Contacts of the helix formed by residues 226 - 244 (chain G) in PDB entry 5N9G
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 226 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377F THR* 5.0 8.0 - - - -
378F VAL 5.0 0.7 + - - -
165G LEU* 4.8 0.2 - - - -
168G ILE* 3.7 14.1 - - - +
224G ALA* 3.5 0.9 - - - +
225G LYS* 1.3 77.9 - - - +
227G GLU* 1.3 61.4 + - - +
228G GLU* 3.4 17.7 + - - +
229G GLN* 3.1 38.4 + - - +
230G SER 2.9 23.7 + - - -
318G ARG* 4.1 13.5 - - - +
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Residues in contact with GLU 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G LEU* 4.1 0.2 - - - +
168G ILE* 4.1 4.6 - - + +
226G SER* 1.3 70.4 - - - +
228G GLU* 1.4 69.9 + - - +
230G SER* 3.1 8.0 + - - -
231G ARG* 2.9 29.3 + - - +
253G PHE* 4.5 3.3 - - - -
255G ILE* 3.6 29.5 - - + +
258G MET* 3.5 27.3 - - + +
316G LYS 6.0 0.2 - - - +
317G VAL* 5.2 0.7 - - - -
318G ARG* 3.3 52.5 + - - +
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Residues in contact with GLU 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378F VAL 3.4 24.7 - - - +
379F THR* 4.6 3.6 - - - -
380F GLY* 3.4 25.1 - - - +
226G SER* 3.4 14.3 + - - +
227G GLU* 1.4 94.8 - - - +
229G GLN* 1.4 56.7 + - - +
231G ARG* 3.3 5.7 + - - +
232G LEU* 2.9 24.7 + - - +
318G ARG* 4.4 5.1 + - - -
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Residues in contact with GLN 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F THR* 3.1 31.5 - - - +
378F VAL* 5.1 9.2 - - + +
206G GLU* 5.4 4.4 - - - +
207G PRO* 3.3 36.3 - - + +
208G ARG 5.6 0.2 + - - -
224G ALA* 4.0 6.3 - - + -
225G LYS* 3.6 25.5 + - - +
226G SER* 3.1 33.4 + - - +
228G GLU* 1.4 74.1 - - - +
230G SER* 1.4 58.6 + - - +
232G LEU* 3.4 4.1 + - + -
233G ALA* 2.9 27.4 + - - +
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Residues in contact with SER 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G ILE* 4.0 20.7 + - - +
170G SER* 2.8 28.2 + - - -
221G CYS* 3.8 7.8 - - - -
224G ALA* 3.5 22.4 - - - +
226G SER 2.9 9.8 + - - -
227G GLU* 3.1 9.6 + - - -
229G GLN* 1.4 75.5 - - - +
231G ARG* 1.4 56.1 + - - +
233G ALA* 3.4 4.7 + - - +
234G ALA* 2.9 30.5 + - - +
253G PHE* 4.1 6.1 - - - -
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Residues in contact with ARG 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380F GLY* 3.7 19.7 + - - +
381F ASP* 2.8 32.5 + - - +
227G GLU 2.9 14.0 + - - +
228G GLU* 3.6 10.5 - - - +
230G SER* 1.4 71.8 - - - +
232G LEU* 1.4 58.9 + - - +
234G ALA* 3.4 2.4 + - - +
235G ARG* 3.0 47.4 + - + +
250G PHE* 3.9 25.8 - - + -
253G PHE* 3.6 34.4 - - + +
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Residues in contact with LEU 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378F VAL* 4.9 8.1 - - + +
379F THR 4.6 2.7 - - - +
380F GLY* 3.8 12.7 + - - +
382F GLU* 3.9 40.8 - - + +
383F ASN 5.5 0.4 - - - +
384F ILE* 4.2 5.2 - - + -
206G GLU* 5.6 1.6 - - + -
