Contacts of the helix formed by residues 272 - 292 (chain A) in PDB entry 4Z30
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 SER 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 3.7 11.2 - - - -
209A GLU* 5.0 1.3 - - - -
270A PHE 2.9 4.4 + - - +
271A ARG* 1.3 75.7 + - - +
273A TYR* 1.3 59.0 + - - +
274A GLU* 3.9 6.5 + - - +
275A ALA* 3.3 22.0 + - - +
276A LEU* 2.8 30.1 + - - +
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Residues in contact with TYR 273 (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 GLU* 3.3 29.4 + - + +
201A LEU* 4.3 14.6 - - + -
202A LYS* 3.9 42.4 - - + -
205A LEU* 3.2 19.2 - - + +
272A SER* 1.3 70.8 - - - +
274A GLU* 1.3 64.0 + - - +
276A LEU* 4.3 5.2 - - + -
277A ARG* 2.8 82.1 + - + +
305A TYR* 4.8 4.0 - + - -
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A SER* 3.3 7.1 + - - +
273A TYR* 1.3 79.3 - - - +
275A ALA* 1.3 63.9 + - - +
277A ARG* 4.1 1.6 - - - +
278A ARG* 3.0 27.5 + - - +
313A HIS* 5.4 2.4 - - - -
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Residues in contact with ALA 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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269A GLU 3.3 26.7 - - - +
270A PHE* 3.6 20.2 - - + -
272A SER* 3.3 19.6 + - - +
274A GLU* 1.3 79.6 - - - +
276A LEU* 1.3 61.1 + - - +
278A ARG* 3.9 5.5 - - - +
279A GLU* 3.3 16.8 + - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.7 42.4 - - + +
204A VAL* 4.8 4.0 - - + -
205A LEU* 4.5 18.4 - - + +
246A LEU* 3.9 28.2 - - + +
251A CYS* 4.1 14.8 - - + -
266A LEU* 4.3 19.3 - - + -
270A PHE* 3.8 13.5 - - + +
272A SER 2.8 18.9 + - - +
273A TYR* 4.1 5.2 - - + +
275A ALA* 1.3 74.5 - - - +
277A ARG* 1.3 67.2 + - - +
278A ARG 3.3 0.2 + - - -
279A GLU* 3.3 2.8 + - - +
280A HIS* 2.9 23.7 + - - +
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Residues in contact with ARG 277 (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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191A PHE* 4.3 8.6 - - - -
194A PRO 4.8 3.4 + - - -
197A GLN* 5.3 2.0 - - - +
198A GLU* 4.5 18.6 - - - +
201A LEU* 3.6 20.4 - - - +
273A TYR* 2.8 62.7 + - + +
274A GLU* 4.2 2.2 - - - +
276A LEU* 1.3 75.0 - - - +
278A ARG* 1.3 50.1 + - - +
280A HIS* 3.2 10.7 + - - +
281A ASP* 2.7 61.4 + - - -
304A LEU* 3.2 33.5 + - - +
305A TYR* 3.3 48.9 + - + +
313A HIS* 5.2 2.5 - - + +
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Residues in contact with ARG 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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274A GLU 3.0 20.3 + - - +
275A ALA* 3.9 6.5 - - - +
277A ARG* 1.3 76.9 - - - +
279A GLU* 1.3 62.6 + - - +
281A ASP* 3.9 2.2 - - - +
282A ALA* 3.0 29.1 + - + +
313A HIS* 4.4 27.3 + - + -
317A ILE* 4.3 15.8 - - + +
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Residues in contact with GLU 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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249A ALA* 3.7 31.4 - - + +
251A CYS* 4.1 10.1 - - - -
270A PHE* 3.4 34.0 - - + -
275A ALA 3.3 14.6 + - - +
276A LEU 3.9 2.7 - - - +
278A ARG* 1.3 81.5 - - - +
280A HIS* 1.3 64.9 + - - +
282A ALA* 3.6 8.9 + - + +
283A GLN* 3.1 23.0 + - - +
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Residues in contact with HIS 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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191A PHE* 3.9 12.1 - + - -
197A GLN* 2.7 27.7 + - + -
201A LEU* 3.9 21.3 - - + +
242A VAL* 5.7 0.2 - - + -
245A LEU* 3.3 32.1 - - + +
246A LEU* 4.1 17.4 - - + +
249A ALA* 5.0 1.8 - - - +
276A LEU 2.9 14.1 + - - +
277A ARG* 3.3 20.0 + - - +
279A GLU* 1.3 75.8 - - - +
281A ASP* 1.3 92.3 + - - +
283A GLN* 3.1 16.5 + - - +
284A ILE* 3.2 33.1 + - + +
304A LEU* 5.5 0.2 - - + -
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Residues in contact with ASP 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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277A ARG* 2.7 33.2 + - - +
278A ARG 3.9 3.4 - - - +
280A HIS* 1.3 101.4 + - - +
282A ALA* 1.3 62.0 + - - +
284A ILE* 3.2 6.3 + - - +
285A VAL* 3.2 25.8 + - - +
304A LEU* 3.9 23.2 - - + +
305A TYR* 2.4 32.7 + - - -
313A HIS* 3.4 10.3 + - - +
314A MET* 4.4 3.1 - - - -
317A ILE* 4.1 14.4 - - + -
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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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278A ARG* 3.0 19.7 + - + +
279A GLU* 3.7 12.8 - - + +
281A ASP* 1.3 77.0 - - - +
283A GLN* 1.3 57.5 + - - +
285A VAL* 3.2 4.7 + - - +
286A HIS* 3.0 27.8 + - - +
317A ILE* 3.9 28.3 - - + +
