Contacts of the helix formed by residues 269 - 279 (chain A) in PDB entry 2OG9
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 SER 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ARG* 3.9 10.5 - - - -
112A SER* 3.5 19.6 - - - -
267A LEU 3.7 1.0 - - - -
268A THR* 1.3 80.7 - - - +
270A ALA* 1.3 64.5 + - - +
271A ALA* 3.6 8.9 + - - +
272A GLU* 3.1 36.1 + - - +
273A HIS* 3.3 20.2 + - - -
292A VAL* 4.0 10.3 - - - +
301A ILE* 4.4 3.4 - - - -
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Residues in contact with ALA 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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269A SER* 1.3 74.5 - - - +
271A ALA* 1.3 57.6 + - - +
273A HIS* 3.2 3.6 + - - +
274A GLY* 2.8 25.8 + - - -
292A VAL 5.0 2.4 + - - -
297A PRO* 4.4 15.5 - - + +
300A LYS* 4.7 15.0 - - + -
301A ILE* 3.6 27.4 - - + +
304A LEU* 4.7 8.1 - - + +
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Residues in contact with ALA 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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269A SER* 3.2 9.5 + - - +
270A ALA* 1.3 80.2 - - - +
272A GLU* 1.3 62.1 + - + +
274A GLY* 3.2 2.8 + - - +
275A ASP* 3.0 22.0 + - - +
245B TYR* 6.0 7.6 - - + -
272B GLU* 5.9 3.6 - - + +
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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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112A SER* 5.6 2.0 - - - -
245A TYR* 2.9 39.2 + - + -
247A HIS* 4.0 5.5 - - + -
267A LEU* 3.3 18.3 - - + +
268A THR* 2.7 38.9 + - - -
269A SER* 3.1 20.9 + - - +
271A ALA* 1.3 77.7 - - + +
273A HIS* 1.3 62.1 + - - +
275A ASP* 3.2 8.9 + - - +
276A LEU* 3.1 21.0 + - - +
111B ARG* 5.1 6.4 + - - +
112B SER* 5.4 4.0 + - - -
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Residues in contact with HIS 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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264A GLY* 3.4 28.6 + - - -
267A LEU* 3.5 24.9 - - + +
269A SER 3.3 20.3 + - - +
270A ALA 3.2 8.2 + - - +
272A GLU* 1.3 76.0 - - - +
274A GLY* 1.3 60.6 + - - +
276A LEU* 3.3 3.3 + - - +
277A ILE* 2.9 37.6 + - + +
285A LEU* 3.6 23.1 - - + +
287A PRO* 3.5 31.4 - - + +
292A VAL* 3.8 11.0 - - + +
301A ILE* 3.5 33.4 - - + -
304A LEU* 6.0 0.4 - - + -
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Residues in contact with GLY 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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270A ALA 2.8 14.4 + - - -
271A ALA* 3.6 5.2 - - - -
272A GLU 3.2 0.6 - - - -
273A HIS* 1.3 77.8 - - - +
275A ASP* 1.3 56.2 + - - +
277A ILE* 3.3 6.3 + - - +
278A ARG* 2.8 29.3 + - - +
304A LEU* 4.2 18.8 - - - +
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Residues in contact with ASP 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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247A HIS* 2.8 25.0 + - + -
271A ALA 3.0 12.6 + - - +
272A GLU* 3.5 11.4 - - - +
273A HIS 3.2 0.2 - - - -
274A GLY* 1.3 74.1 - - - +
276A LEU* 1.3 64.8 + - - +
278A ARG* 2.9 38.6 + - - +
279A HIS* 2.9 35.9 + - - -
275B ASP* 4.7 7.3 - - - +
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Residues in contact with LEU 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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244A ALA 5.4 2.0 - - - +
247A HIS* 3.8 24.1 - - + +
263A THR* 3.6 23.3 - - + +
264A GLY* 4.0 5.8 - - - -
267A LEU* 3.6 22.4 - - + -
272A GLU 3.1 12.6 + - - +
273A HIS 3.5 8.1 - - - +
275A ASP* 1.3 76.9 - - - +
277A ILE* 1.3 66.6 + - + +
279A HIS 3.2 2.4 + - - -
280A ARG 3.2 3.5 + - - -
281A ALA* 3.1 35.9 + - + +
282A ALA* 3.5 33.0 - - + +
285A LEU* 3.7 22.0 - - + -
310A LEU* 5.6 1.3 - - + -
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Residues in contact with ILE 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 HIS* 2.9 25.8 + - + +
274A GLY* 3.6 5.6 - - - +
276A LEU* 1.3 75.7 - - + +
278A ARG* 1.3 67.1 + - - +
280A ARG* 3.0 19.5 + - - +
285A LEU* 3.9 25.1 - - + -
301A ILE* 4.4 1.8 - - + +
304A LEU* 3.8 32.5 - - + +
305A ALA* 3.8 13.2 - - - +
308A ALA* 3.8 27.0 - - + +
310A LEU* 4.1 17.4 - - + +
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Residues in contact with ARG 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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274A GLY 2.8 18.4 + - - +
275A ASP* 2.9 31.2 + - - +
277A ILE* 1.3 76.8 - - - +
279A HIS* 1.3 83.4 + - - +
280A ARG* 3.4 7.3 + - - +
278B ARG* 3.3 54.6 - - - +
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Residues in contact with HIS 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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247A HIS* 3.6 34.7 - - + +
248A GLU* 3.8 30.0 + - + +
251A ALA* 3.1 16.1 - - + +
275A ASP* 2.9 37.7 + - - +
276A LEU 3.6 7.6 - - - +
277A ILE 3.2 0.4 - - - -
278A ARG* 1.3 111.1 + - - +
280A ARG* 1.3 71.8 + - - +
281A ALA* 4.1 1.3 - - + -
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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