Contacts of the helix formed by residues 272 - 285 (chain A) in PDB entry 5OQN
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 GLU 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A ASP 5.4 1.6 - - - +
270A ASP 3.8 13.2 - - - +
271A ILE* 1.3 78.2 - - - +
273A PRO* 1.3 71.3 - - + +
274A HIS* 3.2 32.8 - - + +
275A ILE* 3.3 12.5 + - + +
276A PHE* 2.7 27.4 + - - +
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Residues in contact with PRO 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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271A ILE 4.2 2.9 - - - +
272A GLU* 1.3 91.0 - - + +
274A HIS* 1.3 56.9 + - - +
276A PHE* 2.8 9.1 + - + -
277A ASP* 2.5 48.4 + - - +
317A LYS 6.1 0.7 - - - +
319A ASP* 5.8 5.8 - - + +
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Residues in contact with HIS 274 (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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272A GLU* 3.2 35.6 - - + +
273A PRO* 1.3 81.6 - - - +
275A ILE* 1.3 86.4 + - + +
277A ASP* 4.3 5.4 - - - +
278A GLN* 3.5 18.4 + - - +
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Residues in contact with ILE 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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238A PRO* 5.6 14.8 - - + -
241A LEU* 4.6 13.0 - - + -
271A ILE* 4.5 9.2 - - + -
272A GLU* 3.3 15.8 + - + +
273A PRO 3.2 0.2 - - - -
274A HIS* 1.3 103.9 - - + +
276A PHE* 1.3 65.6 + - - +
278A GLN* 3.2 6.9 + - + +
279A LEU* 3.1 35.7 + - + +
282A TRP* 6.6 0.2 - - + -
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Residues in contact with PHE 276 (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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260A LEU* 6.4 0.7 - - + -
267A CYS* 3.6 39.9 - - + -
268A PHE* 3.8 23.8 - + - -
271A ILE* 4.2 14.1 - - + +
272A GLU 2.7 23.5 + - - +
273A PRO* 2.8 10.6 + - + +
275A ILE* 1.3 73.4 - - - +
277A ASP* 1.3 71.2 + - - +
278A GLN 3.1 1.2 + - - -
279A LEU* 3.2 19.1 + - + +
280A ILE* 3.4 23.0 + - + +
303A TRP* 3.5 28.5 - + - -
317A LYS 4.7 11.2 - - - -
318A LEU* 3.6 25.1 - - + -
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Residues in contact with ASP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A PRO* 2.5 32.6 + - - +
274A HIS* 4.3 5.8 - - - +
276A PHE* 1.3 82.2 - - - +
278A GLN* 1.3 61.3 + - - +
280A ILE* 3.2 25.0 - - + +
281A GLU* 3.4 16.5 + - - +
317A LYS 5.0 1.2 - - - +
318A LEU* 5.4 0.2 - - - -
319A ASP* 4.0 29.6 + - - +
322A ARG* 4.4 8.6 - - - +
323A SER* 4.1 21.2 + - - +
325A VAL* 4.9 1.7 - - - +
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Residues in contact with GLN 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 HIS 3.5 12.8 + - - +
275A ILE* 3.2 12.3 + - + +
276A PHE 3.1 0.8 - - - -
277A ASP* 1.3 77.9 - - - +
279A LEU* 1.3 65.0 + - - +
281A GLU* 3.0 25.6 + - - +
282A TRP* 3.0 70.7 + - + +
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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
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241A LEU* 3.9 48.0 - - + +
244A ALA* 3.5 30.3 - - + -
255A VAL* 5.1 3.6 - - + -
256A TYR* 2.7 37.5 + - + -
260A LEU* 5.2 9.9 - - + -
271A ILE* 4.8 7.0 - - + -
275A ILE* 3.1 24.8 + - + +
276A PHE* 3.2 16.1 + - + +
278A GLN* 1.3 74.8 - - - +
