Contacts of the helix formed by residues 273 - 288 (chain F) in PDB entry 6F0X
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 ALA 273 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216F SER* 3.8 24.5 - - - +
261F ARG* 6.4 0.2 - - - -
272F ASP* 1.3 74.1 - - - +
274F ILE* 1.3 60.4 + - - +
275F ARG 3.4 1.8 - - - -
276F VAL* 3.2 22.0 - - + +
277F VAL* 3.1 29.3 + - + +
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Residues in contact with ILE 274 (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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116E THR* 5.5 4.9 - - - +
117E GLU 5.0 9.6 - - - +
118E ASN* 3.5 38.4 - - + +
261F ARG* 4.6 20.2 - - - +
272F ASP* 3.1 15.8 - - - +
273F ALA* 1.3 78.3 - - - +
275F ARG* 1.3 67.7 + - - +
277F VAL* 2.9 21.7 + - + +
278F ASN* 2.9 20.8 + - + +
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Residues in contact with ARG 275 (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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230F THR* 5.1 15.4 - - - +
272F ASP 4.5 4.8 + - - +
273F ALA 3.4 0.4 - - - -
274F ILE* 1.3 75.1 - - - +
276F VAL* 1.3 61.7 + - - +
278F ASN* 2.6 33.0 - - - +
279F ALA* 2.8 26.1 + - + +
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Residues in contact with VAL 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216F SER* 3.8 22.0 - - - +
227F LYS* 4.2 28.3 - - + -
229F VAL* 3.5 29.8 - - + -
257F LEU* 5.9 5.6 - - + -
272F ASP 5.4 0.4 + - - +
273F ALA* 3.2 26.0 + - + +
275F ARG* 1.3 77.0 - - + +
277F VAL* 1.3 65.4 + - + +
279F ALA* 3.9 1.7 - - - +
280F VAL* 3.0 33.8 + - + +
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Residues in contact with VAL 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ASN* 6.5 0.9 - - + -
257F LEU* 4.5 40.2 - - + +
261F ARG* 5.7 7.9 - - - +
273F ALA* 3.1 18.5 + - + +
274F ILE* 2.9 18.0 + - + +
276F VAL* 1.3 78.6 - - + +
278F ASN* 1.3 59.2 + - + +
280F VAL* 3.2 4.4 + - - +
281F LEU* 2.9 46.7 + - + +
309F PHE* 4.6 8.1 - - + -
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Residues in contact with ASN 278 (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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274F ILE* 2.9 21.1 + - + +
275F ARG* 2.6 42.9 - - - +
277F VAL* 1.3 78.1 - - + +
279F ALA* 1.3 64.3 + - - +
281F LEU* 3.5 14.7 - - + +
282F THR* 2.9 40.2 + - + +
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Residues in contact with ALA 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229F VAL* 3.8 20.2 - - + -
230F THR* 5.8 5.4 - - + -
275F ARG* 2.8 28.6 + - + +
278F ASN* 1.3 82.7 + - - +
280F VAL* 1.3 64.7 + - - +
282F THR* 2.9 19.9 + - - -
283F GLN* 2.9 20.4 + - + +
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Residues in contact with VAL 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F ILE* 5.1 7.9 - - + -
229F VAL* 3.6 17.3 - - + -
232F MET* 4.6 4.5 - - + -
233F PHE* 3.5 32.5 - - + -
251F ILE* 4.4 15.5 - - + -
257F LEU* 6.0 6.1 - - + -
276F VAL* 3.0 24.0 + - + +
277F VAL* 3.6 4.9 - - - +
279F ALA* 1.3 74.8 - - - +
281F LEU* 1.3 58.0 + - + +
283F GLN* 3.4 1.6 + - - +
284F ILE* 2.9 49.6 + - + +
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Residues in contact with LEU 281 (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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277F VAL* 2.9 37.4 + - + +
278F ASN* 3.5 15.7 - - + +
279F ALA 3.2 0.2 - - - -
280F VAL* 1.3 77.0 - - + +
282F THR* 1.3 64.9 + - + +
284F ILE* 3.1 14.6 + - + +
