Contacts of the helix formed by residues 228 - 244 (chain F) in PDB entry 6NZD
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 PHE 228 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170F TYR* 3.3 28.4 + - + -
202F GLU* 6.0 2.2 - - - -
204F LEU* 3.6 28.7 - - + -
206F PHE* 5.3 0.3 - - - -
213F VAL* 3.7 18.6 - - + +
216F HIS* 3.6 51.8 - + + -
227F ARG* 1.3 88.7 - - - +
229F GLU* 1.3 63.5 + - - +
231F ILE* 3.4 4.1 + - - +
232F SER* 3.0 23.7 + - - -
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Residues in contact with GLU 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F GLU* 3.5 31.1 - - - +
170F TYR* 3.7 44.5 - - + -
227F ARG* 3.4 30.1 - - + +
228F PHE* 1.3 80.1 - - - +
230F LYS* 1.3 60.6 + - - +
232F SER* 3.5 1.4 + - - -
233F ASN* 2.9 28.4 + - - +
231H HIS 5.6 2.7 - - - +
232H GLN* 4.7 14.1 - - - +
233H ARG* 5.4 2.6 - - + +
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Residues in contact with LYS 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227F ARG* 3.4 30.3 + - + +
228F PHE 3.2 0.6 - - - -
229F GLU* 1.3 79.2 - - + +
231F ILE* 1.3 60.5 + - - +
233F ASN* 3.2 7.7 + - + +
234F ILE* 2.9 39.4 + - + +
298G ILE* 3.7 28.1 - - + +
232H GLN* 4.4 12.3 - - - +
233H ARG* 4.3 9.6 - - + -
234H ASN 3.4 35.0 - - - +
235H GLY 5.0 3.7 + - - +
237H ALA* 5.6 8.3 - - - +
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Residues in contact with ILE 231 (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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204F LEU* 5.5 2.5 - - + -
206F PHE* 3.7 28.0 - - + -
227F ARG 2.9 21.9 + - - +
228F PHE* 3.9 4.0 - - - +
230F LYS* 1.3 71.6 - - - +
232F SER* 1.3 60.3 + - - +
234F ILE* 3.2 11.8 + - + +
235F ILE* 3.0 36.4 + - + +
273F MET* 4.0 15.5 - - + -
295G VAL* 4.4 13.9 - - + -
298G ILE* 3.7 39.7 - - + -
299G TYR* 3.9 20.6 - - + +
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Residues in contact with SER 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F TYR* 3.3 25.6 + - - -
206F PHE* 5.3 6.5 - - - -
211F PHE* 2.4 37.5 + - - +
213F VAL* 5.5 1.1 - - - -
228F PHE 3.0 9.4 + - - -
229F GLU 3.6 5.2 - - - -
231F ILE* 1.3 78.7 - - - +
233F ASN* 1.3 55.8 + - - +
235F ILE* 4.1 3.0 - - - +
236F LYS* 2.9 45.3 + - - +
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Residues in contact with ASN 233 (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 GLU 2.9 18.3 + - - +
230F LYS* 3.2 9.1 + - - +
232F SER* 1.3 74.3 - - - +
234F ILE* 1.3 61.9 + - - +
236F LYS* 3.8 9.5 - - - +
237F GLN* 2.9 32.5 + - - +
230H LEU* 5.6 2.0 - - - +
233H ARG* 3.5 35.5 + - + +
234H ASN* 5.7 0.2 - - - +
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Residues in contact with ILE 234 (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 LYS* 2.9 29.5 + - + +
231F ILE* 3.2 24.9 + - + +
233F ASN* 1.3 79.5 - - + +
235F ILE* 1.3 61.5 + - + +
237F GLN* 3.3 10.5 + - - +
238F PHE* 3.0 26.2 + - - +
291G VAL* 4.0 27.8 - - + +
294G ASP* 3.7 39.0 - - + +
295G VAL* 4.0 20.9 - - + +
298G ILE* 4.2 5.8 - - + -
234H ASN 5.7 2.5 - - - +
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Residues in contact with ILE 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F PHE* 4.8 9.9 - - + -
211F PHE* 3.6 36.1 - - + -
231F ILE* 3.0 27.8 + - + +
232F SER* 4.3 2.5 - - - +
234F ILE* 1.3 87.9 - - + +
236F LYS* 1.3 57.5 + - - +
238F PHE* 3.3 5.4 + - + +
239F LYS* 2.9 28.5 + - + +
249F PHE* 4.4 19.1 - - + -
252F MET* 3.8 33.0 - - + -
263F ILE* 4.9 13.7 - - + -
273F MET* 6.4 0.2 - - + -
291G VAL* 4.9 1.1 - - + -
295G VAL* 5.0 5.2 - - + -
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Residues in contact with LYS 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F ILE 3.7 6.6 + - - +
27F ILE* 2.5 42.3 + - - +
28F PHE* 5.1 0.2 - - - -
29F ALA* 3.7 28.7 - - + +
