Contacts of the helix formed by residues 223 - 239 (chain C) in PDB entry 4EE5
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C GLN* 3.1 8.5 + - - -
222C PHE* 1.3 78.6 - - - +
224C ARG* 1.3 64.4 + - - +
225C ALA* 3.7 4.9 + - - +
226C LYS* 3.3 27.5 + - - +
227C LEU* 3.3 16.1 + - - +
305C ASN 2.8 28.2 + - - +
307C TYR 3.0 19.1 + - - +
308C TRP* 3.4 41.0 - - + -
309C GLY 5.8 0.2 - - - -
394C ILE* 3.8 9.4 - - + -
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Residues in contact with ARG 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C PRO* 4.0 17.9 - - + +
222C PHE* 3.8 19.9 - - + -
223C ASN* 1.3 71.2 + - - +
225C ALA* 1.3 64.2 - - - +
226C LYS 3.1 1.0 + - - -
227C LEU* 3.1 8.7 + - - +
228C LEU* 3.0 46.9 + - + +
246C PHE* 4.7 6.1 + - - +
247C SER 5.0 0.4 - - - -
248C ASP* 2.7 33.2 + - - +
287C GLY* 5.0 1.8 - - - -
288C GLY 3.7 21.4 + - - +
307C TYR 4.7 1.8 + - - -
309C GLY 5.9 0.6 + - - -
313C GLU* 2.8 44.1 + - + +
314C ASP* 4.6 8.9 - - - +
317C ILE* 5.2 3.8 - - - +
404C UDP 4.2 11.7 - - - +
406C GOL 3.8 21.3 + - - -
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Residues in contact with ALA 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ASN* 3.4 4.8 + - - +
224C ARG* 1.3 78.7 - - - +
226C LYS* 1.3 56.3 + - - +
228C LEU* 3.4 14.2 + - - +
229C ASN* 3.0 30.0 + - - -
303C PHE* 3.9 14.4 - - + +
304C PRO* 3.2 24.7 - - + +
307C TYR* 5.3 2.4 + - + -
313C GLU* 3.8 29.8 - - + +
317C ILE* 4.9 2.0 - - + -
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Residues in contact with LYS 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ASN* 3.3 28.3 + - + +
224C ARG 3.1 0.8 - - - -
225C ALA* 1.3 77.4 - - - +
227C LEU* 1.3 60.3 + - - +
229C ASN* 3.0 3.5 + - - +
230C VAL* 2.8 32.5 + - - +
304C PRO 4.3 0.4 + - - -
305C ASN* 3.2 41.2 - - - +
308C TRP* 4.7 5.8 - - + -
374C LEU* 4.0 13.5 - - + -
375C THR* 3.1 35.7 + - - +
394C ILE* 2.5 48.2 + - + +
395C GLY* 4.9 0.2 - - - -
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Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C PRO* 4.2 7.9 - - + -
184C PHE 4.1 1.8 - - - +
214C ILE* 3.6 44.5 - - + +
216C GLN* 3.7 23.8 - - + +
222C PHE* 3.5 39.9 - - + -
223C ASN 3.3 12.5 + - - +
224C ARG 3.1 5.1 + - - +
226C LYS* 1.3 74.6 - - - +
228C LEU* 1.3 63.4 + - - +
230C VAL* 3.1 5.9 + - - +
231C GLY 2.8 19.1 + - - -
392C VAL* 4.0 6.7 - - + -
394C ILE* 3.8 31.2 - - + -
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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
----------------------------------------------------------
181C ILE* 4.0 19.7 - - + +
183C PRO* 3.6 35.9 - - + -
224C ARG* 3.0 49.0 + - - +
225C ALA* 3.4 11.7 - - - +
227C LEU* 1.3 76.7 - - - +
229C ASN* 1.3 61.9 + - - +
231C GLY* 3.0 10.9 + - - -
232C PHE* 3.1 11.1 + - - +
246C PHE* 3.9 29.1 - - + -
303C PHE* 3.7 32.1 - - + -
317C ILE* 5.1 2.5 - - + -
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Residues in contact with ASN 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C ALA 3.0 15.3 + - - -
226C LYS 3.0 8.0 + - - +
228C LEU* 1.3 72.5 - - - +
230C VAL* 1.3 66.7 + - - +
232C PHE* 3.5 4.9 + - - +
233C GLN* 3.3 16.8 + - - +
297C PHE* 3.3 19.1 - - - -
302C GLY* 4.0 1.7 - - - -
303C PHE* 2.7 50.2 + - - +
304C PRO 4.2 0.6 + - - -
305C ASN* 2.9 24.7 + - - +
370C GLY 4.4 4.6 - - - -
371C LEU* 5.1 3.0 + - + +
374C LEU* 3.6 26.9 - - + +
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Residues in contact with VAL 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ILE* 4.1 16.6 - - + -
226C LYS 2.8 18.7 + - - +
227C LEU* 3.4 7.2 - - - +
229C ASN* 1.3 75.5 - - - +
231C GLY* 1.3 65.5 + - - +
233C GLN* 3.0 3.0 + - - +
234C GLU* 2.9 39.2 + - + +
374C LEU* 4.4 8.5 - - + -
376C TYR* 3.8 38.8 - - + -
390C ILE* 4.8 4.5 - - + -
