Contacts of the helix formed by residues 267 - 276 (chain A) in PDB entry 1OVM
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 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A TYR 4.4 2.5 + - - +
260A THR 5.4 0.4 + - - -
265A ALA 5.6 0.2 - - - +
266A SER* 1.3 78.2 - - - +
268A GLY* 1.3 66.1 + - - +
269A ALA* 3.6 8.1 + - - +
270A VAL* 3.3 27.1 + - + +
271A LYS* 2.9 22.3 + - - +
392A ASP* 5.8 4.0 - - - +
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Residues in contact with GLY 268 (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 SER 3.9 0.6 + - - -
267A THR* 1.3 74.0 - - - +
269A ALA* 1.3 56.9 + - - +
271A LYS* 3.7 10.4 - - - +
272A GLU* 2.9 34.2 + - - +
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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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258A TYR* 4.3 25.7 - - + +
267A THR* 3.2 8.2 + - - +
268A GLY* 1.3 77.0 - - - +
270A VAL* 1.3 57.7 + - - +
272A GLU* 3.3 4.6 + - - +
273A ALA* 2.9 30.3 + - - +
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Residues in contact with VAL 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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241A ALA* 4.9 0.4 - - + -
258A TYR* 3.1 38.6 - - + +
259A GLY* 3.7 16.2 - - - +
260A THR 3.9 5.4 - - - +
261A TYR* 3.8 39.3 - - + -
266A SER* 4.1 5.4 - - - -
267A THR* 3.2 21.8 + - + +
269A ALA* 1.3 71.8 - - - +
271A LYS* 1.3 68.5 + - - +
272A GLU 3.1 0.2 + - - -
273A ALA* 3.1 2.8 + - - -
274A ILE* 2.9 31.7 + - + +
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Residues in contact with LYS 271 (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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261A TYR* 5.0 3.1 - - - -
263A GLY 4.0 1.8 - - - -
264A SER* 2.9 47.5 + - - +
266A SER* 4.0 14.8 + - - -
267A THR 2.9 15.7 + - - +
268A GLY* 3.7 8.7 - - - +
270A VAL* 1.3 77.9 - - - +
272A GLU* 1.3 57.2 + - - +
275A GLU* 3.0 63.0 + - + +
276A GLY 3.5 0.7 + - - -
298A GLN* 6.2 0.2 - - + -
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Residues in contact with GLU 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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211A ARG* 3.0 12.2 + - - -
268A GLY 2.9 18.2 + - - +
269A ALA* 3.6 5.2 - - - +
271A LYS* 1.3 74.2 - - - +
273A ALA* 1.3 61.9 + - - +
276A GLY* 2.9 39.7 + - - +
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Residues in contact with ALA 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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211A ARG* 2.6 23.6 + - - +
213A ALA* 3.5 6.4 - - - +
239A ALA* 3.5 18.7 - - + +
258A TYR* 3.5 37.0 - - + -
269A ALA 2.9 18.3 + - - +
270A VAL* 3.7 4.5 - - - +
272A GLU* 1.3 76.6 - - - +
274A ILE* 1.3 65.6 + - + +
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Residues in contact with ILE 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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213A ALA* 4.0 15.4 - - + +
214A LEU 4.3 5.4 - - - +
215A LEU* 4.3 20.0 - - + -
239A ALA* 4.4 1.3 - - + -
240A HIS* 4.3 9.6 - - - +
241A ALA* 4.1 35.7 - - + +
258A TYR* 6.2 0.4 - - + -
261A TYR* 4.4 17.0 - - + -
270A VAL* 2.9 22.7 + - + +
273A ALA* 1.3 84.8 - - + +
275A GLU* 1.3 64.3 + - - +
276A GLY 3.0 4.7 + - - -
277A ALA* 3.3 18.2 + - - +
280A VAL* 4.3 27.2 - - + +
299A LEU* 4.8 4.9 - - + -
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Residues in contact with GLU 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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261A TYR* 2.6 38.9 + - + +
263A GLY 4.0 12.0 - - - +
264A SER* 4.6 0.5 + - - -
271A LYS* 3.0 37.9 + - + +
274A ILE* 1.3 75.6 - - - +
276A GLY* 1.3 57.6 + - - +
277A ALA 3.7 0.2 - - - +
298A GLN* 3.1 53.6 + - + +
299A LEU* 4.0 11.2 - - + -
303A GLN* 3.1 20.1 + - - +
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Residues in contact with GLY 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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211A ARG* 3.6 12.3 + - - -
271A LYS 3.5 2.0 + - - -
272A GLU* 2.9 36.3 + - - -
275A GLU* 1.3 77.0 - - - +
277A ALA* 1.3 64.5 + - - +
278A ASP* 3.7 1.7 + - - +
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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