Contacts of the helix formed by residues 223 - 238 (chain G) in PDB entry 6K71
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 ASN 223 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G SER* 1.3 78.9 + - - +
224G ALA* 1.3 64.3 + - - +
225G ARG 3.3 2.0 - - - +
226G CYS* 3.6 13.7 + - + +
227G ILE* 3.3 28.6 + - + +
272G SER* 5.3 0.2 - - - -
312G ILE* 3.4 37.0 - - + +
340G SER* 4.0 25.6 + - - -
341G LEU* 6.2 2.3 - - - +
439G GLU* 3.9 14.0 + - - +
441G TYR* 5.2 0.2 - - + -
442G LYS* 4.3 17.0 - - - +
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Residues in contact with ALA 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G VAL* 3.5 12.7 - - + +
221G GLY* 3.8 20.2 - - - -
222G SER 3.4 1.8 - - - +
223G ASN* 1.3 81.0 + - - +
225G ARG* 1.3 58.0 + - - +
227G ILE* 3.2 5.7 + - - +
228G ALA* 2.9 29.3 + - - +
340G SER* 5.4 7.1 + - - +
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Residues in contact with ARG 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G TYR* 3.3 25.6 + - - +
219G VAL* 3.5 21.0 + - - +
220G SER* 2.7 40.8 + - - +
221G GLY 3.3 19.3 + - - +
222G SER 5.1 2.9 - - - +
223G ASN 3.3 0.4 - - - -
224G ALA* 1.3 73.9 - - - +
226G CYS* 1.3 65.6 + - - +
228G ALA* 3.6 0.2 - - - +
229G LEU* 3.0 23.4 + - - +
267G ARG* 3.0 38.9 - - - +
268G PRO 4.6 6.9 + - - -
270G SER* 4.4 26.6 - - - +
273G MET* 4.0 8.6 - - - +
406G HIS* 5.8 0.4 - - - -
417G ARG* 4.1 9.0 - - - +
488G VAL* 6.4 0.2 - - - +
489G TYR* 3.0 27.3 + - - -
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Residues in contact with CYS 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222G SER 5.2 0.6 + - - -
223G ASN* 3.6 14.8 + - + +
225G ARG* 1.3 80.2 - - - +
227G ILE* 1.3 68.9 + - - +
229G LEU* 3.5 1.8 + - - +
230G LEU* 2.8 51.2 + - - +
272G SER* 4.4 9.3 - - - +
273G MET* 4.4 10.4 - - - +
276G ALA* 4.3 2.7 - - - -
307G TYR* 6.3 0.4 - - - -
308G VAL* 5.6 2.9 - - - -
312G ILE* 5.5 3.4 - - - -
441G TYR* 2.7 45.8 - - + +
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Residues in contact with ILE 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G ASN* 3.3 21.3 + - + +
224G ALA* 3.2 7.6 + - - +
226G CYS* 1.3 90.3 - - - +
228G ALA* 1.3 57.2 + - - +
230G LEU* 3.4 10.7 - - + +
231G ARG* 2.9 54.8 + - + +
308G VAL* 4.6 19.5 - - + -
312G ILE* 4.7 16.8 - - + -
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Residues in contact with ALA 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G LEU* 3.7 26.6 - - + +
213G GLN* 4.9 1.3 - - - +
214G TYR* 4.6 0.4 - - - +
219G VAL* 3.8 23.8 - - + -
224G ALA 2.9 17.4 + - - +
225G ARG* 3.6 5.2 - - - +
226G CYS 3.2 0.2 - - - -
227G ILE* 1.3 77.0 - - - +
229G LEU* 1.3 57.9 + - - +
231G ARG* 3.3 6.5 + - - +
232G ALA* 3.0 26.0 + - - +
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Residues in contact with LEU 229 (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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207G MET* 5.4 0.7 - - + -
210G LEU* 4.1 6.8 - - + +
214G TYR* 5.0 1.6 - - + +
225G ARG 3.0 16.0 + - - +
226G CYS 4.0 1.6 - - - +
228G ALA* 1.3 76.5 - - - +
230G LEU* 1.3 70.9 + - + +
232G ALA* 3.6 8.6 - - + +
233G LEU* 2.8 48.3 + - + +
260G MET* 3.7 17.7 - - + -
263G LEU* 3.7 28.5 - - + -
269G LEU* 5.8 1.6 - - + -
273G MET* 3.6 33.2 - - + -
276G ALA* 4.7 11.2 - - + -
277G ILE* 4.9 6.5 - - + -
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Residues in contact with LEU 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G CYS* 2.8 32.5 + - - +
227G ILE* 3.4 12.3 - - + +
228G ALA 3.2 0.2 - - - -
229G LEU* 1.3 84.3 - - + +
231G ARG* 1.3 64.7 + - - +
233G LEU* 3.5 4.0 + - + +
234G GLN* 2.9 43.7 + - - +
276G ALA* 3.8 29.4 - - + -
304G ILE* 3.6 32.7 - - + +
307G TYR* 5.9 0.9 - - + -
308G VAL* 3.7 30.1 - - + -
