Contacts of the helix formed by residues 281 - 291 (chain G) in PDB entry 3DHW
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 PRO 281 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278G VAL 4.3 0.9 - - - +
279G ASP* 3.0 15.7 - - - +
280G ALA* 1.4 80.2 - - - +
282G LEU* 1.3 64.8 + - - +
283G LEU 3.4 3.0 + - - -
284G SER* 3.8 2.1 + - - -
285G GLU* 3.5 21.0 + - + +
293H ASN* 3.8 28.3 - - + +
294H ASN 3.2 31.6 - - - +
295H ASN* 3.3 18.4 - - - +
317H HIS* 5.7 1.8 - - + -
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Residues in contact with LEU 282 (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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273G PHE* 4.4 10.1 - - + -
276G GLN* 2.7 48.7 - - - +
280G ALA* 3.0 13.2 + - + +
281G PRO* 1.3 74.2 - - - +
283G LEU* 1.3 67.8 + - + +
285G GLU* 3.3 3.8 + - + +
286G THR* 3.0 29.1 + - - +
329G TRP* 3.6 30.5 - - + -
330G LEU* 3.3 19.7 - - + -
333G HIS* 4.7 2.7 - - + +
335G VAL* 3.3 22.0 - - + -
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Residues in contact with LEU 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271G LEU* 5.2 11.4 - - + -
273G PHE* 6.0 2.9 - - + -
281G PRO 3.4 1.2 - - - -
282G LEU* 1.3 77.3 - - + +
284G SER* 1.3 58.9 + - - +
286G THR* 3.2 5.6 + - - +
287G ALA* 2.9 22.7 + - - +
294G ASN* 3.0 46.1 + - + +
296G ILE* 3.3 22.4 - - + -
312G MET* 3.2 39.0 - - + -
314G THR* 5.3 7.9 - - + -
316G MET* 6.2 2.0 - - + -
283H LEU* 5.4 1.6 - - + -
294H ASN* 4.8 7.8 + - + +
295H ASN* 6.5 0.2 - - - -
296H ILE* 4.6 6.3 - - + +
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Residues in contact with SER 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G PRO 3.8 3.5 + - - -
282G LEU 3.4 0.4 - - - -
283G LEU* 1.3 78.3 - - - +
285G GLU* 1.3 58.1 + - - +
287G ALA* 3.2 3.1 + - - +
288G ARG* 2.9 36.2 + - - +
294G ASN* 4.8 0.9 - - - +
283H LEU 4.3 2.6 + - - -
287H ALA* 3.6 21.9 - - - +
292H VAL 3.8 8.8 + - - -
293H ASN* 4.0 4.7 - - - -
294H ASN* 3.1 50.6 + - - +
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Residues in contact with GLU 285 (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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281G PRO* 3.5 18.7 + - + +
282G LEU* 3.3 7.0 + - + +
284G SER* 1.3 77.9 - - - +
286G THR* 1.3 62.0 + - + +
288G ARG* 2.6 44.4 + - - +
289G ARG* 3.2 51.2 + - - +
329G TRP* 4.6 18.4 - - + -
293H ASN* 4.3 1.8 - - - +
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Residues in contact with THR 286 (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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282G LEU 3.0 15.7 + - - +
283G LEU* 3.2 13.7 + - - +
285G GLU* 1.3 72.9 - - - +
287G ALA* 1.3 68.7 + - - +
289G ARG* 4.5 3.1 - - - +
290G PHE* 3.0 44.3 + - + +
292G VAL* 3.8 11.1 - - - +
294G ASN* 4.8 2.8 + - - -
316G MET* 5.5 3.7 - - - +
326G ALA* 5.7 3.1 - - - +
329G TRP* 3.4 38.4 - - + -
330G LEU* 4.1 14.4 - - + +
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Residues in contact with ALA 287 (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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283G LEU 2.9 20.7 + - - +
284G SER* 3.2 11.2 - - - +
286G THR* 1.3 80.1 + - - +
288G ARG* 1.3 63.6 + - - +
291G ASN 3.5 12.0 + - - -
292G VAL* 3.7 16.9 + - - +
294G ASN* 4.0 0.9 - - - +
284H SER* 3.7 28.3 - - - +
287H ALA* 4.0 7.4 - - + -
288H ARG* 3.4 18.5 + - - +
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Residues in contact with ARG 288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G SER* 2.9 19.1 + - - +
285G GLU* 2.6 38.5 + - - +
286G THR 3.2 0.2 - - - -
287G ALA* 1.3 79.8 - - - +
289G ARG* 1.4 64.6 + - + +
291G ASN* 4.1 2.6 + - - +
287H ALA 3.1 31.3 + - - +
288H ARG* 3.3 25.5 - - + +
291H ASN* 3.2 36.4 + - - +
292H VAL 3.4 24.0 + - - -
293H ASN* 2.7 24.4 + - - +
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Residues in contact with ARG 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G GLU* 3.2 37.7 + - - +
286G THR* 4.3 3.6 - - - +
288G ARG* 1.4 80.9 - - + +
290G PHE* 1.3 79.4 + - + +
291G ASN* 3.5 0.7 + - - +
329G TRP* 6.1 5.4 - - - -
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Residues in contact with PHE 290 (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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286G THR* 3.0 29.4 + - + +
289G ARG* 1.3 87.2 - - + +
291G ASN* 1.3 72.8 + - - +
292G VAL* 3.6 13.8 - - + +
322G ASP* 3.5 40.0 - - - +
325G ALA* 4.5 13.7 - - + -
326G ALA* 3.9 23.8 - - + -
329G TRP* 3.8 50.5 - + + -
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Residues in contact with ASN 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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287G ALA 3.5 11.7 + - - -
288G ARG 4.1 3.8 + - - +
289G ARG 3.5 3.0 - - - +
290G PHE* 1.3 82.9 - - - +
292G VAL* 1.3 59.8 + - - +
293G ASN* 5.5 0.2 - - - -
317G HIS 4.4 2.6 - - - +
318G GLY* 4.6 7.3 - - - -
319G THR* 5.3 5.7 + - - +
322G ASP* 4.7 10.7 + - - +
288H ARG* 3.6 26.2 + - - +
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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