Contacts of the helix formed by residues 279 - 294 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ILE* 5.7 3.9 - - - +
276A PRO 5.1 1.3 - - - -
277A PHE* 3.0 7.7 + - - +
278A VAL* 1.3 77.8 - - - +
280A GLN* 1.3 61.5 + - - +
282A VAL* 3.3 7.6 + - - -
283A TYR* 3.7 8.3 + - - -
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A PHE 4.6 2.4 + - - -
279A ARG* 1.3 73.9 - - - +
281A GLN* 1.3 55.2 + - - +
282A VAL 3.1 0.2 - - - -
283A TYR* 5.6 0.4 - - - +
284A LYS* 2.9 32.8 + - - +
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Residues in contact with GLN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A PHE 5.2 0.6 + - - -
278A VAL* 3.0 18.4 + - - +
280A GLN* 1.3 73.9 - - - +
282A VAL* 1.3 54.6 + - - +
284A LYS* 4.8 0.7 - - - +
285A LYS* 4.9 5.2 - - - +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A VAL 3.2 7.1 + - - -
279A ARG 3.3 2.4 + - - -
280A GLN 3.1 0.6 + - - -
281A GLN* 1.3 78.8 - - - +
283A TYR* 1.3 60.7 + - - +
284A LYS 3.2 1.1 - - - -
285A LYS* 3.2 5.5 + - - +
286A VAL* 3.0 22.0 + - - -
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Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ARG 3.7 8.0 + - - -
280A GLN* 3.7 2.2 + - - -
282A VAL* 1.3 73.3 - - - +
284A LYS* 1.3 59.1 + - - +
286A VAL* 3.7 4.4 - - - +
287A GLU* 2.7 24.4 + - - -
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A GLN* 2.9 18.3 + - - +
283A TYR* 1.3 75.0 - - - +
285A LYS* 1.3 64.5 + - - +
286A VAL 3.1 0.2 - - - -
287A GLU* 3.1 2.6 + - - +
288A GLU* 3.0 21.5 + - - -
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Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLN 4.5 0.8 + - - -
281A GLN* 4.9 2.9 - - - +
282A VAL* 3.2 10.8 + - - +
284A LYS* 1.3 74.7 - - - +
286A VAL* 1.3 56.9 + - - +
288A GLU* 3.8 1.0 + - - -
289A LYS* 3.1 21.0 + - - -
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A VAL 3.0 14.2 + - - -
283A TYR* 3.7 4.7 - - - +
284A LYS 3.1 0.2 - - - -
285A LYS* 1.3 76.6 - - - +
287A GLU* 1.3 56.2 + - - +
288A GLU 3.2 0.2 - - - -
289A LYS* 3.4 2.9 - - - +
290A VAL* 2.9 28.6 + - - -
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A TYR 2.7 21.5 + - - -
284A LYS* 3.1 4.2 + - - +
286A VAL* 1.3 73.4 - - - +
288A GLU* 1.3 58.5 + - - +
290A VAL* 4.1 0.7 + - - -
291A ARG* 4.0 10.9 + - - -
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LYS 3.0 12.5 + - - -
285A LYS 4.0 1.3 - - - -
287A GLU* 1.3 75.6 - - - +
289A LYS* 1.3 60.4 + - - +
290A VAL 3.4 0.4 - - - -
291A ARG* 3.5 2.8 + - - +
292A LYS* 2.9 25.3 + - - -
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Residues in contact with LYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A LYS 3.1 15.2 + - - -
286A VAL* 3.0 9.6 + - - +
288A GLU* 1.3 79.3 - - - +
290A VAL* 1.3 56.7 + - - +
292A LYS* 3.8 0.4 - - - +
293A GLN* 2.9 26.7 + - - -
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A VAL 2.9 13.6 + - - -
287A GLU 4.1 1.7 + - - -
288A GLU 3.4 0.4 - - - -
289A LYS* 1.3 76.1 - - - +
291A ARG* 1.3 56.9 + - - +
294A THR* 3.3 23.8 + - - +
295A LYS 4.7 2.3 - - - +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A GLU 4.0 6.4 + - - -
288A GLU* 3.5 8.4 + - - +
289A LYS 3.2 0.4 - - - -
290A VAL* 1.3 76.5 - - - +
292A LYS* 1.3 55.8 + - - +
294A THR 2.9 19.8 - - - +
295A LYS* 4.2 12.8 - - - -
296A GLY* 4.8 5.2 + - - +
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Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A GLU 2.9 16.3 + - - -
289A LYS* 3.3 2.0 + - - +
291A ARG* 1.3 77.5 - - - +
293A GLN* 1.3 64.1 + - - +
294A THR 3.5 1.9 - - - +
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Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LYS 2.9 15.3 + - - -
290A VAL* 4.3 0.7 - - - +
291A ARG 3.6 0.2 - - - -
292A LYS* 1.3 80.1 - - - +
294A THR* 1.3 58.1 + - - +
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A VAL 3.3 14.0 + - - -
291A ARG 2.9 22.2 - - - +
292A LYS 3.5 2.6 - - - +
293A GLN* 1.3 76.2 - - - +
295A LYS* 1.3 61.8 + - - +
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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