - - +
224A PRO* 4.4 6.5 - - + +
259A TYR* 2.6 31.7 + - - +
281A VAL 2.8 21.0 + - - +
282A LEU 3.9 1.1 - - - +
284A TYR* 1.3 73.9 - - - +
286A MET* 1.3 58.8 + - + +
289A GLY* 2.8 27.9 + - - -
290A TYR 3.5 26.5 - - - +
291A PRO* 4.1 11.7 - - + +
19I ARG* 3.1 26.2 + - - -
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Residues in contact with MET 286 (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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183A MET* 3.7 38.6 - - - +
187A LEU* 3.8 12.5 - - + +
192A ARG* 3.7 4.2 - - - +
193A PHE* 2.8 43.4 + - + +
198A ALA* 3.4 29.8 - - + +
201A TYR* 3.8 20.2 - - + -
202A ALA 4.2 4.5 - - - +
282A LEU* 2.8 38.3 + - + +
283A ILE* 3.7 26.9 - - + +
285A GLU* 1.3 74.3 - - - +
287A ALA* 1.3 57.9 + - - +
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Residues in contact with ALA 287 (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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192A ARG* 3.3 11.5 + - - +
193A PHE 3.7 11.8 - - - +
195A GLU* 4.8 7.9 - - + -
198A ALA* 4.6 11.0 - - + -
283A ILE* 3.0 17.9 + - + +
286A MET* 1.3 76.4 - - - +
288A ALA* 1.3 58.6 + - - +
315A HIS* 3.2 20.8 - - - -
316A PHE* 3.6 20.6 - - + -
320A LEU* 3.8 17.0 - - + -
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ARG* 3.8 13.8 + - - +
284A TYR* 2.8 26.4 + - + +
287A ALA* 1.3 80.7 - - - +
289A GLY* 1.3 57.9 + - - +
290A TYR* 3.3 31.3 - - + +
313A PRO* 3.7 27.1 - - + -
315A HIS* 4.4 3.8 + - - -
316A PHE* 3.7 5.2 - - + -
7I TYR* 4.2 7.3 - - - +
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Residues in contact with GLY 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 4.7 1.6 - - - -
188A ARG* 3.8 10.5 + - - -
191A GLY 3.1 27.3 - - - +
192A ARG* 3.8 2.6 - - - +
285A GLU* 2.8 18.5 + - - -
287A ALA 3.7 0.8 - - - -
288A ALA* 1.3 77.2 - - - +
290A TYR* 1.3 61.1 + - - +
7I TYR* 3.7 16.2 - - - -
10I PHE* 3.8 11.6 - - - -
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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