Contacts of the helix formed by residues 264 - 271 (chain G) in PDB entry 4HY0
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 264 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260G PRO 5.0 0.2 + - - -
261G SER 4.9 1.5 + - - +
262G MET* 3.1 0.6 - - - +
263G ALA* 1.3 79.2 - - + +
265G TYR* 1.3 81.6 + - - +
266G GLU* 3.1 28.3 + - - +
267G ALA* 3.1 23.9 + - + +
268G ARG* 3.2 15.3 + - - +
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Residues in contact with TYR 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263G ALA 4.0 0.8 + - - -
264G ASP* 1.3 75.7 + - - +
266G GLU* 1.3 70.0 + - + +
268G ARG* 3.0 28.7 + - - +
269G ILE* 2.9 52.3 + - + +
282G GLU* 3.9 17.0 + - - +
285G ALA* 3.4 26.9 - - + -
286G ARG* 3.5 29.9 + - + +
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Residues in contact with GLU 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264G ASP* 3.1 19.6 + - - +
265G TYR* 1.3 82.4 - - + +
267G ALA* 1.3 63.2 + - - +
269G ILE* 3.2 16.4 - - - +
270G PHE* 3.2 25.0 + - - +
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Residues in contact with ALA 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261G SER 3.8 22.4 - - - +
262G MET* 3.7 19.2 - - + +
264G ASP* 3.1 21.0 + - + +
266G GLU* 1.3 79.8 - - - +
268G ARG* 1.3 61.8 + - - +
270G PHE* 3.7 16.4 + - - +
271G THR* 4.0 6.6 + - - +
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Residues in contact with ARG 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262G MET* 2.9 51.1 + - + +
263G ALA 3.0 22.6 + - - -
264G ASP 3.2 3.7 + - - +
265G TYR* 3.0 30.6 + - - +
267G ALA* 1.3 74.8 - - - +
269G ILE* 1.3 64.6 + - - +
271G THR* 2.7 22.2 + - - -
272G PHE* 3.2 12.6 - - - -
285G ALA* 3.0 32.3 + - + -
286G ARG* 4.6 0.4 + - - +
288G GLY* 3.1 24.6 + - - -
289G PHE 3.7 13.9 - - - +
290G TYR* 4.2 4.0 - - + -
301G PHE* 3.6 19.4 - - - -
329G TYR* 3.9 17.2 + - - -
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Residues in contact with ILE 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265G TYR* 2.9 47.5 + - + +
266G GLU* 3.2 27.3 + - - +
268G ARG* 1.3 75.0 - - - +
270G PHE* 1.3 70.3 + - - +
272G PHE* 3.2 21.8 + - + +
273G GLY 4.2 1.9 + - - -
281G LYS* 3.9 20.6 + - + +
282G GLU* 4.0 11.4 - - + -
285G ALA* 3.4 20.2 - - + -
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Residues in contact with PHE 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266G GLU* 3.2 13.2 + - - +
267G ALA* 3.7 9.0 - - - +
268G ARG 3.3 0.2 - - - -
269G ILE* 1.3 85.0 - - + +
271G THR* 1.3 73.6 + - + +
272G PHE 3.2 4.3 + - - -
273G GLY* 3.4 12.6 + - - +
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Residues in contact with THR 271 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262G MET* 4.1 24.0 - - + -
267G ALA 4.0 3.6 + - - +
268G ARG 2.7 21.2 + - - -
270G PHE* 1.3 92.3 - - + +
272G PHE* 1.3 59.2 + - - +
273G GLY 3.5 5.9 + - - +
274G THR 4.7 2.8 - - - +
290G TYR* 3.8 4.0 - - + +
291G ALA* 3.2 46.2 + - - +
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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