207G PRO* 4.1 19.1 - - + -
228G GLU 2.9 17.3 + - - +
229G GLN* 3.4 6.0 + - + +
231G ARG* 1.4 74.0 - - - +
233G ALA* 1.4 58.0 + - - +
235G ARG* 3.5 25.4 + - - +
236G LYS* 3.1 50.7 + - - +
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Residues in contact with ALA 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204G ILE* 3.9 11.0 - - + -
207G PRO* 4.0 9.6 - - + +
209G THR* 3.5 36.6 - - + +
221G CYS* 3.9 5.8 - - - -
229G GLN 2.9 17.7 + - - +
230G SER 3.7 4.0 - - - +
232G LEU* 1.4 74.3 - - - +
234G ALA* 1.4 59.0 + - - +
236G LYS* 2.9 18.9 + - - +
237G TYR* 2.9 20.9 + - + -
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Residues in contact with ALA 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G THR 6.3 0.2 - - - -
172G VAL* 4.5 2.5 - - + -
219G MET* 3.3 27.2 - - + +
221G CYS* 4.1 9.8 - - + -
230G SER 2.9 18.3 + - - +
231G ARG 3.6 5.2 - - - +
233G ALA* 1.4 75.1 - - - +
235G ARG* 1.3 55.3 + - - +
237G TYR* 3.4 3.2 + - - -
238G ALA* 3.1 25.3 + - - +
250G PHE* 3.6 20.3 - - + -
253G PHE* 3.8 14.6 - - + -
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Residues in contact with ARG 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380F GLY 3.0 28.7 + - - -
381F ASP* 3.2 14.8 + - - -
382F GLU 2.7 27.9 + - - +
383F ASN* 5.5 0.8 - - - +
384F ILE* 3.4 28.6 - - + +
231G ARG* 3.0 35.4 + - - +
232G LEU* 3.6 11.9 - - - +
234G ALA* 1.3 73.9 - - - +
236G LYS* 1.4 59.3 + - - +
238G ALA* 3.3 6.0 + - - +
239G ARG* 2.9 32.9 + - - +
250G PHE* 3.6 30.5 - - + -
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Residues in contact with LYS 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F ASN 5.8 0.9 - - - -
384F ILE* 3.8 28.5 - - + +
388F GLU* 3.2 31.6 + - + +
389F ILE* 3.4 13.0 - - + +
392F TYR* 6.2 1.1 - - + -
204G ILE* 3.7 19.7 - - + -
206G GLU* 2.8 34.3 + - - +
207G PRO* 4.5 1.5 - - + +
232G LEU* 3.1 39.7 + - - +
233G ALA 2.9 9.9 + - - +
235G ARG* 1.4 73.9 - - - +
237G TYR* 1.4 59.4 + - - +
239G ARG 3.1 1.6 + - - -
240G VAL* 3.0 32.6 + - - +
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Residues in contact with TYR 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G MET* 3.5 42.7 + - + +
204G ILE* 3.2 31.2 + - + -
209G THR* 2.7 49.1 + - - -
210G THR 3.5 0.5 + - - -
211G ALA* 3.7 27.4 - - + -
213G ILE* 4.8 2.9 - - + -
219G MET* 3.6 23.6 - - + -
221G CYS* 4.2 8.3 - - - -
233G ALA* 2.9 34.2 + - + -
234G ALA* 4.1 4.5 - - - -
236G LYS* 1.4 74.2 - - - +
238G ALA* 1.4 56.6 + - - +
240G VAL* 3.2 7.6 + - - +
241G VAL* 3.1 33.6 + - - +
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Residues in contact with ALA 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G LEU* 3.6 30.3 - - + -
219G MET* 4.5 0.8 - - - +
234G ALA 3.1 14.8 + - - +
235G ARG* 3.4 10.1 - - - +
236G LYS 3.2 0.2 - - - -
237G TYR* 1.4 76.0 - - - +
239G ARG* 1.3 56.9 + - + +
241G VAL* 3.5 5.5 + - - +
242G GLN* 3.0 39.6 + - - +
248G ALA* 4.0 2.7 - - + +
249G LYS 4.8 2.7 - - - +