170F TYR* 6.0 0.8 - - - -
209F ALA 5.5 2.2 - - - +
210F THR 3.6 18.2 + - - +
211F PHE* 4.2 15.1 + - + -
212F LEU* 5.0 2.6 - - - +
232F SER* 2.9 32.1 + - - +
233F ASN* 3.8 9.9 - - - +
235F ILE* 1.3 78.1 - - - +
237F GLN* 1.3 57.6 + - - +
239F LYS* 3.4 6.5 + - + +
240F LEU* 2.9 31.2 + - + +
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Residues in contact with GLN 237 (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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233F ASN* 2.9 23.0 + - - +
234F ILE* 3.6 5.6 - - - +
236F LYS* 1.3 74.4 - - - +
238F PHE* 1.3 63.0 + - - +
240F LEU* 3.6 10.1 - - + +
241F SER* 2.9 32.4 + - - -
287G ASP* 4.6 16.9 - - - +
290G ASP* 5.3 11.2 + - - +
291G VAL* 3.8 18.9 - - - +
294G ASP* 5.7 1.2 - - - +
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Residues in contact with PHE 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F ILE 3.0 16.5 + - - +
235F ILE* 3.7 8.3 - - + +
236F LYS 3.3 0.2 - - - -
237F GLN* 1.3 79.9 + - - +
239F LYS* 1.3 55.9 + - - +
241F SER* 3.4 1.0 + - - -
242F CYS* 2.9 56.1 + - - -
249F PHE* 3.5 40.6 - + + -
252F MET* 4.6 7.2 - - + -
284G LEU* 4.9 5.4 - - + -
287G ASP* 3.2 38.1 - - - -
288G MET* 4.0 22.2 - - + -
291G VAL* 3.6 26.5 - - + -
318G ILE* 3.9 22.0 - - + -
320G LEU* 5.3 2.7 - - + -
326G LEU* 6.3 0.9 - - + -
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Residues in contact with LYS 239 (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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208F ARG* 4.2 22.2 + - - +
209F ALA* 5.9 1.5 - - - +
211F PHE* 3.6 24.5 - - + -
235F ILE* 2.9 18.0 + - + +
236F LYS* 3.8 6.1 - - + +
238F PHE* 1.3 75.4 - - - +
240F LEU* 1.3 61.8 + - - +
242F CYS* 3.8 4.3 - - - +
243F SER* 2.9 33.0 + - - -
248F SER* 5.5 7.0 - - - -
249F PHE* 4.5 26.4 + - + +
271F TYR* 3.5 25.9 + - - -
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Residues in contact with LEU 240 (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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29F ALA* 3.7 36.1 - - + +
236F LYS* 2.9 21.4 + - + +
237F GLN* 3.6 11.2 - - + +
239F LYS* 1.3 78.1 - - - +
241F SER* 1.3 59.4 + - - +
243F SER* 2.6 20.7 + - - +
244F LYS* 3.7 13.5 + - - +
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Residues in contact with SER 241 (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 GLN* 2.9 21.6 + - - -
238F PHE 3.4 0.6 + - - -
240F LEU* 1.3 77.5 - - - +
242F CYS* 1.3 60.4 + - - +
244F LYS* 3.3 15.2 + - - +
245F LEU* 3.3 26.4 - - - +
283G GLU* 4.9 1.7 + - - -
287G ASP* 2.9 37.2 + - - +
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Residues in contact with CYS 242 (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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238F PHE* 2.9 55.8 + - - +
239F LYS* 4.2 3.4 - - - +
241F SER* 1.3 75.3 - - - +
243F SER* 1.3 64.4 + - - +
245F LEU* 3.5 17.8 + - + +
247F ALA 2.9 33.9 - - - +
248F SER* 4.3 8.9 + - - -
249F PHE* 4.5 4.7 - - - +
284G LEU* 3.8 20.6 - - - -
287G ASP* 4.5 2.5 - - - -
320G LEU* 4.3 6.3 - - - -
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Residues in contact with SER 243 (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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239F LYS* 2.9 17.4 + - - -
240F LEU* 2.6 33.3 + - - +
242F CYS* 1.3 78.6 - - - +
244F LYS* 1.3 65.5 + - - +
245F LEU 3.2 8.0 + - - +
248F SER* 5.4 5.4 - - - +
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Residues in contact with LYS 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F LEU* 4.1 12.4 - - - +
241F SER* 3.3 8.3 + - - +
243F SER* 1.3 82.5 + - - +
245F LEU* 1.3 67.6 + - - +
280G GLN* 5.8 0.2 - - - +
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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