Contacts of the helix formed by residues 266 - 278 (chain A) in PDB entry 1OV1
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 LEU 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LEU* 2.8 11.4 + - + +
263A ILE* 3.1 30.7 - - + +
265A TRP* 1.3 80.7 - - - +
267A PRO* 1.4 59.6 - - + +
269A ALA* 3.6 0.3 - - - +
270A GLY* 2.7 35.6 + - - -
291A PRO* 3.7 23.3 - - + +
294A PHE* 3.6 42.8 - - + +
295A ALA* 3.7 12.1 - - + -
298A SER* 3.8 22.0 - - - +
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Residues in contact with PRO 267 (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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263A ILE 3.9 3.1 - - - +
264A CYS 3.6 12.6 - - - +
265A TRP 3.5 2.9 - - - -
266A LEU* 1.4 99.3 - - + +
268A TYR* 1.3 71.5 + - + +
270A GLY* 3.2 2.0 + - - -
271A VAL* 3.1 30.2 + - - +
291A PRO* 4.7 6.3 - - - +
292A ALA* 5.5 2.9 - - - -
295A ALA* 3.8 13.9 - - + -
400A RET 3.5 45.5 - - + -
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Residues in contact with TYR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 3.7 34.1 - - + +
191A TYR* 4.8 11.1 + + - -
203A PHE* 5.2 9.4 - + - -
207A MET* 3.7 29.2 - - + -
265A TRP* 5.6 3.1 - - + +
267A PRO* 1.3 80.5 - - + +
269A ALA* 1.3 61.6 + - - +
271A VAL* 3.3 7.1 + - - +
272A ALA* 2.9 29.1 + - + +
400A RET 4.4 44.6 - - + +
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Residues in contact with ALA 269 (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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207A MET* 4.5 13.2 - - + +
211A HIS* 5.9 2.0 - - + +
265A TRP* 3.0 38.0 + - + +
266A LEU 3.4 0.8 + - - +
267A PRO 3.3 0.4 - - - -
268A TYR* 1.3 79.8 - - - +
270A GLY* 1.3 53.7 - - - +
272A ALA* 3.6 8.1 - - - +
273A PHE* 2.8 34.7 + - - +
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Residues in contact with GLY 270 (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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266A LEU* 2.7 20.0 + - - -
267A PRO* 3.2 3.1 + - - -
268A TYR 3.1 0.6 - - - -
269A ALA* 1.3 78.4 - - - +
271A VAL* 1.3 61.9 + - - +
273A PHE* 3.3 11.2 + - - +
274A TYR* 3.2 19.2 + - - +
291A PRO* 4.6 17.4 - - - +
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TYR* 3.6 38.4 + - + +
267A PRO 3.1 17.1 + - - +
268A TYR* 3.8 5.8 - - - +
270A GLY* 1.3 75.0 - - - +
272A ALA* 1.3 64.6 + - - +
274A TYR* 3.1 40.3 - - + +
275A ILE* 3.9 1.4 + - - +
287A PHE* 5.5 4.5 - - + -
288A MET* 5.3 18.8 - - + -
291A PRO* 4.5 18.4 - - + -
292A ALA* 5.7 4.3 - - + +
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Residues in contact with ALA 272 (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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191A TYR* 4.0 11.8 + - - +
203A PHE* 5.5 4.3 - - + +
204A CYS* 3.2 27.7 - - - +
207A MET* 3.8 28.5 - - + -
268A TYR* 2.9 18.7 + - + +
269A ALA* 3.6 6.1 - - - +
271A VAL* 1.3 77.9 - - - +
273A PHE* 1.3 60.6 + - - +
275A ILE* 3.6 18.4 + - + +
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Residues in contact with PHE 273 (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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204A CYS* 4.0 8.7 - - - -
269A ALA 2.8 16.6 + - - +
270A GLY* 3.4 11.0 - - - +
271A VAL 3.1 0.2 - - - -
272A ALA* 1.3 75.9 - - - +
274A TYR* 1.3 53.6 + - - +
275A ILE 3.0 2.5 - - - -
276A CYS* 3.0 15.3 + - + -
277A THR* 2.7 63.4 + - + -
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Residues in contact with TYR 274 (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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12A PRO* 4.8 8.1 + - + +
191A TYR* 4.9 11.7 - + - -
270A GLY 3.2 11.7 + - - +
271A VAL* 3.1 29.2 - - + +
273A PHE* 1.3 79.1 - - - +
275A ILE* 1.3 70.6 + - + +
277A THR* 3.4 8.2 - - - -
278A HIS* 2.7 45.8 + + + -
283A PHE* 3.1 41.3 - + - -
287A PHE* 3.4 47.7 - + + +
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Residues in contact with ILE 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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191A TYR* 4.1 22.4 - - + +
200A ASN* 3.6 47.8 - - - +
201A GLU* 4.8 11.4 - - + -
204A CYS* 5.1 1.3 - - + -
271A VAL 4.0 7.9 - - - +
272A ALA* 3.7 17.0 - - + +
273A PHE 3.0 0.6 - - - -
274A TYR* 1.3 96.6 - - + +
276A CYS* 1.3 66.6 + - - +
277A THR 3.0 2.0 + - - -
278A HIS 3.4 4.2 - - - +
279A GLN* 3.3 29.4 + - + +
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Residues in contact with CYS 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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201A GLU* 4.2 13.7 - - - -
204A CYS* 2.0 58.3 - - - -
205A ILE* 4.7 7.2 - - - -
273A PHE* 3.0 15.3 + - + +
275A ILE* 1.3 81.1 - - - +
277A THR* 1.3 61.9 + - - +
279A GLN* 4.6 9.5 + - - +
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Residues in contact with THR 277 (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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273A PHE* 2.7 48.9 + - + -
274A TYR* 3.4 10.1 - - - -
276A CYS* 1.3 81.3 - - - +
278A HIS* 1.3 84.9 + - + +
279A GLN* 3.5 3.5 + - - +
281A SER* 4.8 2.3 + - - -
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Residues in contact with HIS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR* 2.7 35.3 + + + +
275A ILE* 3.4 9.1 - - - +
277A THR* 1.3 91.9 + - + +
279A GLN* 1.3 58.9 + - - +
280A GLY* 3.0 8.9 + - - -
281A SER* 3.7 21.8 + - - +
282A ASP 4.7 4.5 + - - -
283A PHE* 3.8 42.8 - - + +
287A PHE* 4.7 9.1 - - + +
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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