Contacts of the helix formed by residues 267 - 276 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D TYR 4.4 2.7 + - - +
260D THR 5.5 0.6 + - - -
265D ALA 5.6 0.2 - - - +
266D SER* 1.3 76.6 - - - +
268D GLY* 1.3 60.4 + - - +
269D ALA* 3.8 7.9 + - - +
270D VAL* 3.2 27.4 + - + +
271D LYS* 2.9 26.8 + - - +
392D ASP* 5.8 4.0 - - - +
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Residues in contact with GLY 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D SER 3.9 0.8 + - - -
267D THR* 1.3 72.6 - - - +
269D ALA* 1.3 56.3 + - - +
271D LYS* 3.8 10.7 - - - +
272D GLU* 2.9 33.6 + - - +
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Residues in contact with ALA 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D TYR* 4.3 25.8 - - + +
267D THR* 3.2 8.8 + - - +
268D GLY* 1.3 75.7 - - - +
270D VAL* 1.3 58.0 + - - +
272D GLU* 3.2 5.9 + - - +
273D ALA* 2.8 30.7 + - - +
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Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D ALA* 4.9 0.9 - - + -
258D TYR* 3.1 40.2 - - - +
259D GLY* 3.6 16.6 - - - +
260D THR 4.0 4.9 - - - +
261D TYR* 3.8 39.5 - - + -
266D SER* 4.1 6.3 - - - -
267D THR* 3.2 20.5 + - + +
269D ALA* 1.3 74.6 - - - +
271D LYS* 1.3 65.1 + - - +
272D GLU 3.1 0.2 + - - -
273D ALA* 3.1 3.0 + - - -
274D ILE* 2.9 31.3 + - + +
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Residues in contact with LYS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D TYR* 5.0 2.7 - - - -
263D GLY 3.9 2.9 - - - +
264D SER* 2.9 49.4 + - - +
266D SER* 3.9 15.0 + - - -
267D THR 2.9 15.4 + - - +
268D GLY* 3.8 8.9 - - - +
270D VAL* 1.3 77.4 - - - +
272D GLU* 1.3 57.1 + - - +
275D GLU* 2.9 64.2 + - + +
276D GLY 3.4 0.3 + - - -
298D GLN* 6.1 0.7 - - + -
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Residues in contact with GLU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ARG* 2.9 12.7 + - - -
268D GLY 2.9 18.4 + - - +
269D ALA* 3.5 5.8 - - - +
271D LYS* 1.3 75.6 - - - +
273D ALA* 1.3 60.3 + - - +
276D GLY* 2.9 40.7 + - - +
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ARG* 2.6 23.3 + - - +
213D ALA* 3.5 6.4 - - - +
239D ALA* 3.5 19.4 - - + +
258D TYR* 3.6 36.6 - - + -
269D ALA 2.8 20.4 + - - +
270D VAL* 3.7 4.7 - - - +
272D GLU* 1.3 73.2 - - - +
274D ILE* 1.3 63.9 + - + +
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Residues in contact with ILE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ALA* 4.1 16.1 - - + +
214D LEU 4.1 6.5 - - - +
215D LEU* 4.3 24.5 - - + -
239D ALA* 4.5 1.1 - - + -
240D HIS* 4.3 8.7 - - - +
241D ALA* 4.1 36.1 - - + +
261D TYR* 4.3 18.2 - - + -
270D VAL* 2.9 24.0 + - + +
273D ALA* 1.3 84.9 - - + +
275D GLU* 1.3 64.0 + - - +
276D GLY 3.0 4.6 + - - -
277D ALA* 3.3 18.4 + - - +
280D VAL* 4.3 20.8 - - + +
299D LEU* 4.6 5.4 - - + -
303D GLN* 4.5 0.5 + - - -
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Residues in contact with GLU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D TYR* 2.6 39.5 + - + +
263D GLY 4.0 13.0 - - - +
264D SER* 4.6 0.6 + - - -
271D LYS* 2.9 37.9 + - + +
274D ILE* 1.3 76.7 - - - +
276D GLY* 1.3 56.7 + - - +
277D ALA 3.4 0.2 - - - -
296D THR 4.6 0.2 - - - +
298D GLN* 3.0 52.5 + - + +
299D LEU* 3.9 7.2 - - + -
303D GLN* 3.0 24.0 + - - +
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Residues in contact with GLY 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D ARG* 3.7 12.2 + - - -
271D LYS 3.4 1.6 + - - -
272D GLU* 2.9 36.5 + - - -
275D GLU* 1.3 77.7 - - - +
277D ALA* 1.3 63.2 + - - +
278D ASP* 3.6 2.3 + - - +
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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