Contacts of the helix formed by residues 271 - 281 (chain A) in PDB entry 4U6Q
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 ASP 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A HIS* 3.8 31.0 + - + +
247A ILE* 3.0 19.3 + - - +
248A ASN* 4.3 13.5 - - + +
249A ASP* 4.5 8.0 - - - +
270A VAL* 1.3 70.6 - - - +
272A GLU* 1.3 64.0 + - - +
273A LYS* 3.0 29.5 + - - +
274A ALA* 3.1 24.1 + - + +
275A LEU* 3.1 11.8 + - - +
293A GLU* 3.8 5.3 - - - +
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Residues in contact with GLU 272 (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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267A GLY 5.1 0.7 - - - +
270A VAL* 4.1 10.5 - - + +
271A ASP* 1.3 71.0 - - - +
273A LYS* 1.3 56.7 + - - +
275A LEU* 3.8 11.3 - - + +
276A ALA* 2.9 30.1 + - - +
289A LEU* 5.5 2.8 - - + +
292A HIS* 3.5 15.6 - - - +
293A GLU* 2.8 58.7 + - + +
294A SER 4.6 1.1 + - - -
297A PHE* 5.1 2.4 - - - -
303A PRO* 3.8 23.8 - - + +
304A LEU* 3.3 36.8 - - + +
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Residues in contact with LYS 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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249A ASP* 5.8 2.0 - - - +
271A ASP* 3.0 18.2 + - - +
272A GLU* 1.3 80.1 - - - +
274A ALA* 1.3 62.5 + - - +
276A ALA* 3.4 4.4 + - - +
277A GLN* 3.2 22.9 + - - +
293A GLU* 5.8 0.7 - - - +
303A PRO* 4.2 22.0 - - + +
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Residues in contact with ALA 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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247A ILE 5.2 0.2 - - - +
248A ASN* 3.9 7.0 - - - +
249A ASP* 3.3 51.4 - - - +
252A VAL* 4.4 10.3 - - + +
271A ASP* 3.1 15.8 + - + +
273A LYS* 1.3 79.5 - - - +
275A LEU* 1.3 62.3 + - - +
277A GLN* 4.0 3.7 - - - +
278A ALA* 3.1 24.8 + - - +
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Residues in contact with LEU 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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247A ILE* 5.9 2.0 - - + -
252A VAL* 5.1 4.2 - - - +
261A LEU* 4.0 19.3 - - + -
270A VAL* 4.0 20.4 - - + -
271A ASP 3.1 13.9 + - - +
272A GLU* 3.9 7.6 - - + +
273A LYS 3.3 0.2 - - - -
274A ALA* 1.3 75.4 - - - +
276A ALA* 1.3 65.2 + - - +
278A ALA* 3.3 3.1 + - - +
279A LEU* 2.9 40.0 + - + +
284A ILE* 3.9 25.1 - - + -
287A ALA* 4.1 17.0 - - + -
289A LEU* 3.9 31.2 - - + -
304A LEU* 4.2 9.4 - - + -
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Residues in contact with ALA 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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272A GLU 2.9 20.1 + - - +
273A LYS 3.6 5.2 - - - +
275A LEU* 1.3 76.6 - - - +
277A GLN* 1.3 63.8 + - - +
279A LEU* 3.0 6.3 + - - +
280A LYS* 3.0 36.3 + - - +
303A PRO* 3.5 28.0 - - + +
304A LEU* 4.4 3.1 - - + +
307A ALA* 4.1 17.2 - - + +
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Residues in contact with GLN 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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249A ASP* 5.7 2.5 - - - +
273A LYS 3.2 13.1 + - - +
274A ALA* 4.0 5.4 - - - +
276A ALA* 1.3 77.9 - - - +
278A ALA* 1.3 57.5 + - - +
280A LYS* 3.3 16.9 + - + +
281A GLU* 2.8 58.6 + - + +
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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
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252A VAL* 4.0 23.6 - - + -
274A ALA 3.1 19.3 + - - +
275A LEU* 3.5 4.9 - - - +
276A ALA 3.2 0.2 - - - -
277A GLN* 1.3 76.3 - - - +
279A LEU* 1.3 57.8 + - - +
281A GLU* 4.5 3.6 - - - -
282A GLY 2.9 7.3 + - - -
283A ARG* 2.9 39.2 + - + -
284A ILE* 3.1 24.2 + - + -
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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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275A LEU* 2.9 34.5 + - + +
276A ALA* 3.3 7.2 - - - +
278A ALA* 1.3 75.8 - - - +
280A LYS* 1.3 64.7 + - - +
282A GLY* 3.2 11.8 + - - -
284A ILE* 3.5 34.8 - - + +
286A GLY* 3.9 8.5 - - - -
287A ALA* 4.3 0.9 - - + -
304A LEU* 4.7 1.8 - - + -
307A ALA* 4.2 12.8 - - + -
308A PRO* 3.5 40.6 - - + +
309A ASN* 3.8 21.0 - - + +
310A LEU* 4.1 23.1 - - + -
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Residues in contact with LYS 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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276A ALA* 3.0 35.5 + - - +
277A GLN* 3.8 15.5 - - + +
279A LEU* 1.3 76.4 - - - +
281A GLU* 1.3 64.3 + - + +
282A GLY* 3.1 1.3 + - - -
303A PRO 4.6 6.2 + - - -
306A ASP* 4.3 21.5 - - - +
307A ALA* 4.3 7.4 - - - +
308A PRO* 3.7 22.0 - - + -
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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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257A GLN* 5.3 1.0 + - - -
277A GLN* 2.8 40.6 + - + +
278A ALA* 3.9 4.6 - - - +
280A LYS* 1.3 78.3 - - + +
282A GLY* 1.3 58.3 + - - +
283A ARG* 3.2 14.3 + - + +
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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
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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