Contacts of the helix formed by residues 238 - 260 (chain C) in PDB entry 4HYY
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 GLU 238 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C PHE* 3.9 27.6 - - + +
235C GLY 3.2 11.9 + - - +
236C ARG 3.1 1.0 - - - -
237C GLY* 1.3 82.6 - - - +
239C LEU* 1.3 61.4 + - - +
240C ALA* 3.9 6.6 + - - +
241C GLU* 3.4 41.4 + - + +
242C ARG* 3.4 18.0 + - - +
240D ALA* 5.5 12.1 - - + -
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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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233C PHE 5.8 1.3 - - - +
235C GLY 5.2 0.4 - - - +
236C ARG* 3.4 35.5 + - + +
237C GLY 3.7 0.8 + - - -
238C GLU* 1.3 75.1 - - - +
240C ALA* 1.3 63.7 + - - +
242C ARG* 3.2 29.7 + - - +
243C GLN* 2.8 56.5 + - - +
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Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C GLY 5.3 0.2 + - - -
238C GLU* 3.4 7.2 + - - +
239C LEU* 1.3 80.0 - - - +
241C GLU* 1.3 63.9 + - - +
243C GLN* 3.3 7.4 + - - +
244C GLN* 3.2 21.7 + - - +
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Residues in contact with GLU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C PHE* 3.9 15.4 - - + -
238C GLU* 3.4 35.6 + - + +
240C ALA* 1.3 77.9 - - - +
242C ARG* 1.3 66.0 + - - +
244C GLN* 2.9 28.0 + - - +
245C LYS* 3.2 52.3 + - - +
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Residues in contact with ARG 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C MET* 5.0 9.0 - - - +
229C PHE* 3.4 36.7 - - + +
230C ARG* 3.8 27.9 - - - +
233C PHE* 3.5 42.2 + - + -
234C SER* 5.7 0.6 - - - +
238C GLU 3.4 7.0 + - - +
239C LEU* 3.2 32.2 + - - +
241C GLU* 1.3 78.2 - - - +
243C GLN* 1.3 72.0 + - - +
245C LYS* 3.5 2.4 + - - +
246C LEU* 2.9 35.6 + - + +
288C ILE* 5.2 6.7 - - - +
289C GLY* 4.9 17.4 - - - +
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Residues in contact with GLN 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C LEU* 2.8 53.6 + - - +
240C ALA* 3.8 6.5 - - - +
241C GLU 3.2 0.2 - - - -
242C ARG* 1.3 92.1 + - - +
244C GLN* 1.3 68.3 + - - +
246C LEU* 3.1 5.8 + - - +
247C ALA* 2.7 30.6 + - + +
289C GLY 5.3 0.3 - - - +
292C ILE* 3.3 34.5 - - + +
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Residues in contact with GLN 244 (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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240C ALA 3.2 10.5 + - - +
241C GLU* 2.9 38.2 + - - +
243C GLN* 1.3 79.0 - - - +
245C LYS* 1.3 63.3 + - + +
247C ALA* 4.0 3.1 - - - +
248C GLN* 3.0 48.9 + - - +
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Residues in contact with LYS 245 (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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196C SER* 6.1 0.9 - - - -
197C GLU* 5.9 7.0 - - - +
200C MET* 5.2 7.5 - - + +
229C PHE* 3.9 18.5 - - + -
233C PHE* 4.3 16.1 - - + -
241C GLU* 3.2 35.2 + - - +
242C ARG* 3.6 4.9 - - - +
243C GLN 3.2 0.6 - - - -
244C GLN* 1.3 82.6 + - + +
246C LEU* 1.3 66.9 + - - +
248C GLN* 3.3 18.8 + - - +
249C MET* 3.0 22.3 + - - +
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Residues in contact with LEU 246 (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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226C MET* 3.7 40.8 - - + -
229C PHE* 3.8 23.3 - - + -
242C ARG* 2.9 26.3 + - + +
243C GLN* 3.7 9.9 - - - +
245C LYS* 1.3 69.6 - - - +
247C ALA* 1.3 67.2 + - - +
249C MET* 2.9 18.7 + - + +
250C LEU* 2.8 45.8 + - + +
289C GLY* 4.3 7.2 - - - +
292C ILE* 4.0 30.3 - - + -
293C LEU* 5.2 1.1 - - + +
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Residues in contact with ALA 247 (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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243C GLN* 2.7 22.5 + - + +
244C GLN* 4.1 2.9 - - - +
246C LEU* 1.3 74.4 - - - +
248C GLN* 1.4 55.7 + - - +
250C LEU* 3.1 3.0 + - - +
251C SER* 2.9 32.6 + - - -
292C ILE* 3.7 25.4 - - + -
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Residues in contact with GLN 248 (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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200C MET* 3.7 14.3 - - + +
244C GLN* 3.0 39.6 + - - +
245C LYS* 3.4 23.5 + - + +
247C ALA* 1.4 72.0 - - - +
249C MET* 1.3 65.7 - - - +
251C SER* 3.3 7.7 + - - -
252C ARG* 3.0 26.9 + - - +
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Residues in contact with MET 249 (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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199C GLN* 3.4 25.1 - - - +
200C MET* 3.7 30.3 - - + -
203C LEU* 4.3 17.0 - - + +
222C ILE* 5.8 0.2 - - - -
225C ILE* 3.7 28.5 - - + +
229C PHE* 3.8 21.3 - - + -
245C LYS 3.0 10.3 + - - +
246C LEU* 2.9 13.1 + - + +
248C GLN* 1.3 78.0 - - - +
250C LEU* 1.3 90.8 + - + +
252C ARG* 3.2 4.0 + - - +
253C LEU* 2.9 28.3 + - + +
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Residues in contact with LEU 250 (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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121C ILE* 4.3 5.1 - - + +
