Contacts of the helix formed by residues 223 - 242 (chain C) 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 SER 223 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B HIS 5.5 0.2 - - - -
218B PHE* 3.1 41.8 + - - -
219B SER* 2.9 25.6 + - - -
220B LYS 3.1 2.3 + - - -
221C TRP* 4.3 0.6 - - - +
222C PHE* 1.3 83.3 - - - +
224C GLU* 1.3 64.6 + - - +
225C SER* 2.5 21.1 + - - -
226C GLY* 3.2 12.1 + - - -
227C LYS* 3.7 6.8 + - - +
275C ARG* 4.5 11.6 + - - +
276C VAL* 5.0 1.4 - - - +
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Residues in contact with GLU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B THR* 6.0 1.2 - - - -
218B PHE 5.4 0.2 - - - +
219B SER* 4.7 2.1 - - - -
220B LYS* 2.5 67.3 + - + +
114C GLU* 5.4 6.2 - - - +
219C SER* 3.9 16.2 - - - +
221C TRP* 4.4 13.2 - - + +
223C SER* 1.3 79.5 + - - +
225C SER* 1.3 62.6 + - - +
226C GLY 3.5 0.4 - - - -
227C LYS* 3.1 26.5 + - - +
228C LEU* 2.9 34.7 + - + +
231C LYS* 5.9 1.4 + - - -
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Residues in contact with SER 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LEU 4.2 2.0 - - - +
218C PHE* 4.0 9.3 - - - +
219C SER* 2.7 47.2 + - - +
221C TRP 4.7 4.5 + - - -
222C PHE 5.3 2.4 + - - -
223C SER 2.5 8.8 + - - -
224C GLU* 1.3 73.4 - - - +
226C GLY* 1.3 65.5 + - - -
228C LEU* 3.1 7.6 + - - +
229C VAL* 3.0 24.3 + - - +
272C ASP* 5.9 2.5 - - - +
276C VAL* 3.5 18.6 - - - -
222D PHE* 5.1 5.7 - - - -
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Residues in contact with GLY 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B HIS* 4.9 11.9 - - - -
223C SER 3.2 5.9 + - - -
225C SER* 1.3 79.0 - - - +
227C LYS* 1.3 63.1 + - - +
229C VAL* 2.8 30.1 + - - +
230C THR* 3.3 10.2 + - - +
275C ARG* 6.2 0.2 - - - -
276C VAL* 3.2 21.0 - - - +
279C ALA* 4.7 8.2 - - - +
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Residues in contact with LYS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU 5.1 1.2 + - - -
116B THR* 3.4 30.6 + - - -
117B GLU* 4.3 3.0 - - - +
120B ILE* 2.9 51.6 - - + +
215B HIS* 5.3 14.7 + - + +
216B SER* 5.2 4.0 - - - +
218B PHE 5.8 4.5 - - - +
223C SER* 3.7 5.8 + - - +
224C GLU* 3.1 41.4 + - - +
226C GLY* 1.3 74.6 - - - +
228C LEU* 1.3 51.4 + - + +
230C THR* 2.2 32.9 + - - +
231C LYS* 4.3 9.5 - - - +
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Residues in contact with LEU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU* 4.8 15.9 - - + +
216C SER 5.4 0.4 - - - +
217C LEU* 3.1 35.4 - - + +
218C PHE 5.0 2.2 - - - +
219C SER* 4.2 15.5 - - - +
224C GLU* 2.9 31.4 + - + +
225C SER 3.3 3.8 - - - +
227C LYS* 1.3 76.7 - - + +
229C VAL* 1.3 67.7 + - - +
230C THR 3.0 1.3 - - - -
231C LYS* 3.0 27.7 + - + +
232C MET* 2.9 21.3 + - - +
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Residues in contact with VAL 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LEU* 3.7 27.8 - - + +