280A ILE* 1.3 65.4 + - + +
282A TRP* 3.0 17.6 + - + +
283A GLY 3.1 0.2 + - - -
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Residues in contact with ILE 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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256A TYR* 4.8 1.8 - - + -
260A LEU* 6.5 0.7 - - + -
276A PHE* 3.4 16.8 - - + +
277A ASP* 3.2 32.3 - - + +
279A LEU* 1.3 77.1 - - + +
281A GLU* 1.3 61.1 + - - +
283A GLY 3.4 0.2 + - - -
284A LEU* 3.1 37.4 + - + +
295A CYS* 4.4 10.8 - - - -
299A ILE* 4.6 9.9 - - + -
303A TRP* 4.1 31.9 - - + -
318A LEU* 3.9 30.5 - - + -
323A SER* 5.0 5.2 - - - +
325A VAL* 4.5 15.2 - - + +
326A CYS* 6.3 0.7 - - - -
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Residues in contact with GLU 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 ASP* 3.4 13.1 - - - +
278A GLN* 3.0 28.4 + - - +
280A ILE* 1.3 84.0 - - - +
282A TRP* 1.3 66.3 + - + +
284A LEU* 3.6 2.9 + - - -
285A GLU* 2.7 45.6 - - - +
323A SER* 5.5 1.0 + - - -
324A SER* 5.1 10.4 + - - -
325A VAL* 3.7 23.6 - - + +
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Residues in contact with TRP 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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241A LEU 4.9 4.0 - - - -
242A GLU* 5.2 4.0 - - - -
244A ALA* 3.9 24.0 - - + +
245A ARG* 3.5 57.0 + - + +
256A TYR* 3.7 4.9 - - - +
275A ILE* 6.6 0.2 - - + -
278A GLN* 3.0 58.2 + - + +
279A LEU* 3.0 15.9 + - + +
281A GLU* 1.3 80.1 - - + +
283A GLY* 1.3 62.6 + - - +
285A GLU* 3.6 4.1 + - + +
286A ASP* 3.1 27.4 + - - +
291A VAL* 6.0 0.2 - - - -
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Residues in contact with GLY 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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256A TYR* 2.9 36.5 + - - -
279A LEU 3.1 3.0 + - - -
280A ILE 4.0 2.2 - - - -
281A GLU 3.3 0.2 - - - -
282A TRP* 1.3 79.5 - - - +
284A LEU* 1.3 59.6 + - - +
285A GLU 3.4 0.3 + - - -
286A ASP* 3.7 2.3 + - - +
291A VAL* 4.7 4.3 - - - -
292A ARG* 3.3 28.8 + - - +
295A CYS* 4.0 12.3 - - - -
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Residues in contact with LEU 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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280A ILE* 3.1 30.6 + - + +
281A GLU* 4.3 2.9 - - - +
282A TRP 3.4 0.2 - - - -
283A GLY* 1.3 76.1 - - - +
285A GLU* 1.3 62.2 + - - +
286A ASP 3.7 0.4 - - - -
292A ARG* 3.0 20.1 - - - -
295A CYS* 3.5 20.4 - - - -
296A LYS* 3.7 35.2 - - + +
299A ILE* 3.6 18.2 - - + -
325A VAL* 5.3 4.9 - - + +
328A LYS* 4.1 41.2 + - + +
329A ALA* 4.5 11.9 - - + +
332A ALA* 4.7 1.6 - - + -
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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
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281A GLU* 2.7 35.2 - - - +
282A TRP* 3.6 4.5 + - + +
283A GLY 3.2 0.2 - - - -
284A LEU* 1.3 78.0 - - - +
286A ASP* 1.3 66.5 + - - +
287A ARG* 3.7 1.0 + - - -
292A ARG* 4.2 4.6 + - - +
325A VAL* 3.4 24.1 - - - +
328A LYS* 3.8 27.5 - - - +
501B ASP* 5.0 0.2 - - - +
503B HIS* 3.0 48.2 + - + +
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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
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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