Contacts of the helix formed by residues 270 - 286 (chain F) in PDB entry 6O81
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 270 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F SER* 4.7 12.3 + - - -
225F ARG* 3.4 26.5 + - - +
269F LEU* 1.3 78.5 - - - +
271F ALA* 1.3 64.2 + - - +
272F SER* 2.9 23.3 + - - -
273F MET* 3.3 17.1 + - - +
274F HIS* 3.2 21.0 + - - -
406F HIS* 6.0 2.0 - - - -
415F MET* 5.8 2.7 - - - -
489F TYR* 4.1 17.3 - - - -
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Residues in contact with ALA 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270F SER* 1.3 73.2 - - - +
272F SER* 1.3 61.8 + - - +
274F HIS* 3.2 13.5 + - + +
275F ASN* 2.9 36.3 + - - +
406F HIS 4.9 1.4 + - - +
407F ALA* 3.7 20.6 - - + +
415F MET* 4.8 10.1 - - + +
442F LYS* 5.2 1.6 - - - +
443F PHE 4.9 0.2 - - - +
444F CYS* 3.6 31.6 - - - -
446F ARG* 5.0 3.4 - - - +
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Residues in contact with SER 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F SER* 3.6 21.8 + - - -
226F CYS* 4.0 10.3 - - - +
270F SER* 2.9 18.4 + - - -
271F ALA* 1.3 78.0 - - - +
273F MET* 1.3 56.4 + - - +
275F ASN* 3.8 1.7 - - - +
276F ALA* 2.9 28.9 + - - +
406F HIS 5.0 3.8 + - - -
441F TYR* 3.7 36.6 - - - -
442F LYS* 3.7 17.6 - - - +
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Residues in contact with MET 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214F TYR* 3.6 26.5 - - + -
225F ARG* 3.3 49.6 - - + +
226F CYS* 4.8 1.1 - - - +
229F LEU* 3.8 37.8 - - + +
263F LEU* 4.1 7.0 - - + -
269F LEU* 3.8 25.8 - - + -
270F SER* 3.3 20.5 + - - +
271F ALA 3.3 0.2 - - - -
272F SER* 1.3 76.7 + - - +
274F HIS* 1.3 59.3 + - - +
276F ALA* 3.3 1.8 + - - +
277F ILE* 2.9 37.7 + - + +
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Residues in contact with HIS 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F THR* 6.0 2.2 - - + -
269F LEU* 3.7 40.0 + - + +
270F SER 3.2 25.0 + - - -
271F ALA* 3.2 12.5 + - + +
273F MET* 1.3 76.4 - - - +
275F ASN* 1.3 59.3 + - - +
277F ILE* 3.3 10.4 + - - +
278F LYS* 2.9 50.7 + - - +
446F ARG* 6.1 4.0 - - - -
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Residues in contact with ASN 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F ALA* 2.9 20.8 + - - +
272F SER 3.9 2.5 - - - +
273F MET 3.3 0.2 - - - -
274F HIS* 1.3 75.1 - - - +
276F ALA* 1.3 61.0 + - - +
278F LYS* 3.7 17.4 + - - +
279F PHE* 2.9 29.5 + - - +
307F TYR* 4.5 6.1 + - - +
441F TYR* 2.8 30.6 + - + +
442F LYS 3.8 2.6 - - - -
443F PHE 2.6 33.8 + - - +
444F CYS* 5.2 0.4 - - - -
445F GLU* 4.4 10.9 - - - +
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Residues in contact with ALA 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F CYS* 3.9 21.3 - - - -
229F LEU* 4.1 12.1 - - + -
230F LEU* 4.5 17.6 - - + +
233F LEU* 5.8 2.0 - - + -
272F SER 2.9 18.0 + - - +
273F MET 3.7 4.9 - - - +
274F HIS 3.3 0.2 - - - -
275F ASN* 1.3 73.8 - - - +
277F ILE* 1.3 59.0 + - - +
279F PHE* 3.8 3.5 - - - +
280F LEU* 2.9 31.5 + - - +
307F TYR* 4.5 13.4 + - + +
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Residues in contact with ILE 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229F LEU* 4.9 7.9 - - + -
233F LEU* 5.8 3.6 - - + -
260F MET* 3.7 44.9 - - + -
269F LEU* 4.1 20.6 - - + -
273F MET* 2.9 27.1 + - + +
274F HIS* 3.3 12.3 + - - +
276F ALA* 1.3 77.1 - - - +
278F LYS* 1.3 59.6 + - + +
280F LEU* 3.4 3.6 + - - -
281F ASN* 2.5 50.9 + - - +
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Residues in contact with LYS 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F HIS* 2.9 40.7 + - - +
275F ASN* 3.7 18.0 + - - +
