Contacts of the helix formed by residues 246 - 257 (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 ASP 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ARG* 2.7 52.5 + - - +
242A LEU* 3.7 12.1 - - + +
243A ASP* 2.9 25.8 + - + +
244A ALA 3.5 0.4 - - - -
245A TYR* 1.3 73.4 - - - +
247A HIS* 1.3 56.9 + - - +
248A GLU* 3.9 1.2 + - - +
249A GLY* 2.9 11.3 + - - -
250A HIS* 3.0 31.5 + - - -
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Residues in contact with HIS 247 (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 3.8 22.3 + - - -
245A TYR* 3.0 26.5 + + - +
246A ASP* 1.3 69.2 - - - +
248A GLU* 1.3 61.3 + - - +
250A HIS* 3.4 3.0 + + - -
251A ALA* 2.9 29.8 + - - +
267A LEU* 4.7 6.0 - - + +
272A GLU* 4.0 8.1 + - - -
275A ASP* 2.8 41.9 + - + +
276A LEU* 3.8 32.1 + - + +
279A HIS* 3.6 26.8 - - + +
281A ALA* 3.4 11.3 - - + +
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Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 3.9 17.5 + - - +
246A ASP* 3.4 1.0 + - - +
247A HIS* 1.3 77.6 - - - +
249A GLY* 1.3 63.7 + - - +
251A ALA* 3.3 5.2 + - - +
252A ALA* 3.0 24.6 + - - +
279A HIS* 3.8 24.0 + - + +
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Residues in contact with GLY 249 (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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220A ARG* 3.6 15.2 - - - +
242A LEU* 3.5 10.7 - - - +
246A ASP* 2.9 29.8 + - - -
248A GLU* 1.3 77.7 - - - +
250A HIS* 1.3 61.4 + - - +
252A ALA* 3.3 8.4 + - - +
253A LEU* 3.2 24.8 + - - +
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Residues in contact with HIS 250 (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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240A GLU* 3.9 4.2 + - - -
241A PRO* 3.4 27.1 - - + +
242A LEU* 3.3 37.8 + - + +
243A ASP 3.3 21.9 + - - -
244A ALA 4.6 4.9 - - - -
246A ASP 3.0 27.9 + - - +
247A HIS* 4.7 2.5 - + - -
249A GLY* 1.3 74.8 - - - +
251A ALA* 1.3 64.2 + - - +
253A LEU* 3.2 6.1 + - - +
254A ALA* 3.0 23.0 + - - +
261A ILE* 3.9 8.7 - - + +
263A THR* 3.8 23.9 + - + -
281A ALA* 3.3 29.1 - - + +
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Residues in contact with ALA 251 (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 2.9 17.8 + - - +
248A GLU* 3.7 7.0 - - - +
250A HIS* 1.3 77.1 - - - +
252A ALA* 1.3 57.6 + - - +
254A ALA* 3.3 2.1 + - - +
255A LEU* 3.0 30.1 + - - +
279A HIS* 3.1 30.5 - - + +
280A ARG 3.7 14.5 - - - +
281A ALA* 3.8 1.5 - - - +
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Residues in contact with ALA 252 (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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224A GLN* 5.5 5.1 - - - +
248A GLU 3.0 17.7 + - - +
249A GLY* 3.5 7.4 - - - +
251A ALA* 1.3 77.6 - - - +
253A LEU* 1.3 63.2 + - + +
255A LEU* 3.4 8.3 + - - +
256A GLN* 3.1 23.9 + - - +
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Residues in contact with LEU 253 (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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220A ARG 5.3 1.1 - - - +
223A ALA* 4.0 8.1 - - + -
224A GLN* 3.6 26.5 - - - +
227A CYS* 4.1 11.9 - - - -
241A PRO* 3.8 24.9 - - + -
242A LEU* 3.6 31.4 - - + -
249A GLY 3.2 8.3 + - - +
250A HIS* 3.2 8.0 + - - +
252A ALA* 1.3 78.3 - - + +
254A ALA* 1.3 58.3 + - - +
256A GLN* 3.2 1.4 + - - -
257A PHE* 2.9 61.7 + - + +
261A ILE* 4.3 13.2 - - + -
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Residues in contact with ALA 254 (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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250A HIS 3.0 16.5 + - - +
251A ALA 3.7 4.7 - - - +
253A LEU* 1.3 76.5 - - - +
255A LEU* 1.3 59.8 + - - +
257A PHE 3.4 2.7 - - - +
261A ILE* 3.9 15.2 - - + +
280A ARG 4.3 13.9 - - - +
281A ALA 4.9 4.7 - - - +
282A ALA 5.2 0.4 - - - +
283A ASP* 3.8 22.2 - - - +
401A CA 2.3 33.0 - - - -
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Residues in contact with LEU 255 (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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251A ALA 3.0 18.0 + - - +
252A ALA* 3.8 7.6 - - - +
253A LEU 3.2 0.2 - - - -
254A ALA* 1.3 77.6 - - - +
256A GLN* 1.3 61.6 + - - +
257A PHE 4.9 0.5 - - - +
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Residues in contact with GLN 256 (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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224A GLN* 3.7 24.7 - - - +
228A ARG* 2.9 33.2 + - - +
231A GLU* 4.7 1.0 - - - +
252A ALA 3.1 16.8 + - - +
253A LEU 3.2 2.9 + - - +
255A LEU* 1.3 80.2 - - - +
257A PHE* 1.3 72.1 + - + +
258A ASP* 4.2 2.3 + - - +
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Residues in contact with PHE 257 (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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224A GLN* 3.4 47.6 - - - -
227A CYS* 3.6 23.6 - - + -
228A ARG* 3.4 45.5 - - - -
231A GLU* 3.6 26.9 - - + +
238A ILE* 6.4 0.2 - - + -
253A LEU* 2.9 45.8 + - + +
254A ALA 3.4 1.6 - - - +
255A LEU 5.3 0.2 - - - -
256A GLN* 1.3 82.7 - - + +
258A ASP* 1.3 60.4 + - - +
259A THR* 3.3 14.4 - - - +
261A ILE* 5.6 2.2 - - + -
401A CA 2.4 31.5 - - - -
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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