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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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245A LEU* 3.9 22.2 - - + +
248A ARG* 2.6 51.4 + - + +
249A ALA* 3.7 30.1 - - + +
279A GLU 3.1 12.8 + - - +
280A HIS* 3.1 10.4 + - - +
282A ALA* 1.3 75.7 - - - +
284A ILE* 1.3 58.0 + - - +
286A HIS* 3.3 16.9 + - - +
287A ILE* 2.9 30.9 + - + +
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Residues in contact with ILE 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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180A LEU* 4.2 12.3 - - + +
181A TRP* 4.5 12.8 - - + -
184A VAL* 4.5 11.0 - - + -
191A PHE* 3.7 22.9 - - + -
245A LEU* 3.9 19.7 - - + -
280A HIS* 3.2 43.9 + - + +
281A ASP* 3.2 8.5 + - - +
283A GLN* 1.3 74.3 - - - +
285A VAL* 1.3 60.4 + - - +
287A ILE* 3.5 8.3 + - + +
288A ALA* 3.0 19.4 + - - +
300A TRP* 3.5 25.7 - - + -
304A LEU* 4.4 9.2 - - + -
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Residues in contact with VAL 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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281A ASP 3.2 12.9 + - - +
282A ALA* 3.5 9.0 - - - +
284A ILE* 1.3 75.1 - - - +
286A HIS* 1.3 61.4 + - - +
288A ALA* 2.8 20.1 + - + +
289A MET* 2.9 30.7 + - + +
300A TRP* 3.5 33.9 - - + +
314A MET* 3.8 19.5 - - + -
317A ILE* 4.5 9.2 - - + -
318A ILE* 4.4 18.2 - - + -
321A LEU* 4.7 11.9 - - + -
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Residues in contact with HIS 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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248A ARG* 4.0 9.3 + - - -
282A ALA 3.0 13.2 + - - +
283A GLN* 3.3 21.9 + - - +
285A VAL* 1.3 76.8 - - - +
287A ILE* 1.3 56.8 + - - +
289A MET* 3.5 17.9 + - + +
290A GLU* 2.8 62.0 + - + +
321A LEU* 6.0 4.0 - - + -
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Residues in contact with ILE 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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180A LEU* 4.8 1.8 - - + -
183A ALA* 3.8 26.9 - - + +
184A VAL* 3.9 28.5 - - + +
187A ARG* 3.7 14.7 - - - -
189A CYS* 4.6 12.3 - - + -
245A LEU* 4.3 14.8 - - + -
248A ARG* 3.6 24.5 - - - +
283A GLN* 2.9 30.0 + - + +
284A ILE* 3.7 9.2 - - - +
286A HIS* 1.3 74.5 - - - +
288A ALA* 1.3 66.7 + - - +
290A GLU* 3.2 7.6 + - - +
291A ALA* 3.0 22.7 + - - +
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Residues in contact with ALA 288 (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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180A LEU* 4.1 14.4 - - + -
284A ILE 3.0 8.4 + - - +
285A VAL* 2.8 15.1 + - + +
287A ILE* 1.3 70.8 - - - +
289A MET* 1.3 56.6 + - + +
291A ALA* 3.2 3.5 + - - +
292A GLY 3.0 22.7 + - - -
293A LEU* 3.0 31.3 + - + +
295A ILE* 4.4 4.7 - - + -
300A TRP* 3.6 30.1 - - + -
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Residues in contact with MET 289 (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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285A VAL* 2.9 31.8 + - + +
286A HIS* 3.7 18.6 - - + +
288A ALA* 1.3 74.4 - - + +
290A GLU* 1.3 64.0 + - + +
292A GLY* 3.2 13.4 + - - +
293A LEU 4.7 7.4 - - - +
321A LEU* 3.7 33.0 - - - +
322A GLN* 4.0 40.2 - - + +
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Residues in contact with GLU 290 (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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187A ARG* 3.0 33.0 + - - +
248A ARG* 2.9 36.2 + - - -
286A HIS* 2.8 49.6 + - + +
287A ILE* 3.2 8.6 + - - +
289A MET* 1.3 77.2 - - - +
291A ALA* 1.3 57.8 + - - +
292A GLY* 3.6 0.5 + - - -
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Residues in contact with ALA 291 (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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179A ASN 5.4 0.2 - - - +
183A ALA* 3.7 20.4 - - + -
187A ARG* 4.5 7.0 - - - +
287A ILE 3.0 16.6 + - - +
288A ALA 3.2 0.4 + - - -
290A GLU* 1.3 74.4 - - - +
292A GLY* 1.3 60.5 + - - +
293A LEU* 3.7 28.0 - - + +
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Residues in contact with GLY 292 (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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288A ALA 3.0 2.6 + - - -
289A MET 3.2 12.5 + - - -
290A GLU 3.3 0.6 - - - -
291A ALA* 1.3 79.2 - - - +
293A LEU* 1.3 64.1 + - - +
294A ARG 4.1 1.3 + - - -
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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
------------------------------------------------------------
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