277F ILE* 1.3 80.4 - - + +
279F PHE* 1.3 56.7 + - - +
281F ASN* 3.4 6.1 + - - +
282F LYS* 2.9 28.8 + - - +
445F GLU* 4.5 15.9 - - - +
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Residues in contact with PHE 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230F LEU* 6.4 0.7 - - + -
275F ASN 2.9 18.3 + - - +
276F ALA 3.9 3.1 - - - +
278F LYS* 1.3 76.1 - - - +
280F LEU* 1.3 62.9 + - + +
282F LYS* 3.3 26.2 + - - +
283F GLU* 2.9 62.3 + - + +
303F ALA* 4.7 7.6 - - + -
304F ILE* 5.5 5.4 - - + -
307F TYR* 3.4 63.9 - + + +
311F LYS* 5.7 3.8 - - - -
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Residues in contact with LEU 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230F LEU* 5.4 2.5 - - + -
233F LEU* 3.7 45.8 - - + -
237F ILE* 4.7 9.2 - - + -
256F LEU* 4.2 15.9 - - + -
276F ALA 2.9 19.1 + - - +
277F ILE* 3.9 5.2 - - - +
279F PHE* 1.3 80.0 - - + +
281F ASN* 1.3 58.9 + - - +
283F GLU* 3.3 9.3 + - + -
284F ILE* 2.9 49.1 + - + +
300F LEU* 4.9 2.9 - - + -
304F ILE* 3.7 30.5 - - + -
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Residues in contact with ASN 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F VAL* 3.7 32.1 - - + +
256F LEU* 5.2 10.2 - - - +
257F LYS* 4.9 5.4 + - - +
277F ILE* 2.5 47.4 + - - +
278F LYS* 3.8 6.7 - - - +
279F PHE 3.3 0.2 - - - -
280F LEU* 1.3 78.5 - - - +
282F LYS* 1.3 54.1 + - - +
284F ILE* 3.7 8.8 - - - +
285F THR* 2.3 41.7 + - - +
28M GLU* 6.1 6.0 - - - -
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Residues in contact with LYS 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278F LYS 2.9 17.6 + - - +
279F PHE* 3.7 30.2 - - - +
280F LEU 3.3 0.2 - - - -
281F ASN* 1.3 76.1 - - - +
283F GLU* 1.3 66.3 + - - +
285F THR* 4.0 5.8 - - - -
286F SER* 3.3 23.3 + - - -
519F LYS 5.2 6.9 + - - -
520F SER* 5.7 3.0 - - - +
521F SER* 4.4 15.4 + - - +
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Residues in contact with GLU 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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279F PHE* 2.9 56.7 + - + +
280F LEU* 3.7 11.2 - - + +
281F ASN 3.2 0.2 - - - -
282F LYS* 1.3 84.0 - - + +
284F ILE* 1.3 60.7 + - - +
286F SER* 3.3 21.6 + - - -
287F VAL* 3.6 13.5 - - - +
300F LEU* 4.2 15.0 - - + +
303F ALA* 4.0 21.5 - - + +
304F ILE* 6.4 0.7 - - + -
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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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237F ILE* 5.4 0.9 - - + -
248F LEU* 5.0 1.8 - - + -
249F SER* 3.4 15.9 - - - +
252F LEU* 3.8 36.3 - - + -
253F VAL* 3.7 29.2 - - + +
256F LEU* 4.1 15.5 - - + -
280F LEU* 2.9 35.2 + - + +
281F ASN* 3.7 11.0 - - - +
283F GLU* 1.3 72.6 - - - +
285F THR* 1.3 64.5 + - - +
287F VAL* 3.3 23.5 - - - +
300F LEU* 3.7 31.6 - - + -
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Residues in contact with THR 285 (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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249F SER* 4.1 16.2 + - - +
250F ARG* 5.9 0.2 - - - +
253F VAL* 4.8 3.8 - - - +
281F ASN* 2.3 28.2 + - - +
282F LYS* 4.0 7.1 - - - -
283F GLU 3.2 0.2 - - - -
284F ILE* 1.3 79.8 - - - +
286F SER* 1.3 57.0 + - - +
287F VAL 3.3 11.2 + - - +
28M GLU 4.8 4.7 - - - +
29M MET* 3.8 41.1 + - + +
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Residues in contact with SER 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282F LYS* 3.3 12.7 + - - -
283F GLU* 3.3 20.1 + - - -
285F THR* 1.3 77.0 - - - +
287F VAL* 1.3 59.9 + - - +
288F GLY 3.9 0.9 + - - -
291F LYS* 4.9 4.5 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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