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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
----------------------------------------------------------
227G ILE* 2.9 37.3 + - + +
228G ALA* 3.3 5.6 + - - +
230G LEU* 1.3 84.6 - - - +
232G ALA* 1.3 57.2 + - - +
234G GLN* 3.6 34.7 + - - +
235G GLN* 3.0 34.9 + - + +
305G ASP* 5.3 6.6 + - - -
308G VAL* 5.2 13.3 - - - +
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Residues in contact with ALA 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G ALA* 3.4 28.0 - - + +
207G MET* 4.9 8.3 - - + -
210G LEU* 3.7 28.2 - - + +
228G ALA 3.0 14.0 + - - +
229G LEU* 3.6 9.2 - - + +
231G ARG* 1.3 76.2 - - - +
233G LEU* 1.3 57.9 + - - +
235G GLN* 3.2 2.7 + - - -
236G VAL* 2.9 29.1 + - - +
263G LEU* 6.5 0.4 - - + -
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Residues in contact with LEU 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207G MET* 3.7 24.7 - - + -
229G LEU* 2.8 42.0 + - + +
230G LEU* 4.2 4.7 - - + +
232G ALA* 1.3 70.6 - - - +
234G GLN* 1.3 61.6 + - + +
236G VAL* 3.4 17.8 - - + +
237G ILE* 2.9 30.6 + - + +
252G LEU* 6.0 0.4 - - + -
256G LEU* 3.8 28.5 - - + -
259G TYR* 4.1 3.1 - - + -
260G MET* 4.3 10.8 - - + -
277G ILE* 4.3 7.9 - - + -
280G LEU* 4.2 26.5 - - + +
304G ILE* 6.2 0.2 - - - -
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Residues in contact with GLN 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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230G LEU* 2.9 29.4 + - - +
231G ARG* 3.6 29.3 + - - +
232G ALA 3.3 0.2 - - - -
233G LEU* 1.3 76.1 - - - +
235G GLN* 1.3 64.3 + - - +
237G ILE* 3.7 4.0 - - + -
238G GLN* 2.8 51.8 + - - +
301G ARG* 5.4 4.9 - - - +
304G ILE* 3.3 52.4 + - + +
305G ASP* 4.9 6.4 + - - +
308G VAL* 5.3 2.0 - - - +
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Residues in contact with GLN 235 (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 HIS* 2.9 12.9 + - - +
206G ALA* 4.4 11.7 - - + -
231G ARG* 3.0 22.4 + - + +
232G ALA 3.2 4.2 + - - +
234G GLN* 1.3 78.5 - - - +
236G VAL* 1.3 59.7 + - - +
238G GLN* 4.5 6.4 - - - +
239G ASP* 2.8 29.4 + - - +
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Residues in contact with VAL 236 (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 HIS* 3.4 32.7 - - + +
206G ALA* 4.6 1.1 - - + -
207G MET* 4.2 10.8 - - + -
232G ALA 2.9 21.4 + - - +
233G LEU* 3.4 25.4 - - + +
234G GLN 3.2 0.2 - - - -
235G GLN* 1.3 77.9 - - - +
237G ILE* 1.3 64.8 + - + +
239G ASP* 2.9 17.3 - - - +
240G TYR* 3.6 21.0 - - + +
252G LEU* 5.1 8.1 - - + -
259G TYR* 3.7 29.6 - - + +
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Residues in contact with ILE 237 (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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233G LEU* 2.9 24.2 + - + +
234G GLN* 3.7 5.8 - - + -
236G VAL* 1.3 76.6 - - + +
238G GLN* 1.3 84.3 + - - +
239G ASP 3.1 5.1 + - - -
240G TYR* 3.2 19.8 + - + +
252G LEU* 4.2 26.0 - - + -
280G LEU* 5.7 9.6 - - + -
284G ILE* 4.7 4.5 - - + -
297G LYS* 3.2 28.3 - - + +
300G LEU* 3.7 38.8 - - + -
304G ILE* 6.0 3.1 - - + -
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Residues in contact with GLN 238 (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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234G GLN* 2.8 51.8 + - - +
235G GLN* 4.9 5.6 - - - +
237G ILE* 1.3 92.4 - - - +
239G ASP* 1.3 59.6 - - - +
297G LYS* 3.8 24.3 + - + +
298G SER* 5.8 1.1 - - - +
300G LEU 4.6 1.6 - - - -
301G ARG* 3.3 50.4 - - + +
304G ILE* 4.9 1.6 - - - +
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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
------------------------------------------------------------
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