Contacts of the helix formed by residues 222 - 240 (chain C) in PDB entry 5KX8
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 THR 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221C ILE* 1.3 75.4 - - - +
223C THR* 1.3 59.1 + - - +
224C GLU* 3.8 8.2 + - - +
225C GLU* 3.0 40.6 + - - +
226C LEU* 2.9 29.6 + - - +
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Residues in contact with THR 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C THR* 1.3 70.7 - - - +
224C GLU* 1.3 64.6 + - - +
226C LEU* 3.4 12.0 + - + +
227C LYS* 3.1 22.9 + - - +
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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
----------------------------------------------------------
222C THR* 3.2 9.2 + - - +
223C THR* 1.3 77.7 - - - +
225C GLU* 1.4 63.2 + - - +
227C LYS* 3.4 4.6 + - - +
228C GLN* 3.1 30.7 + - + +
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Residues in contact with GLU 225 (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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221C ILE* 3.5 11.7 + - - +
222C THR* 3.0 43.1 + - - +
224C GLU* 1.4 82.4 - - + +
226C LEU* 1.3 56.0 + - - +
228C GLN* 3.3 7.4 + - - +
229C GLN* 3.1 36.0 + - - +
347C ARG* 3.6 45.2 + - - +
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Residues in contact with LEU 226 (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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197C PHE* 4.3 31.9 - - + +
215C LEU* 3.8 30.1 - - + +
216C ALA 4.2 2.9 - - - -
217C ALA* 3.7 40.2 - - - +
221C ILE* 6.2 2.7 - - - +
222C THR 2.9 15.7 + - - +
223C THR* 3.7 12.3 - - + +
224C GLU 3.3 0.2 - - - -
225C GLU* 1.3 77.3 - - - +
227C LYS* 1.3 58.0 + - - +
229C GLN* 3.4 12.0 + - + +
230C PHE* 3.1 24.1 + - - +
258C LEU* 4.4 6.7 - - + -
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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
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223C THR 3.1 16.0 + - - +
224C GLU* 4.2 5.2 - - - +
226C LEU* 1.3 73.5 - - - +
228C GLN* 1.3 62.1 + - - +
230C PHE* 3.2 11.0 + - + +
231C ASP* 2.8 61.4 + - - +
253C SER* 4.8 11.4 - - - -
258C LEU* 3.8 38.5 - - + +
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Residues in contact with GLN 228 (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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224C GLU* 3.1 25.9 + - + +
225C GLU* 3.3 7.6 + - - +
227C LYS* 1.3 77.3 - - - +
229C GLN* 1.3 57.5 + - - +
231C ASP* 3.4 29.2 + - - +
232C GLN* 2.8 30.4 + - - +
331C GLY 5.0 0.2 - - - -
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Residues in contact with GLN 229 (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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197C PHE* 3.2 50.1 - - - +
215C LEU* 5.2 3.3 - - + +
225C GLU* 3.1 19.6 + - - +
226C LEU* 3.5 16.1 - - + +
228C GLN* 1.3 74.9 - - - +
230C PHE* 1.3 58.7 + - - +
232C GLN 3.3 0.5 + - - -
233C GLU* 2.9 27.3 + - - +
331C GLY* 3.4 35.5 - - - +
332C LEU* 3.3 27.7 - - + +
347C ARG* 4.0 13.6 - - - +
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Residues in contact with PHE 230 (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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215C LEU* 3.7 13.8 - - + +
226C LEU 3.1 13.4 + - - +
227C LYS* 3.4 20.9 - - + +
229C GLN* 1.3 74.8 - - - +
231C ASP* 1.3 71.2 + - - +
233C GLU* 3.4 8.2 + - - +
234C ILE* 3.2 52.6 + - + +
251C PHE* 3.9 20.6 - + + -
252C SER 4.0 12.3 - - - -
253C SER* 4.6 5.8 - - - -
258C LEU* 3.6 42.2 - - + -
259C CYS 3.7 21.3 - - - -
260C LEU* 4.0 18.2 - - + -
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Residues in contact with ASP 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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227C LYS* 2.8 53.5 + - - +
228C GLN* 3.4 27.2 + - - +
230C PHE* 1.3 77.3 - - - +
232C GLN* 1.4 60.5 + - - +
234C ILE* 3.5 7.7 + - - +
235C LYS* 2.9 28.8 + - - +
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Residues in contact with GLN 232 (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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228C GLN 2.8 18.4 + - - +
229C GLN 3.7 0.4 - - - +
