Contacts of the helix formed by residues 279 - 294 (chain G) in PDB entry 5ZRV
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 ARG 279 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275G ILE* 5.7 3.8 - - - +
276G PRO 5.9 1.3 - - - -
277G PHE* 3.0 7.7 - - - +
278G VAL* 1.3 77.7 - - - +
280G GLN* 1.3 62.3 + - - +
282G VAL* 3.3 7.1 + - - -
283G TYR* 3.7 8.3 + - - -
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Residues in contact with GLN 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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277G PHE 4.6 2.8 + - - -
278G VAL 3.5 0.2 - - - -
279G ARG* 1.3 74.0 - - - +
281G GLN* 1.3 56.5 + - - +
282G VAL 3.1 0.4 - - - -
283G TYR 4.9 0.2 - - - +
284G LYS* 2.9 32.0 + - - +
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Residues in contact with GLN 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G PHE 5.2 0.6 + - - -
278G VAL* 3.0 17.9 + - - +
280G GLN* 1.3 73.4 - - - +
282G VAL* 1.3 55.9 + - - +
284G LYS 4.8 0.2 - - - -
285G LYS* 4.9 4.6 - - - +
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Residues in contact with VAL 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G VAL 3.2 6.5 + - - -
279G ARG 3.3 2.6 + - - -
280G GLN 3.1 0.6 - - - -
281G GLN* 1.3 79.3 - - - +
283G TYR* 1.3 61.5 + - - +
284G LYS 3.2 1.3 - - - -
285G LYS* 3.2 4.9 + - - +
286G VAL* 3.0 22.5 + - - -
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Residues in contact with TYR 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G ARG 3.7 9.0 + - - -
280G GLN* 3.7 2.3 + - - +
282G VAL* 1.3 72.8 - - - +
284G LYS* 1.3 61.1 + - - +
286G VAL* 3.7 4.4 - - - +
287G GLU* 2.7 24.3 + - - -
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Residues in contact with LYS 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G GLN 2.9 18.8 + - - -
283G TYR* 1.3 76.4 - - - +
285G LYS* 1.3 64.2 + - - +
286G VAL 3.1 0.2 - - - -
287G GLU* 3.5 1.9 - - - +
288G GLU* 3.0 21.1 + - - -
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Residues in contact with LYS 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G GLN 4.5 1.2 + - - -
281G GLN* 4.9 3.3 - - - +
282G VAL* 3.2 10.9 + - - +
284G LYS* 1.3 74.5 - - - +
286G VAL* 1.3 57.6 + - - +
288G GLU* 4.0 0.7 - - - -
289G LYS* 3.1 21.5 + - - -
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Residues in contact with VAL 286 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G VAL 3.0 14.0 + - - -
283G TYR* 3.7 4.9 - - - +
284G LYS 3.1 0.2 - - - -
285G LYS* 1.3 76.8 - - - +
287G GLU* 1.3 58.6 + - - +
288G GLU 3.2 0.4 - - - -
289G LYS* 4.1 2.2 - - - +
290G VAL* 2.9 28.9 + - - -
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Residues in contact with GLU 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 TYR 2.7 20.5 + - - -
284G LYS* 3.1 5.1 + - - +
286G VAL* 1.3 73.4 - - - +
288G GLU* 1.3 59.2 + - - +
290G VAL* 4.1 1.0 + - - -
291G ARG* 4.0 10.2 + - - -
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Residues in contact with GLU 288 (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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284G LYS 3.0 13.7 + - - -
285G LYS 4.0 0.7 - - - -
287G GLU* 1.3 75.4 - - - +
289G LYS* 1.3 59.2 + - - +
290G VAL 3.4 0.7 - - - -
291G ARG* 3.5 3.2 + - - +
292G LYS* 2.9 25.3 + - - -
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Residues in contact with LYS 289 (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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285G LYS 3.1 15.0 + - - -
286G VAL* 3.0 8.6 + - - +
288G GLU* 1.3 77.0 - - - +
290G VAL* 1.3 57.1 + - - +
292G LYS* 3.3 1.6 + - - +
293G GLN* 2.9 26.2 + - - -
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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
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286G VAL 2.9 13.4 + - - -
287G GLU 4.1 1.5 + - - -
288G GLU 3.4 0.2 - - - -
289G LYS* 1.3 76.8 - - - +
291G ARG* 1.3 57.3 + - - +
293G GLN* 5.3 0.4 - - - +
294G THR* 3.3 23.4 + - - +
295G LYS 4.7 2.6 - - - +
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Residues in contact with ARG 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G GLU 4.0 7.6 + - - -
288G GLU* 3.5 8.2 + - - +
289G LYS 3.2 0.4 - - - -
290G VAL* 1.3 74.9 - - - +
292G LYS* 1.3 55.7 + - - +
294G THR 2.9 19.1 - - - +
295G LYS* 4.2 12.8 - - - -
296G GLY* 4.8 4.8 + - - +
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Residues in contact with LYS 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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288G GLU 2.9 15.7 + - - -
289G LYS* 3.3 1.5 + - - +
291G ARG* 1.3 77.7 - - - +
293G GLN* 1.3 64.8 + - - +
294G THR 3.5 2.2 - - - +
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Residues in contact with GLN 293 (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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289G LYS 2.9 16.4 + - - -
290G VAL* 4.3 0.4 - - - +
292G LYS* 1.3 79.6 - - - +
294G THR* 1.3 58.1 + - - +
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Residues in contact with THR 294 (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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290G VAL 3.3 13.1 + - - -
291G ARG 2.9 22.2 - - - +
292G LYS 3.5 2.4 - - - +
293G GLN* 1.3 76.7 - - - +
295G LYS* 1.3 62.1 + - - +
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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