Contacts of the helix formed by residues 276 - 285 (chain G) in PDB entry 2VKZ
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 GLY 276 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160G PHE* 3.4 13.6 - - - +
161G GLY 3.1 23.7 + - - -
245G GLN* 4.1 9.4 - - - -
272G GLY* 3.3 7.5 - - - -
273G HIS 2.9 9.9 + - - -
275G GLN* 1.3 75.0 - - - +
277G LEU* 1.3 65.9 + - - +
278G VAL 3.2 2.5 - - - -
279G THR* 3.2 20.3 + - - -
280G ALA 3.4 2.4 + - - -
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Residues in contact with LEU 277 (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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272G GLY* 3.3 24.1 - - - +
274G SER 3.3 13.9 + - - +
275G GLN 3.2 0.2 - - - -
276G GLY* 1.3 76.4 - - - +
278G VAL* 1.3 66.0 + - - +
280G ALA* 3.0 12.0 + - - +
281G VAL* 3.1 15.0 + - + +
459G VAL* 4.3 5.4 - - + -
460G TYR 5.0 5.4 - - - +
461G ASP* 5.4 0.2 - - - -
462G THR* 3.6 27.1 - - - +
468G LEU* 3.7 18.6 - - + -
479G ILE* 3.4 42.0 - - + +
482G CYS* 4.0 20.0 - - + -
483G ILE* 4.4 5.2 - - + -
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Residues in contact with VAL 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G GLN 3.7 3.1 - - - +
276G GLY 3.2 0.8 - - - -
277G LEU* 1.3 78.4 - - - +
279G THR* 1.3 64.9 + - - +
281G VAL* 3.2 4.9 + - - +
282G ALA* 3.0 19.1 + - - +
299G ALA* 3.6 26.0 - - + +
302G VAL* 3.7 24.7 - - + -
303G LEU* 3.4 36.1 - - + -
306G ILE* 4.2 2.2 - - + -
450G PHE* 5.3 2.9 - - + -
479G ILE* 4.3 19.3 - - + -
483G ILE* 3.7 23.3 - - + -
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Residues in contact with THR 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160G PHE* 3.3 25.9 - - - +
242G GLY* 4.2 14.6 - - - +
245G GLN* 3.5 22.7 + - + +
246G LEU* 4.1 25.4 - - + -
275G GLN 5.3 1.6 - - - +
276G GLY 3.2 13.9 + - - +
278G VAL* 1.3 76.3 - - - +
280G ALA* 1.3 51.9 + - - +
282G ALA* 3.6 7.0 - - - +
283G ILE* 2.7 38.6 + - - +
299G ALA* 4.6 9.9 - - + -
303G LEU* 4.7 8.1 - - + -
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Residues in contact with ALA 280 (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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160G PHE* 3.7 26.7 - - + -
270G ALA* 4.1 4.9 - - + +
271G THR* 3.7 33.9 - - - +
272G GLY 3.9 1.3 - - - +
276G GLY 3.4 1.0 + - - +
277G LEU 3.0 10.3 + - - +
279G THR* 1.3 78.6 + - - +
281G VAL* 1.3 69.1 + - - +
283G ILE* 3.2 17.4 - - - +
284G ALA* 3.3 7.6 + - - +
459G VAL* 4.0 7.7 - - + +
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Residues in contact with VAL 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G LEU* 3.1 10.1 + - + +
278G VAL 3.4 8.1 - - - +
280G ALA* 1.3 80.1 - - - +
282G ALA* 1.3 64.3 + - - +
284G ALA* 3.1 12.0 + - - +
285G GLU* 3.4 11.1 + - - +
450G PHE* 3.3 47.3 - - + -
455G ILE* 5.1 9.8 - - + +
459G VAL* 3.6 28.4 - - + +
468G LEU* 4.0 15.7 - - + -
475G ILE* 4.4 8.5 - - + -
479G ILE* 4.0 17.3 - - + -
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Residues in contact with ALA 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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246G LEU* 5.9 1.8 - - + -
278G VAL 3.0 10.8 + - - +
279G THR 3.9 2.7 - - - +
281G VAL* 1.3 82.1 - - - +
283G ILE* 1.3 62.7 + - - +
285G GLU* 3.4 9.0 + - - +
286G THR* 4.0 1.2 + - - -
295G SER* 2.9 35.8 + - - +
298G LYS* 5.1 0.2 - - + -
299G ALA* 3.7 31.2 - - + -
450G PHE* 4.1 17.3 - - + -
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Residues in contact with ILE 283 (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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160G PHE* 4.1 15.9 - - + -
246G LEU* 3.9 26.7 - - + -
249G TYR* 3.3 61.9 - - + +
264G ARG* 4.0 4.4 - - + +
267G LEU* 5.1 8.3 - - + -
270G ALA* 4.5 8.7 - - + -
279G THR 2.7 18.3 + - - +
280G ALA* 3.2 16.8 - - - +
281G VAL 3.1 0.6 + - - -
282G ALA* 1.3 74.0 - - - +
284G ALA* 1.3 65.3 + - + +
286G THR* 3.0 32.3 - - + +
292G PHE* 4.9 7.2 - - + -
457G ILE* 5.2 0.2 - - + -
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Residues in contact with ALA 284 (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 ARG* 3.3 21.1 - - - +
280G ALA 3.8 6.7 - - - +
281G VAL 3.1 10.3 + - - +
283G ILE* 1.3 76.0 - - + +
285G GLU* 1.3 57.3 + - - +
286G THR 3.0 9.0 + - - -
455G ILE* 4.3 3.8 - - + -
456G GLN* 3.2 26.4 + - - +
457G ILE* 3.5 37.9 - - + +
459G VAL* 4.2 6.7 - - + -
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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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264G ARG* 5.2 0.2 - - - -
281G VAL 3.4 4.9 + - - +
282G ALA 3.4 11.1 + - - +
283G ILE 3.2 0.4 - - - -
284G ALA* 1.3 76.7 - - - +
286G THR* 1.3 59.9 + - - +
287G ASP* 3.9 2.3 + - - +
291G SER* 5.4 2.8 + - - -
295G SER* 4.0 11.3 + - - +
298G LYS* 3.2 40.0 + - - +
450G PHE* 3.3 35.5 - - + +
451G ASN 3.9 1.9 + - - +
454G ASP* 3.8 41.7 - - + +
455G ILE* 4.1 10.3 - - + +
456G GLN* 5.6 0.7 - - - -
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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