231C ASP* 1.4 73.8 - - - +
233C GLU* 1.4 57.0 + - - +
235C LYS* 3.7 23.6 + - - +
236C VAL* 2.9 54.9 + - - +
307C HIS* 5.0 4.9 + - - -
330C PHE 3.4 16.6 - - - +
331C GLY 3.5 17.5 - - - +
333C ALA* 3.1 30.4 + - - +
334C ARG* 4.3 4.2 - - - +
335C ALA* 5.2 1.0 - - - +
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Residues in contact with GLU 233 (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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213C LYS* 5.5 2.6 + - - -
229C GLN 2.9 12.8 + - - +
230C PHE* 3.5 12.1 - - - +
231C ASP 3.4 0.2 - - - -
232C GLN* 1.4 75.3 - - - +
234C ILE* 1.4 55.6 + - - +
236C VAL* 3.9 1.2 - - - +
237C MET* 2.9 40.0 + - + +
246C VAL* 5.0 0.2 - - - +
248C LEU* 5.3 0.9 - - + -
260C LEU* 3.9 20.6 - - + -
262C TYR* 2.7 36.7 + - + +
329C ASP* 3.7 9.7 + - - +
330C PHE* 2.8 53.5 + - - -
331C GLY* 3.3 6.3 + - - +
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Residues in contact with ILE 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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165C PHE* 3.9 12.6 - - + -
230C PHE* 3.2 58.3 + - + +
231C ASP* 3.5 8.7 + - - +
233C GLU* 1.4 74.1 - - - +
235C LYS* 1.3 60.1 + - - +
237C MET* 3.3 1.0 + - - +
238C ALA* 2.8 31.4 + - + +
248C LEU* 4.1 8.3 - - + -
251C PHE* 3.8 39.9 - - + -
260C LEU* 3.8 11.4 - - + -
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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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231C ASP 2.9 19.0 + - - +
232C GLN* 3.7 28.4 + - - +
234C ILE* 1.3 75.7 - - - +
236C VAL* 1.3 64.0 + - + +
238C ALA* 3.4 5.7 + - - +
239C LYS* 3.3 30.6 + - + +
307C HIS* 5.4 11.5 - - + -
335C ALA* 5.5 8.3 - - - +
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Residues in contact with VAL 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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232C GLN* 2.9 41.9 + - - +
233C GLU 4.1 0.2 - - - +
235C LYS* 1.3 76.8 - - + +
237C MET* 1.4 56.9 + - - +
239C LYS* 3.5 6.8 + - - +
240C CYS* 2.8 33.4 + - + +
302C LEU* 4.4 15.0 - - + -
307C HIS* 4.0 23.1 - - + +
330C PHE* 3.7 36.6 - - + -
333C ALA* 4.0 14.4 - - + -
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Residues in contact with MET 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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165C PHE* 3.7 20.9 - - + -
233C GLU* 2.9 35.1 + - - +
234C ILE 4.0 0.9 - - - +
236C VAL* 1.4 75.2 - - - +
238C ALA* 1.3 64.0 + - - +
240C CYS 3.3 36.9 + - - +
241C GLN* 4.0 11.8 + - + +
245C LEU* 5.1 2.2 - - + -
246C VAL* 3.3 31.4 - - - +
247C GLU* 4.2 5.2 - - + -
248C LEU* 3.9 31.4 - - + +
262C TYR* 4.9 0.7 - - + -
330C PHE* 3.6 25.6 - - + -
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Residues in contact with ALA 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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165C PHE* 3.6 18.8 - - + -
234C ILE* 2.8 23.5 + - + +
235C LYS* 3.7 6.7 - - - +
236C VAL 3.3 0.2 - - - -
237C MET* 1.3 71.8 - - - +
239C LYS* 1.3 55.4 + - + +
241C GLN* 2.7 24.6 + - - -
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Residues in contact with LYS 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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235C LYS* 3.3 21.6 + - - +
236C VAL 3.8 2.7 - - - +
238C ALA* 1.3 81.1 - - + +
240C CYS* 1.4 61.6 + - - +
241C GLN* 3.9 6.6 + - - +
301C PHE* 5.0 2.6 - - - -
305C ASN* 3.9 42.9 + - - +
306C HIS* 5.9 1.4 - - - -
307C HIS* 3.4 29.3 + - + +
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Residues in contact with CYS 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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236C VAL* 2.8 25.4 + - + +
237C MET* 3.3 27.6 - - - +
238C ALA 3.5 0.4 - - - -
239C LYS* 1.4 78.0 - - - +
241C GLN* 1.4 61.8 + - - +
245C LEU* 3.8 16.9 - - + +
301C PHE* 3.6 24.7 - - + -
302C LEU* 4.5 8.1 - - + -
305C ASN* 3.9 15.5 - - - -
307C HIS* 3.8 28.9 - - - -
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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
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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