225C ILE* 3.8 13.0 - - + -
246C LEU* 2.8 39.7 + - + +
247C ALA* 3.9 3.8 - - - +
249C MET* 1.3 97.9 - - + +
251C SER* 1.3 58.4 + - - +
253C LEU* 3.1 12.7 + - + +
254C GLN* 2.8 34.6 + - - +
266C VAL* 6.3 0.2 - - + -
292C ILE* 3.8 21.5 - - + +
293C LEU* 3.7 35.9 - - + -
296C ALA* 3.7 17.5 - - + -
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Residues in contact with SER 251 (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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247C ALA 2.9 14.0 + - - -
248C GLN* 3.3 12.3 + - - -
250C LEU* 1.3 77.6 - - - +
252C ARG* 1.3 62.7 + - - +
254C GLN* 3.6 15.3 - - - +
255C LYS* 3.0 34.9 + - - +
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Residues in contact with ARG 252 (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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200C MET* 3.6 23.8 - - + -
203C LEU* 5.3 7.1 + - + +
204C ASP* 4.6 16.3 + - - +
207C ALA* 3.8 26.4 - - - +
248C GLN 3.0 19.2 + - - +
249C MET 3.4 9.0 - - - +
251C SER* 1.3 74.3 + - - +
253C LEU* 1.3 59.7 + - - +
255C LYS* 3.4 37.1 + - - +
256C ILE* 2.9 46.3 + - + +
259C GLU* 5.3 4.9 + - - -
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Residues in contact with LEU 253 (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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121C ILE* 4.0 11.4 - - + -
203C LEU* 4.2 16.6 - - + -
220C LEU* 3.7 29.6 - - + -
222C ILE* 3.7 23.6 - - + -
225C ILE* 4.0 16.2 - - + -
249C MET* 2.9 16.9 + - + +
250C LEU* 3.1 20.8 + - + +
252C ARG* 1.3 73.3 - - - +
254C GLN* 1.3 67.9 + - - +
256C ILE* 3.1 7.7 + - + +
257C SER* 3.0 24.3 + - - -
264C VAL* 4.2 22.2 - - + -
266C VAL* 4.6 1.8 - - + -
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Residues in contact with GLN 254 (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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121C ILE* 3.6 19.5 - - + +
250C LEU 2.8 23.6 + - - +
251C SER* 3.6 15.0 - - - +
253C LEU* 1.3 72.2 - - - +
255C LYS* 1.3 59.6 + - + +
257C SER* 2.8 23.8 - - - -
258C GLU* 3.1 28.7 + - - +
295C HIS* 3.8 21.3 - - - +
296C ALA* 3.0 32.3 - - + +
298C THR* 5.2 3.0 - - + +
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Residues in contact with LYS 255 (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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251C SER* 3.0 25.8 + - - +
252C ARG* 3.7 33.8 - - - +
254C GLN* 1.3 76.2 - - - +
256C ILE* 1.3 55.1 + - - +
258C GLU* 4.1 4.7 - - - +
259C GLU* 2.7 48.3 + - + +
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Residues in contact with ILE 256 (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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203C LEU* 4.1 32.5 - - + +
206C VAL* 4.6 1.6 - - + -
207C ALA* 4.1 25.8 - - + +
210C PHE* 3.5 35.4 - - + -
220C LEU* 4.6 9.4 - - + -
252C ARG* 2.9 40.6 + - + +
253C LEU* 3.4 10.5 - - + +
255C LYS* 1.3 73.6 - - - +
257C SER* 1.3 66.7 + - - +
260C TYR* 2.9 39.8 + - + +
262C VAL* 4.5 3.8 - - + +
264C VAL* 5.5 0.9 - - + -
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Residues in contact with SER 257 (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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119C MET* 3.1 9.6 + - - -
120C ALA* 2.8 42.4 + - - -
121C ILE* 4.3 0.8 - - - +
253C LEU 3.0 9.5 + - - -
254C GLN* 2.8 19.3 - - - -
256C ILE* 1.3 77.1 - - - +
258C GLU* 1.3 58.2 + - - -
261C ASN 3.3 4.5 + - - -
262C VAL* 3.1 37.5 + - - +
264C VAL* 3.9 12.3 - - - +
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Residues in contact with GLU 258 (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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91C TYR* 5.7 2.1 + - - +
94C LYS* 2.5 31.3 + - - +
119C MET* 3.5 43.7 - - + +
120C ALA* 5.7 0.5 - - - -
254C GLN* 3.1 36.1 + - - +
255C LYS* 4.1 3.4 - - - +
257C SER* 1.3 78.2 + - - +
259C GLU* 1.3 57.9 + - - +
260C TYR 3.3 0.8 + - - -
261C ASN 4.0 4.0 + - - -
298C THR* 5.9 3.1 - - - +
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Residues in contact with GLU 259 (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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94C LYS* 4.0 10.1 + - - +
211C HIS* 4.9 6.1 - - - -
252C ARG* 5.3 4.9 + - - -
255C LYS* 2.7 33.3 + - + +
258C GLU* 1.3 75.5 - - - +
260C TYR* 1.3 97.4 + - + +
261C ASN* 3.8 0.5 + - - +
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Residues in contact with TYR 260 (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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207C ALA* 3.9 26.5 + - + +
210C PHE* 3.6 42.0 - + + -
211C HIS* 2.9 53.3 + + - +
214C ALA* 6.1 3.6 - - + -
215C GLY* 5.3 8.0 + - - -
217C PHE 5.0 0.7 - - - +
256C ILE* 2.9 24.7 + - + +
259C GLU* 1.3 109.5 + - + +
261C ASN* 1.3 72.0 + - - +
262C VAL* 3.2 10.3 + - + +
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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