Contacts of the helix formed by residues 272 - 283 (chain N) in PDB entry 3O3U
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 ASN 272 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3N GLU 2.9 25.5 + - - -
4N GLU* 3.5 4.5 - - - +
5N GLY* 2.9 24.1 + - - -
6N LYS 2.9 18.3 + - - -
7N LEU* 3.9 12.8 - - + -
58N ASP* 2.9 18.4 + - - +
270N SER* 2.9 10.5 + - - +
271N PRO* 1.3 87.7 - - - +
273N LYS* 1.3 59.9 + - - +
274N GLU 3.3 2.7 - - - -
275N LEU* 3.2 17.4 + - + +
276N ALA* 2.9 27.4 + - - +
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Residues in contact with LYS 273 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77N ALA* 3.7 29.2 - - + -
266N ILE* 4.0 19.8 - - + +
267N ASN 3.7 5.2 - - - -
268N ALA* 2.8 28.0 + - - +
269N ALA 4.4 0.6 - - - -
270N SER* 2.7 30.3 + - - +
271N PRO 3.6 2.4 + - - -
272N ASN* 1.3 77.5 - - - +
274N GLU* 1.3 58.0 + - - +
276N ALA* 3.4 7.9 + - - +
277N LYS* 3.0 27.5 + - - +
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Residues in contact with GLU 274 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N THR* 5.6 0.2 + - - -
272N ASN 3.3 0.4 - - - -
273N LYS* 1.3 76.0 - - - +
275N LEU* 1.3 66.5 + - + +
277N LYS* 3.3 32.5 + - - +
278N GLU* 3.0 26.1 + - + +
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Residues in contact with LEU 275 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5N GLY* 4.5 6.7 - - - -
6N LYS 4.6 1.8 - - - +
7N LEU* 4.1 14.1 - - + -
27N PHE* 3.7 15.4 - - + -
31N THR* 5.4 3.6 - - + +
33N ILE* 4.0 44.0 - - + -
272N ASN* 3.2 33.0 + - + +
274N GLU* 1.3 77.6 - - - +
276N ALA* 1.3 57.1 + - - +
278N GLU* 3.2 7.3 + - + +
279N PHE* 2.9 30.0 + - - +
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Residues in contact with ALA 276 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N LEU* 4.0 11.4 - - + +
58N ASP* 5.1 1.8 - - + +
59N ILE* 3.9 26.0 - - + -
266N ILE* 3.8 22.7 - - + -
272N ASN 2.9 17.2 + - - +
273N LYS* 3.6 7.2 - - - +
274N GLU 3.2 0.2 - - - -
275N LEU* 1.3 76.4 - - - +
277N LYS* 1.3 58.1 + - - +
279N PHE* 3.3 1.7 + - - +
280N LEU* 2.9 35.6 + - - +
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Residues in contact with LYS 277 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N THR* 3.0 42.4 + - - +
81N PRO* 4.6 0.4 - - - -
82N ASP 5.4 0.9 - - - +
106N TYR* 3.6 18.6 - - - +
266N ILE* 4.2 7.8 - - + +
273N LYS 3.0 16.5 + - - +
274N GLU* 3.6 29.4 + - - +
276N ALA* 1.3 76.8 - - - +
278N GLU* 1.3 58.5 + - - +
280N LEU* 4.8 1.8 - - - -
281N GLU* 2.9 62.4 + - - +
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Residues in contact with GLU 278 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27N PHE* 3.8 18.2 - - + -
31N THR* 5.4 4.0 - - + -
274N GLU* 3.0 20.0 + - + +
275N LEU* 3.7 7.9 - - + +
277N LYS* 1.3 77.0 - - - +
279N PHE* 1.3 63.5 + - - +
282N ASN* 2.7 56.7 + - - +
283N TYR* 3.5 20.1 + - + -
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Residues in contact with PHE 279 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7N LEU* 3.9 13.7 - - + -
9N ILE* 3.7 23.3 - - + -
20N LEU* 4.1 21.3 - - + -
23N VAL* 3.7 26.0 - - + -
24N GLY* 3.7 28.7 - - - -
27N PHE* 3.7 32.2 - + + -
35N VAL* 4.5 5.4 - - + -
59N ILE* 4.2 8.3 - - + -
61N PHE* 5.3 0.2 - + - -
275N LEU 2.9 16.3 + - - +
276N ALA 3.6 2.7 - - - +
278N GLU* 1.3 77.8 - - - +
280N LEU* 1.3 76.9 + - + +
283N TYR* 3.1 10.0 + - + +
284N LEU* 2.9 33.4 + - + -
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Residues in contact with LEU 280 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N ILE* 4.1 19.3 - - + -
61N PHE* 4.1 6.1 - - + -
106N TYR* 3.6 39.0 - - + -
108N ILE* 5.2 1.8 - - + -
264N ALA* 3.8 28.0 - - + +
266N ILE* 4.2 15.3 - - + -
276N ALA 2.9 21.2 + - - +
277N LYS 4.1 1.6 - - - +
279N PHE* 1.3 89.3 - - + +
281N GLU* 1.3 57.4 + - - +
284N LEU* 3.9 22.2 - - + -
285N LEU* 2.9 39.1 + - + +
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Residues in contact with GLU 281 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81N PRO* 3.3 22.3 - - - +
82N ASP* 5.2 0.9 + - - -
85N PHE* 3.5 45.7 - - + +
88N LYS* 4.7 2.8 + - - -
106N TYR* 2.6 39.4 + - + +
277N LYS* 2.9 38.6 + - - +
280N LEU* 1.3 78.0 - - - +
282N ASN* 1.3 76.4 + - - +
283N TYR 3.6 0.2 - - - -
285N LEU 3.6 12.8 - - - +
286N THR* 4.1 2.4 - - - +
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Residues in contact with ASN 282 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85N PHE* 5.3 2.6 - - - -
88N LYS* 5.4 2.6 + - - -
278N GLU* 2.7 50.8 + - - +
281N GLU* 1.3 94.4 + - - +
283N TYR* 1.3 71.2 + - + +
286N THR* 3.5 15.6 - - - +
288N GLU* 5.1 2.1 - - - +
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Residues in contact with TYR 283 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23N VAL* 3.9 17.9 - - + +
26N LYS* 4.0 20.4 - - + -
27N PHE* 3.6 50.3 - + - -
30N ASP* 2.7 39.7 + - + +
31N THR* 4.4 4.3 - - + +
278N GLU* 3.5 34.0 + - + -
279N PHE* 3.1 14.1 + - + +
282N ASN* 1.3 89.2 - - + +
284N LEU* 1.3 61.4 + - - +
286N THR* 2.9 20.9 + - - -
288N GLU* 5.0 1.7 - - - +
289N GLY* 3.3 10.6 - - - -
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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
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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