Contacts of the strand formed by residues 286 - 292 (chain G) in PDB entry 2HU4
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 286 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233G VAL* 4.9 0.2 - - - +
282G PRO* 3.5 1.5 - - - +
283G ASN* 2.7 42.1 + - - +
284G ALA* 4.1 7.6 - - + +
285G GLY* 1.3 85.1 - - - +
287G ILE* 1.3 67.6 + - - +
288G THR* 4.0 1.9 + - - +
304G SER* 5.4 4.3 - - - -
305G PHE* 3.4 23.1 + - - +
306G ASN* 4.3 18.4 + - - +
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Residues in contact with ILE 287 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G ALA* 4.1 17.5 - - + +
233G VAL* 4.6 7.4 - - + -
238G PHE* 3.8 38.1 - - + +
280G CYS* 3.7 26.9 - - + -
281G TYR 3.5 7.9 - - - +
282G PRO* 4.8 3.8 - - + -
285G GLY 4.6 4.5 - - - +
286G GLU* 1.3 83.6 - - - +
288G THR* 1.3 66.4 + - - +
289G CYS* 4.0 2.2 - - - -
303G VAL 4.7 0.2 - - - -
304G SER* 3.2 6.6 - - - -
305G PHE* 3.1 68.5 + - + +
306G ASN 4.9 1.6 - - - +
308G GLN* 5.1 0.9 - - + -
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Residues in contact with THR 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G SER 3.6 0.5 - - - +
280G CYS* 3.2 0.9 - - - -
281G TYR* 2.9 75.7 + - + +
283G ASN* 5.2 4.2 - - - +
286G GLU* 4.0 3.7 + - - +
287G ILE* 1.3 76.2 + - - +
289G CYS* 1.3 67.1 + - - +
290G VAL* 4.7 2.2 - - + -
302G TRP* 5.9 0.9 - - + -
303G VAL 3.7 4.7 - - - +
304G SER* 4.4 9.9 - - - +
355G LYS* 5.1 5.5 - - + +
383G TRP* 4.6 20.0 - - + -
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Residues in contact with CYS 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240G VAL* 3.8 16.2 - - - -
278G CYS* 4.1 0.9 - - + -
279G SER 3.4 3.6 - - - -
280G CYS* 2.0 46.0 - - - -
287G ILE* 4.0 9.6 - - - -
288G THR* 1.3 75.9 - - - +
290G VAL* 1.3 62.2 + - - +
291G CYS* 4.0 15.3 - - - -
302G TRP* 3.1 9.2 - - - +
303G VAL* 2.8 42.4 + - + +
305G PHE* 4.1 12.1 - - - -
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Residues in contact with VAL 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G SER* 3.0 32.3 + - - +
281G TYR* 5.0 0.4 - - + -
288G THR* 4.7 6.5 - - + -
289G CYS* 1.3 75.7 - - - +
291G CYS* 1.3 63.0 + - - +
300G ARG* 3.8 34.1 - - + -
301G PRO 3.6 4.5 - - - +
302G TRP* 4.3 1.3 - - + -
317G ILE* 4.1 5.2 - - + -
351G GLY 3.8 4.7 - - - +
352G PHE* 3.9 2.5 - - - -
353G SER* 3.5 52.3 - - - +
383G TRP* 4.4 21.3 - - + -
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Residues in contact with CYS 291 (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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275G TYR* 3.7 15.7 - - + -
276G GLU 3.5 11.9 - - - +
277G GLU 4.6 2.0 - - - -
278G CYS* 2.0 52.7 - - - +
289G CYS* 4.0 13.2 - - - -
290G VAL* 1.3 76.5 - - - +
292G ARG* 1.3 62.6 + - - +
300G ARG* 3.0 35.2 + - - +
301G PRO* 2.9 26.0 + - + +
303G VAL* 4.7 0.4 - - - -
351G GLY 5.2 1.8 - - - -
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Residues in contact with ARG 292 (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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274G HIS* 3.3 7.4 + - - +
275G TYR 3.7 0.7 - - - -
276G GLU* 3.0 33.7 + - + +
277G GLU* 2.6 41.8 + - + +
291G CYS* 1.3 80.5 - - - +
293G ASP* 1.3 69.6 + - - +
294G ASN* 2.9 30.9 + - + +
300G ARG* 3.6 5.8 - - - +
301G PRO* 4.0 1.1 - - - -
324G ASP* 4.5 1.6 - - - +
347G TYR* 3.7 9.9 - - - -
348G GLY* 3.0 22.8 + - - -
349G VAL* 3.4 32.9 - - - +
350G LYS* 4.6 4.9 - - - -
406G TYR* 2.8 20.4 + - - -
806G G39 3.3 34.2 + - - +
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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
------------------------------------------------------------
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