Contacts of the helix formed by residues 269 - 279 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ARG* 3.9 10.3 - - - -
112B SER* 3.5 18.9 - - - -
267B LEU 3.8 1.2 - - - -
268B THR* 1.3 80.7 - - - +
270B ALA* 1.3 64.3 + - - +
271B ALA* 3.6 9.5 + - - +
272B GLU* 3.2 35.4 + - - +
273B HIS* 3.3 20.3 + - - -
292B VAL* 4.0 10.5 - - - +
301B ILE* 4.3 3.1 - - - -
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B SER* 1.3 75.1 - - - +
271B ALA* 1.3 57.7 + - - +
273B HIS* 3.3 2.8 + - - +
274B GLY* 2.8 26.3 + - - -
292B VAL* 5.0 2.2 + - - +
297B PRO* 4.4 15.5 - - + +
300B LYS* 4.8 14.8 - - + -
301B ILE* 3.6 27.4 - - + +
304B LEU* 4.7 8.3 - - + +
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Residues in contact with ALA 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A TYR* 6.0 7.0 - - + -
272A GLU* 5.9 3.8 - - + +
269B SER* 3.1 10.1 + - - +
270B ALA* 1.3 79.8 - - - +
272B GLU* 1.3 63.8 + - + +
274B GLY* 3.2 2.5 + - - -
275B ASP* 3.0 22.3 + - - +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 5.1 5.5 + - - +
112A SER* 5.3 3.8 + - - -
112B SER* 5.5 2.0 - - - -
245B TYR* 2.9 41.0 + - + -
247B HIS* 4.1 5.6 - - + -
267B LEU* 3.3 19.0 - - + +
268B THR* 2.7 37.7 + - - -
269B SER* 3.2 20.5 + - - +
271B ALA* 1.3 77.9 - - + +
273B HIS* 1.3 63.1 + - - +
275B ASP* 3.2 9.1 + - - +
276B LEU* 3.0 21.1 + - - +
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Residues in contact with HIS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLY* 3.4 25.7 + - - -
267B LEU* 3.5 27.8 - - + +
269B SER 3.3 20.6 + - - +
270B ALA 3.6 7.2 - - - +
272B GLU* 1.3 75.4 - - - +
274B GLY* 1.3 60.7 + - - +
276B LEU* 3.2 3.6 + - - +
277B ILE* 2.9 37.2 + - + +
285B LEU* 3.7 23.3 - - + +
287B PRO* 3.6 26.4 - - + +
292B VAL* 3.8 16.2 - - + +
301B ILE* 3.5 34.5 - - + -
304B LEU* 6.0 0.4 - - + -
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Residues in contact with GLY 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ALA 2.8 15.2 + - - -
271B ALA* 3.2 5.8 + - - -
273B HIS* 1.3 77.8 - - - +
275B ASP* 1.3 56.2 + - - +
277B ILE* 3.3 5.4 + - - +
278B ARG* 2.8 29.6 + - - +
304B LEU* 4.2 20.1 - - - +
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ASP* 4.7 6.7 - - - +
247B HIS* 2.8 26.6 + - + -
271B ALA 3.0 12.1 + - - +
272B GLU* 3.4 11.7 - - - +
273B HIS 3.2 0.2 - - - -
274B GLY* 1.3 74.1 - - - +
276B LEU* 1.3 65.0 + - - +
278B ARG* 2.9 38.5 + - - +
279B HIS* 2.9 34.6 + - - -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ALA 5.4 1.8 - - - +
247B HIS* 4.0 23.7 - - + +
263B THR* 3.6 22.7 - - + +
264B GLY* 3.9 7.0 - - - -
267B LEU* 3.6 22.2 - - + -
272B GLU 3.0 12.8 + - - +
273B HIS 3.5 8.3 - - - +
275B ASP* 1.3 75.5 - - - +
277B ILE* 1.3 66.6 + - + +
279B HIS 3.3 2.1 + - - -
280B ARG 3.2 3.3 + - - -
281B ALA* 3.1 40.4 + - + +
282B ALA* 3.5 29.2 - - + +
285B LEU* 3.7 22.2 - - + -
310B LEU* 5.7 1.1 - - + -
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Residues in contact with ILE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B HIS* 2.9 26.2 + - + +
274B GLY* 3.6 5.2 - - - +
276B LEU* 1.3 77.0 - - - +
278B ARG* 1.3 65.3 + - - +
280B ARG* 2.9 20.1 + - - +
285B LEU* 4.0 24.7 - - + -
301B ILE 4.4 1.3 - - - +
304B LEU* 3.6 33.7 - - + +
305B ALA* 3.8 13.0 - - - +
308B ALA* 3.7 27.7 - - + +
310B LEU* 4.2 17.4 - - + +
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Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ARG* 3.3 55.1 - - - +
274B GLY 2.8 17.4 + - - +
275B ASP* 2.9 30.8 + - - +
277B ILE* 1.3 78.9 - - - +
279B HIS* 1.3 83.8 + - - +
280B ARG* 3.5 5.5 + - - +
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Residues in contact with HIS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B HIS* 3.6 30.5 + - + +
248B GLU* 3.8 35.9 + - + +
251B ALA* 3.1 15.9 - - + +
275B ASP* 2.9 39.6 + - - -
276B LEU 3.6 7.9 - - - +
277B ILE 3.1 0.4 - - - -
278B ARG* 1.3 104.5 + - - +
280B ARG* 1.3 71.0 + - - +
281B ALA* 4.1 4.9 - - + -
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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