225C SER 3.0 17.3 + - - +
226C GLY* 2.8 17.4 + - - +
228C LEU* 1.3 75.8 - - - +
230C THR* 1.3 64.3 + - - +
232C MET* 3.1 3.1 + - - +
233C PHE* 3.0 51.7 + - + -
276C VAL* 3.6 20.9 - - + +
279C ALA* 4.8 3.6 - - + -
280C VAL* 3.9 20.9 - - + +
283C GLN* 4.4 8.1 - - + -
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Residues in contact with THR 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 5.6 1.6 - - - -
120B ILE* 4.1 22.9 - - + +
213B ASN* 4.6 13.5 - - - +
215B HIS* 6.1 2.7 - - + -
226C GLY 3.6 9.0 - - - +
227C LYS* 2.2 35.7 + - - +
229C VAL* 1.3 76.0 - - + +
231C LYS* 1.3 71.7 + - - +
233C PHE* 2.9 5.7 + - - +
234C GLN* 2.7 22.9 + - - +
279C ALA* 6.2 2.5 - - + -
283C GLN* 4.4 25.1 - - + +
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B THR* 5.4 7.9 - - - -
118B ASN* 5.7 12.6 - - + -
113C GLU* 3.5 36.6 - - + +
114C GLU* 3.6 23.8 - - - +
224C GLU* 5.9 1.6 + - - -
227C LYS* 4.3 8.1 - - - +
228C LEU* 3.0 26.8 + - + +
230C THR* 1.3 85.2 + - - +
232C MET* 1.3 63.2 + - - +
234C GLN* 3.0 10.5 + - - +
235C LYS* 2.9 29.7 + - - +
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Residues in contact with MET 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ALA 5.4 7.6 - - - +
122C ALA* 6.3 2.9 - - + -
210C ILE* 6.2 0.2 - - + -
212C ILE* 3.5 46.2 - - + -
213C ASN 5.7 1.6 - - - +
216C SER* 6.0 0.4 - - - -
217C LEU* 3.8 34.5 - - + -
228C LEU* 2.9 12.4 + - + +
229C VAL 3.4 4.7 - - - +
230C THR 3.1 0.2 - - - -
231C LYS* 1.3 77.0 - - - +
233C PHE* 1.3 98.0 + - + +
235C LYS* 2.9 18.4 + - + +
236C ILE* 2.9 25.2 + - + +
251C ILE* 5.9 0.9 - - + -
257C LEU* 5.8 1.1 - - + -
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Residues in contact with PHE 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C VAL* 3.0 38.0 + - + +
230C THR 2.9 6.5 + - - +
232C MET* 1.3 99.9 - - + +
234C GLN* 1.3 56.7 + - - +
236C ILE* 3.1 26.3 - - + +
237C GLN* 2.8 26.2 + - - +
240C ILE* 5.1 0.7 - - - +
249C VAL* 5.8 2.5 - - + -
251C ILE* 5.0 12.6 - - + -
257C LEU* 5.8 0.4 - - + -
280C VAL* 4.3 20.0 - - + -
283C GLN* 3.4 54.5 - - + +
284C ILE* 4.4 8.1 - - + -
287C ILE* 4.5 17.5 - - + +
295C ILE* 5.5 5.4 - - + -
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Residues in contact with GLN 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ASN* 5.7 8.1 - - + -
119B ILE* 3.2 34.7 - - + +
230C THR 2.7 11.9 + - - +
231C LYS* 3.2 15.0 - - - +
232C MET 3.0 0.2 - - - -
233C PHE* 1.3 74.4 - - - +
235C LYS* 1.3 65.4 + - - +
236C ILE 3.0 1.3 - - - -
237C GLN* 3.0 23.0 + - - +
238C ASP* 2.9 34.7 + - - +
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Residues in contact with LYS 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLU* 3.2 31.1 + - + +
111C ASN 2.6 30.7 + - - -
112C LEU* 4.7 0.8 - - - +
113C GLU* 4.5 13.4 - - - +
121C ALA* 5.2 1.4 - - - +
122C ALA* 5.2 5.8 - - + -
231C LYS* 2.9 18.9 + - - +
232C MET* 2.9 15.2 + - + +
