Contacts of the helix formed by residues 267 - 276 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C TYR 4.4 2.2 + - - +
260C THR 5.4 0.4 + - - +
265C ALA 5.6 0.7 - - - +
266C SER* 1.3 77.6 - - - +
268C GLY* 1.3 64.4 + - - +
269C ALA* 3.6 8.4 + - - +
270C VAL* 3.2 28.3 + - + +
271C LYS* 2.9 21.2 + - - +
392C ASP* 5.8 4.0 - - - +
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Residues in contact with GLY 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C SER 3.9 0.4 + - - -
267C THR* 1.3 74.9 - - - +
269C ALA* 1.3 57.4 + - - +
271C LYS* 3.7 9.2 - - - +
272C GLU* 2.9 35.0 + - - +
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Residues in contact with ALA 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C TYR* 4.3 25.7 - - + +
267C THR* 3.2 9.0 + - - +
268C GLY* 1.3 76.7 - - - +
270C VAL* 1.3 57.4 + - - +
272C GLU* 3.6 4.3 - - - +
273C ALA* 2.8 31.0 + - - +
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Residues in contact with VAL 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ALA* 4.9 0.9 - - + -
258C TYR* 3.2 38.6 - - + +
259C GLY* 3.7 15.0 - - - +
260C THR 4.0 4.9 - - - +
261C TYR* 3.8 41.3 - - + +
266C SER* 4.1 5.6 - - - -
267C THR* 3.2 21.7 + - + +
269C ALA* 1.3 73.2 - - - +
271C LYS* 1.3 67.6 + - - +
273C ALA* 3.1 3.6 + - - -
274C ILE* 2.9 31.0 + - + +
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Residues in contact with LYS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C TYR* 5.0 3.6 - - - -
263C GLY 4.0 2.9 - - - +
264C SER* 2.9 47.9 + - - +
266C SER* 3.9 15.7 + - - -
267C THR 2.9 15.1 + - - +
268C GLY* 3.7 7.8 - - - +
270C VAL* 1.3 78.4 - - - +
272C GLU* 1.3 57.9 + - - +
275C GLU* 2.9 65.1 + - + +
276C GLY 3.4 0.3 + - - -
298C GLN* 6.1 0.4 - - + -
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Residues in contact with GLU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C ARG* 3.0 16.6 + - - -
268C GLY 2.9 19.6 + - - +
269C ALA* 3.6 4.7 - - - +
271C LYS* 1.3 76.9 - - - +
273C ALA* 1.3 61.5 + - - +
276C GLY* 2.9 35.6 + - - +
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Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C ARG* 2.6 22.6 + - - +
213C ALA* 3.5 6.8 - - - +
239C ALA* 3.5 18.7 - - + +
258C TYR* 3.6 36.3 - - + -
269C ALA 2.8 17.1 + - - +
270C VAL* 3.1 5.1 + - - +
272C GLU* 1.3 76.0 - - - +
274C ILE* 1.3 64.0 + - + +
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Residues in contact with ILE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ALA* 4.0 15.4 - - + +
214C LEU 4.3 6.3 - - - +
215C LEU* 4.3 25.1 - - + -
239C ALA* 4.4 1.3 - - + -
240C HIS* 4.3 9.9 - - - +
241C ALA* 4.2 34.5 - - + +
258C TYR* 6.2 0.4 - - + -
261C TYR* 4.3 17.5 - - + -
270C VAL* 2.9 23.8 + - + +
273C ALA* 1.3 85.5 - - + +
275C GLU* 1.3 64.5 + - - +
276C GLY 3.0 4.9 + - - -
277C ALA* 3.2 18.0 + - - +
280C VAL* 4.3 21.3 - - + +
299C LEU* 4.7 5.2 - - + -
303C GLN* 4.5 0.3 + - - -
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Residues in contact with GLU 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C TYR* 2.7 39.1 + - + +
263C GLY 4.1 10.0 - - - +
264C SER* 5.7 0.3 - - - -
271C LYS* 2.9 39.4 + - + +
274C ILE* 1.3 75.5 - - - +
276C GLY* 1.3 57.8 + - - +
277C ALA 3.4 0.4 - - - +
296C THR 4.5 0.2 - - - +
297C HIS* 4.0 2.8 - - - -
298C GLN* 3.2 51.9 + - + +
299C LEU* 3.9 11.7 - - + -
303C GLN* 3.1 18.8 + - - -
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Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211C ARG* 3.6 13.0 + - - -
271C LYS 3.4 1.8 + - - -
272C GLU* 2.9 35.6 + - - -
275C GLU* 1.3 77.6 - - - +
277C ALA* 1.3 62.5 + - - +
278C ASP* 3.7 2.1 + - - +
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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