285F ASP* 3.0 28.7 + - - +
308F ALA* 3.8 35.2 - - + +
309F PHE* 3.8 30.5 - - + -
312F ARG* 4.1 8.0 + - - +
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Residues in contact with THR 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E PRO* 4.4 24.0 - - + -
278F ASN* 2.9 24.8 + - + +
279F ALA* 2.9 20.4 + - - -
281F LEU* 1.3 74.1 - - + +
283F GLN* 1.3 62.2 + - - +
285F ASP* 3.3 4.9 + - - +
286F GLN* 2.9 54.8 + - - +
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Residues in contact with GLN 283 (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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229F VAL* 5.4 0.2 - - + -
233F PHE* 3.3 55.4 - - + +
279F ALA* 2.9 24.9 + - + +
280F VAL 3.7 0.7 - - - +
282F THR* 1.3 82.7 + - - +
284F ILE* 1.3 63.6 + - - +
286F GLN* 4.1 14.3 + - - +
287F ILE* 2.9 47.5 + - - +
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Residues in contact with ILE 284 (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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174F VAL* 5.3 1.3 - - + -
233F PHE* 4.7 5.6 - - + -
249F VAL* 5.5 4.0 - - + -
251F ILE* 4.6 14.8 - - + -
280F VAL* 2.9 44.2 + - + +
281F LEU* 3.2 16.6 - - + +
283F GLN* 1.3 80.0 - - - +
285F ASP* 1.3 69.3 + - - +
286F GLN 3.1 0.2 + - - -
287F ILE* 4.1 6.5 - - - +
288F LYS* 3.0 43.5 + - - +
295F ILE* 4.2 21.6 - - + +
297F THR* 5.8 2.7 - - + -
309F PHE* 5.8 2.2 - - + -
312F ARG* 3.7 27.4 - - - +
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Residues in contact with ASP 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E GLY* 6.5 0.9 - - - -
107E PRO* 6.0 4.0 - - + -
131E GLU* 5.8 4.4 - - - +
281F LEU* 3.0 13.5 + - - +
282F THR* 4.1 5.5 - - - +
284F ILE* 1.3 79.4 - - - +
286F GLN* 1.3 61.1 + - + +
288F LYS* 2.7 45.2 + - - +
289F ARG* 5.6 2.6 + - - +
308F ALA 5.0 0.5 - - - +
312F ARG* 3.1 27.2 + - - -
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Residues in contact with GLN 286 (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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104E GLU 4.9 14.2 + - - +
105E ASP* 4.9 11.5 + - - +
106E GLY* 5.1 4.4 - - - +
107E PRO 5.7 1.8 - - - -
282F THR* 2.9 41.7 + - - +
283F GLN* 4.0 17.3 + - - +
284F ILE 3.1 0.2 - - - -
285F ASP* 1.3 81.6 - - + +
287F ILE* 1.3 65.9 + - + +
288F LYS 3.4 2.4 + - - -
289F ARG* 4.6 10.9 + - - +
290F HIS* 4.6 5.5 + - - -
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Residues in contact with ILE 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F PHE* 4.5 15.9 - - + +
236F ILE* 3.7 29.4 - - + -
237F GLN* 5.1 5.4 - - + +
240F ILE* 4.1 9.9 - - + -
249F VAL* 4.7 9.0 - - + -
283F GLN* 2.9 40.4 + - - +
284F ILE* 4.1 5.6 - - - +
286F GLN* 1.3 79.2 - - + +
288F LYS* 1.3 65.3 + - - +
289F ARG 3.2 2.5 - - - -
290F HIS* 3.3 26.2 + - + +
293F VAL* 3.2 33.8 - - + +
295F ILE* 5.8 1.8 - - + -
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Residues in contact with LYS 288 (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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171F TRP* 5.3 4.3 - - + -
172F ASN* 5.1 13.6 - - + +
173F ARG* 2.0 43.7 + - + +
174F VAL* 4.6 7.9 - - - +
284F ILE* 3.0 33.8 + - - +
285F ASP* 2.7 40.3 + - - +
286F GLN 3.4 1.8 - - - -
287F ILE* 1.3 77.0 - - - +
289F ARG* 1.3 57.9 + - + +
290F HIS 3.0 5.0 + - - +
293F VAL* 4.7 6.3 - - - -
295F ILE* 3.7 18.6 - - + -
312F ARG* 3.0 26.8 - - - +
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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