234C GLN* 1.3 75.6 - - + +
236C ILE* 1.3 62.9 + - + +
238C ASP* 3.0 30.8 - - - +
239C LEU* 3.7 9.5 + - - +
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Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ILE* 5.0 16.4 - - + -
212C ILE* 4.6 14.4 - - + -
232C MET* 2.9 16.1 + - + +
233C PHE* 3.1 53.8 - - + +
234C GLN 3.0 0.2 - - - -
235C LYS* 1.3 75.1 - - + +
237C GLN* 1.3 64.7 + - - +
239C LEU* 3.0 13.1 + - - +
240C ILE* 2.9 38.5 + - + +
247C VAL* 4.3 15.9 - - + -
249C VAL* 4.4 20.4 - - + -
287C ILE* 5.2 2.7 - - + -
293C VAL* 5.1 2.0 - - + -
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Residues in contact with GLN 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C PHE 2.8 15.9 + - - +
234C GLN* 3.4 27.6 - - - +
236C ILE* 1.3 73.8 - - - +
238C ASP* 1.3 64.2 + - - +
240C ILE* 3.1 30.9 - - - +
241C ASP* 2.9 50.3 + - - +
287C ILE* 4.9 4.0 - - - +
290C HIS* 3.3 33.7 + - - -
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Residues in contact with ASP 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C GLN* 2.9 25.5 + - - +
235C LYS* 3.0 32.9 + - - +
237C GLN* 1.3 76.9 - - - +
239C LEU* 1.3 68.2 + - + +
241C ASP* 3.2 21.8 + - - +
242C ASP* 3.7 3.3 + - - +
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C HIS* 3.3 31.6 - - + +
206C TYR* 6.2 0.9 - - + -
208C GLN* 3.6 35.2 - - + -
210C ILE* 3.7 22.0 - - + -
235C LYS 4.2 9.4 - - - +
236C ILE* 3.0 8.5 + - - +
238C ASP* 1.3 82.9 - - + +
240C ILE* 1.3 54.5 + - - +
242C ASP* 2.7 41.0 + - + +
245C ALA* 4.7 5.5 - - + +
247C VAL* 3.8 16.8 - - + +
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Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C PHE 5.1 0.2 - - - +
236C ILE* 2.9 27.4 + - + +
237C GLN* 2.9 48.9 + - + +
239C LEU* 1.3 76.1 - - - +
241C ASP* 1.3 63.0 + - - +
242C ASP 3.2 1.0 + - - +
243C LYS* 4.5 3.8 + - - -
247C VAL* 3.6 11.4 - - + -
287C ILE* 4.2 15.9 - - + -
290C HIS* 3.5 28.0 - - + +
292C ASN* 3.1 33.3 + - - +
293C VAL* 3.5 22.0 - - + -
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Residues in contact with ASP 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C GLN* 2.9 39.1 + - - +
238C ASP* 3.4 12.4 - - - +
239C LEU 3.0 0.4 + - - -
240C ILE* 1.3 75.4 - - - +
242C ASP* 1.3 57.0 + - - +
243C LYS* 2.8 22.8 + - - +
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Residues in contact with ASP 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C TYR* 2.2 37.4 + - - -
238C ASP 3.7 1.9 + - - +
239C LEU* 2.7 31.3 + - + +
240C ILE 4.0 3.5 - - - +
241C ASP* 1.3 71.5 - - - +
243C LYS* 1.3 57.4 + - - +
244C ASP* 2.8 30.7 + - - +
245C ALA* 3.0 35.1 + - + +
247C VAL* 5.9 0.2 - - - +
292C ASN* 4.5 2.4 + - - -
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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
------------------------------------------------------------
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