Contacts of the helix formed by residues 274 - 284 (chain A) in PDB entry 2VWJ
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 THR 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A TYR* 4.2 1.8 - - - -
272A THR* 3.4 17.9 + - - +
273A TYR* 1.3 78.5 - - - +
275A LEU* 1.3 64.8 + - - +
276A GLU* 3.3 18.4 + - + +
277A ALA* 2.8 27.3 + - - +
278A VAL* 3.0 25.9 + - - +
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Residues in contact with LEU 275 (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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141A ASP* 4.9 3.1 - - - +
209A TYR* 3.4 51.9 - - + -
274A THR* 1.3 73.8 - - - +
276A GLU* 1.3 66.9 + - - +
278A VAL* 3.8 3.0 - - - +
279A TYR* 3.0 29.3 + - - +
287A LYS* 4.0 7.2 - - - -
315A ASP* 3.4 35.2 - - + +
318A VAL* 3.7 22.2 - - + -
319A THR* 4.0 11.2 - - - +
322A LEU* 4.4 13.4 - - + +
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Residues in contact with GLU 276 (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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274A THR* 3.7 14.8 - - + +
275A LEU* 1.3 86.9 + - - +
277A ALA* 1.3 63.7 + - - +
279A TYR* 4.2 1.5 - - - +
280A GLU* 3.3 25.6 + - - +
287A LYS* 3.3 67.7 + - + +
289A LYS* 3.5 35.3 - - + +
311A TYR* 4.1 8.7 + - - -
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 4.3 11.8 - - + +
272A THR* 3.7 29.2 - - + -
274A THR* 2.8 23.7 + - - +
276A GLU* 1.3 74.5 - - - +
278A VAL* 1.3 65.8 + - - +
280A GLU* 3.1 7.5 + - - +
281A ALA* 2.9 24.9 + - - +
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Residues in contact with VAL 278 (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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209A TYR* 3.4 23.6 - - + +
264A ILE* 3.7 48.0 - - + -
268A ILE* 5.2 0.4 - - + -
270A LEU* 4.5 11.9 - - + -
273A TYR* 4.3 11.4 - - + -
274A THR 3.0 17.8 + - - +
275A LEU* 3.8 4.7 - - - +
277A ALA* 1.3 75.8 - - - +
279A TYR* 1.3 64.8 + - - +
280A GLU 3.2 0.3 + - - -
281A ALA* 3.3 1.5 + - - +
282A ILE* 3.1 31.7 + - + +
322A LEU* 3.9 17.5 - - + -
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Residues in contact with TYR 279 (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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275A LEU 3.0 18.8 + - - +
276A GLU* 4.2 4.9 - - - +
278A VAL* 1.3 77.4 - - - +
280A GLU* 1.3 57.4 + - - +
282A ILE* 4.2 0.2 - - - +
283A PHE* 2.9 59.4 + + + +
285A GLN* 3.7 30.8 + - + +
286A PRO 4.4 7.4 - - - -
287A LYS* 4.3 14.8 - - + -
318A VAL* 3.6 45.2 - - + +
321A GLU* 3.7 22.6 + - + -
322A LEU* 4.6 12.3 - - + +
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Residues in contact with GLU 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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276A GLU 3.3 17.6 + - - +
277A ALA* 3.1 7.0 + - - +
279A TYR* 1.3 77.9 - - - +
281A ALA* 1.3 64.4 - - - +
284A GLY* 2.8 47.2 + - - +
285A GLN 3.2 12.3 + - - +
286A PRO* 3.3 37.2 - - + +
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Residues in contact with ALA 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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268A ILE* 4.0 24.0 - - + -
270A LEU* 4.3 15.5 - - + -
277A ALA 2.9 16.1 + - - +
278A VAL 3.7 4.0 - - - +
280A GLU* 1.3 77.9 - - - +
282A ILE* 1.3 61.3 + - - +
284A GLY* 4.8 0.5 + - - -
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Residues in contact with ILE 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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264A ILE* 5.4 0.2 - - + -
267A THR* 5.6 0.4 - - + -
268A ILE* 4.0 30.5 - - + -
278A VAL* 3.1 24.9 + - + +
279A TYR 4.2 1.3 - - - +
281A ALA* 1.3 81.1 - - + +
283A PHE* 1.3 78.5 + - + +
322A LEU* 4.3 10.8 - - + -
325A GLU* 4.6 9.6 - - + -
326A PHE* 3.7 37.7 - - + -
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Residues in contact with PHE 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 TYR* 2.9 49.5 + + + +
282A ILE* 1.3 96.9 - - + +
284A GLY* 1.3 59.7 + - - +
285A GLN* 3.4 13.0 + - + +
321A GLU* 4.3 42.4 - - + -
322A LEU* 4.7 5.2 - - + -
325A GLU* 4.7 17.7 - - + -
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Residues in contact with GLY 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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279A TYR 4.0 0.2 + - - -
280A GLU* 2.8 36.6 + - - +
281A ALA 4.7 0.8 + - - -
282A ILE 3.7 0.6 - - - -
283A PHE* 1.3 71.8 - - - +
285A GLN* 1.3 66.5 + - - +
286A PRO* 4.6 0.2 - - - +
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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