250G PHE* 4.0 15.7 - - + -
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Residues in contact with ARG 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F ASN* 5.3 2.0 - - - +
384F ILE* 2.8 49.3 + - + +
385F SER 3.9 6.3 + - - -
386F ASP* 3.1 26.5 + - - -
389F ILE* 3.8 16.5 - - + +
235G ARG* 2.9 18.2 + - + +
236G LYS* 3.1 8.5 + - - +
238G ALA* 1.3 73.0 - - + +
240G VAL* 1.4 64.4 + - - +
242G GLN* 3.5 25.7 + - - +
243G LYS* 3.1 41.5 + - - +
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Residues in contact with VAL 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389F ILE* 3.7 26.5 - - + -
392F TYR* 4.4 24.5 - - + -
393F LEU* 4.3 12.5 - - + +
187G ALA* 4.8 5.2 - - + -
189G ASN* 4.9 0.2 - - - +
202G MET* 3.8 33.4 - - + -
204G ILE* 5.0 4.7 - - + -
236G LYS 3.0 20.1 + - - +
237G TYR* 3.2 9.6 + - - +
239G ARG* 1.4 75.0 - - - +
241G VAL* 1.3 62.2 + - - +
243G LYS* 3.3 6.6 + - - +
244G LEU* 3.2 33.0 + - + +
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Residues in contact with VAL 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174G LEU* 4.1 18.6 - - + -
178G LEU* 3.7 30.7 - - + -
183G ILE* 4.5 11.0 - - + -
202G MET* 5.2 2.7 - - + -
213G ILE* 4.1 22.9 - - + -
237G TYR 3.1 15.8 + - - +
238G ALA 3.7 5.2 - - - +
239G ARG 3.4 0.2 - - - -
240G VAL* 1.3 75.5 - - - +
242G GLN* 1.4 61.3 + - - +
244G LEU* 3.2 25.0 + - + +
246G PHE* 3.5 20.2 + - + -
248G ALA* 4.0 12.1 - - + -
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Residues in contact with GLN 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238G ALA* 3.0 27.5 + - - +
239G ARG* 3.6 27.0 + - - +
240G VAL 3.3 0.2 - - - -
241G VAL* 1.4 74.7 - - - +
243G LYS* 1.4 55.7 + - + +
245G GLY* 3.0 22.3 + - - -
246G PHE 3.5 15.1 + - - +
247G PRO* 5.1 0.4 - - + -
248G ALA* 2.9 37.0 + - + +
249G LYS* 4.9 2.8 - - - +
250G PHE* 6.3 0.2 - - - +
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Residues in contact with LYS 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F ASP* 2.8 49.7 + - - +
389F ILE* 3.7 22.7 - - + +
390F GLU* 3.3 26.5 - - + +
393F LEU* 4.0 23.1 - - + +
186G ARG* 4.7 5.5 + - - -
239G ARG* 3.1 29.0 + - - +
240G VAL 3.3 8.9 + - - +
242G GLN* 1.4 74.6 - - + +
244G LEU* 1.3 56.6 + - - +
245G GLY* 3.1 4.2 + - - -
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Residues in contact with LEU 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393F LEU* 3.9 15.5 - - + -
182G THR* 4.7 5.6 - - + +
183G ILE* 4.0 35.9 - - + +
186G ARG* 3.4 64.2 + - + +
187G ALA* 4.5 3.8 - - + +
202G MET* 4.8 0.2 - - + -
240G VAL* 3.2 31.0 + - + +
241G VAL* 3.4 17.5 - - - +
242G GLN 3.1 1.2 - - - -
243G LYS* 1.3 74.7 - - - +
245G GLY* 1.3 57.1 + - - +
246G PHE* 3.7 18.9 - - + -
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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
------------------------------------------------------------
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