Contacts of the helix formed by residues 247 - 256 (chain F) in PDB entry 2OX4
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 PRO 247 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244F PRO 3.9 9.9 - - - +
245F LEU 3.4 10.3 - - - +
246F ASN* 1.3 85.7 - - - +
248F ARG* 1.3 62.7 + - - +
250F LEU* 3.1 21.0 + - - +
251F LYS 4.0 1.9 + - - -
275F PRO* 3.8 38.4 - - + -
276F PHE* 3.6 31.3 - - + +
279F ASP* 4.2 5.2 - - - +
281F SER* 4.7 0.5 + - - -
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Residues in contact with ARG 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A GLU* 4.3 19.3 + - - +
246F ASN* 3.2 12.5 + - - +
247F PRO* 1.3 78.7 - - - +
249F LEU* 1.3 63.8 + - + +
251F LYS* 3.1 22.4 + - + +
252F GLU* 3.2 28.8 + - + +
279F ASP* 3.8 16.5 + - - +
278H GLU* 3.1 40.0 + - - +
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Residues in contact with LEU 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ARG* 4.1 14.4 - - + -
307A ILE 3.5 22.2 - - - +
308A PHE* 3.5 25.6 - - + +
309A GLU* 3.6 32.1 - - + +
220F LEU* 3.8 16.4 - - + +
242F ASN* 3.7 14.1 - - - +
243F THR 5.3 2.0 - - - +
246F ASN* 3.1 32.3 + - + +
248F ARG* 1.3 78.9 - - + +
250F LEU* 1.3 56.6 + - - +
252F GLU* 3.2 8.5 + - + +
253F ALA* 2.9 26.5 + - - +
271H TRP* 6.0 0.2 - - - +
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Residues in contact with LEU 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F ILE* 3.7 38.4 - - + +
242F ASN* 3.9 16.5 - - - +
246F ASN 4.5 0.2 + - - -
247F PRO* 3.1 12.8 + - + +
249F LEU* 1.3 74.1 - - - +
251F LYS* 1.3 59.8 + - - +
253F ALA* 3.3 2.7 + - + +
254F LYS* 2.9 29.3 + - - +
261F LEU* 3.9 12.6 - - + -
262F ALA 5.7 0.9 - - - +
263F SER* 4.8 9.0 - - - -
276F PHE* 3.9 14.6 - - + -
281F SER* 3.6 22.4 - - - +
282F ILE* 3.5 32.5 - - + -
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Residues in contact with LYS 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D LYS* 4.7 16.5 - - - +
247F PRO 4.0 0.8 + - - -
248F ARG* 3.1 20.4 + - + +
250F LEU* 1.3 78.8 - - - +
252F GLU* 1.3 63.2 + - - +
254F LYS* 3.4 6.6 + - - +
255F LYS* 3.3 41.0 + - + +
279F ASP* 3.9 51.7 + - + +
281F SER* 3.7 10.5 - - - -
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Residues in contact with GLU 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LYS* 6.1 0.7 - - - +
278A GLU 5.3 1.4 - - - +
279A ASP 4.4 11.4 - - - +
280A ARG* 4.1 33.6 - - + +
220F LEU* 4.6 10.8 - - + -
224F ILE* 4.6 1.4 - - - +
248F ARG* 3.2 30.7 + - + +
249F LEU* 3.2 13.7 + - + +
251F LYS* 1.3 78.4 - - - +
253F ALA* 1.3 62.2 + - - +
255F LYS* 2.9 54.1 + - - +
256F LYS* 4.0 7.8 + - - +
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Residues in contact with ALA 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F LEU* 4.3 15.1 - - + +
224F ILE* 4.2 11.4 - - + -
241F ILE* 3.8 29.4 - - + -
242F ASN* 5.8 0.9 - - - +
249F LEU 2.9 13.3 + - - +
250F LEU* 3.3 11.9 + - + +
252F GLU* 1.3 75.8 - - - +
254F LYS* 1.3 58.1 + - - +
256F LYS* 2.9 19.6 + - - +
257F ILE* 3.2 23.1 + - + +
261F LEU* 4.7 0.2 - - + -
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Residues in contact with LYS 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D LEU* 6.3 0.2 - - - +
224D ILE* 6.2 1.4 - - - +
252D GLU* 6.1 0.4 - - - +
256D LYS* 2.6 50.7 + - - +
250F LEU 2.9 17.1 + - - +
251F LYS* 3.7 8.7 - - + +
252F GLU 3.3 0.2 - - - -
253F ALA* 1.3 75.2 - - - +
255F LYS* 1.3 54.3 + - - +
256F LYS 3.0 0.9 + - - -
257F ILE* 3.2 10.7 + - - +
258F ASP 5.8 0.8 + - - -
259F ILE 4.7 4.9 + - - -
260F PRO* 4.8 0.8 - - - +
261F LEU* 4.1 18.3 - - + +
279F ASP 5.7 0.2 - - - +
280F ARG* 3.7 19.4 - - - +
281F SER* 3.3 30.5 - - - +
283F ASP* 2.6 35.1 + - - -
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Residues in contact with LYS 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A LYS* 4.8 16.4 - - - +
279A ASP 5.6 0.4 + - - -
255D LYS* 6.3 1.1 - - + +
256D LYS* 4.1 7.8 + - - +
251F LYS* 3.3 33.3 + - + +
252F GLU* 2.9 46.2 + - - +
253F ALA 3.1 0.8 - - - -
254F LYS* 1.3 75.2 - - - +
256F LYS* 1.3 69.3 + - + +
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Residues in contact with LYS 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LYS* 2.7 45.9 + - - +
255A LYS* 3.9 11.7 + - - +
256A LYS 4.9 0.2 - - - -
257A ILE 2.9 19.4 + - - -
258A ASP* 3.1 27.7 + - - +
256D LYS* 5.0 0.4 - - - -
224F ILE* 3.8 43.2 - - + +
227F ALA* 5.5 0.3 - - - +
228F LYS* 5.8 3.6 - - - +
252F GLU 4.4 5.4 - - - +
253F ALA 2.9 2.8 + - - -
255F LYS* 1.3 86.9 - - + +
257F ILE* 1.3 64.1 - - - +
258F ASP* 4.3 0.6 + - - -
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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