392C VAL* 4.1 11.9 - - + -
394C ILE* 3.9 20.6 - - + -
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Residues in contact with GLY 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ILE* 3.6 16.2 - - - -
212C TYR* 5.4 1.8 - - - -
214C ILE* 3.7 27.4 - - - -
227C LEU 2.8 11.4 + - - -
228C LEU 3.0 5.0 + - - -
230C VAL* 1.3 76.2 - - - +
232C PHE* 1.3 62.9 - - - +
234C GLU* 4.0 1.6 - - - +
235C ALA* 2.9 28.6 + - - +
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Residues in contact with PHE 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ILE* 3.6 10.9 - - - +
228C LEU 3.1 10.8 + - - +
229C ASN 3.6 7.4 - - - +
231C GLY* 1.3 78.6 - - - +
233C GLN* 1.3 74.0 + - + +
236C LEU* 3.3 44.9 + - + +
244C PHE* 3.4 46.7 - + + -
246C PHE* 4.7 2.5 - - + -
294C LYS* 4.1 9.6 - - + -
297C PHE* 3.4 55.0 - + + -
298C LEU* 3.8 16.6 - - + -
371C LEU* 4.0 17.3 - - + -
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Residues in contact with GLN 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C ASN 3.3 7.9 + - - +
230C VAL 3.0 6.7 + - - +
232C PHE* 1.3 88.6 - - + +
234C GLU* 1.3 64.0 + - - +
236C LEU* 3.6 11.7 + - - +
237C LYS* 3.6 22.1 - - - +
371C LEU* 3.8 31.4 - - + +
374C LEU* 4.3 6.5 + - + +
376C TYR* 3.2 35.5 + - + +
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Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C TYR* 5.3 0.2 - - - -
230C VAL* 2.9 30.4 + - + +
231C GLY 4.2 0.7 - - - +
233C GLN* 1.3 73.6 - - - +
235C ALA* 1.3 65.2 + - - +
236C LEU 3.1 2.0 - - - -
237C LYS* 2.5 53.4 + - - +
238C ASP* 3.5 7.8 + - - +
376C TYR* 2.4 27.9 + - - +
378C VAL* 3.5 27.1 - - + +
390C ILE* 3.6 27.7 - - + +
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Residues in contact with ALA 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ALA* 3.8 20.6 - - + -
181C ILE* 4.7 0.9 - - + -
212C TYR* 3.7 39.6 - - + -
231C GLY 2.9 20.2 + - - +
232C PHE 4.1 2.9 - - - +
234C GLU* 1.3 75.7 - - - +
236C LEU* 1.3 64.5 + - - +
238C ASP* 3.0 13.2 + - - +
239C TYR 3.3 8.5 + - - -
241C TYR* 3.4 12.4 - - + -
244C PHE* 4.4 1.8 - - + -
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Residues in contact with LEU 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C PHE* 3.3 52.9 + - + +
233C GLN* 3.7 8.3 - - - +
234C GLU 3.1 0.6 - - - -
235C ALA* 1.3 79.9 - - - +
237C LYS* 1.3 58.9 + - + +
238C ASP 3.4 0.2 - - - -
239C TYR 3.2 23.5 + - - +
240C ASP* 4.7 4.8 - - - +
241C TYR* 3.5 26.9 - - - +
244C PHE* 3.8 8.3 - - + -
294C LYS* 3.7 25.1 - - - +
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Residues in contact with LYS 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C GLN* 3.6 18.4 - - - +
234C GLU* 2.5 49.8 + - - +
236C LEU* 1.3 76.9 - - + +
238C ASP* 1.3 65.9 + - - +
376C TYR* 4.1 4.7 + - - -
378C VAL* 5.6 0.6 - - - +
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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
----------------------------------------------------------
166C ARG* 4.5 12.0 + - - +
212C TYR* 2.6 37.9 + - - +
234C GLU 3.5 4.6 + - - +
235C ALA 3.0 4.7 + - - +
237C LYS* 1.3 82.0 - - - +
239C TYR* 1.3 66.2 + - + +
383C ARG* 2.9 43.5 + - - -
388C THR* 5.0 0.2 - - - +
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Residues in contact with TYR 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C ARG* 3.4 24.7 - - - +
177C LYS* 4.1 23.6 - - + +
208C ASP* 2.5 40.7 + - - -
235C ALA 3.3 7.9 + - - +
236C LEU* 3.2 19.5 + - - +
237C LYS 3.5 1.6 - - - -
238C ASP* 1.3 83.5 - - + +
240C ASP* 1.3 68.3 + - + +
241C TYR* 2.9 49.3 + + + -
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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
------------------------------------------------------------
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