Contacts of the helix formed by residues 231 - 247 (chain C) in PDB entry 4QUL
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 231 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A HIS* 2.5 44.1 + - + +
230C LEU* 1.3 76.4 - - - +
232C PHE* 1.3 76.1 + - - +
233C MET* 3.0 33.6 + - - +
234C HIS* 3.1 10.6 + - - +
235C ILE* 3.1 16.6 + - - +
269C LEU* 5.4 1.7 - - - +
271C LYS 4.5 1.7 - - - +
272C GLU* 3.4 26.4 - - + -
273C LEU* 2.8 30.8 + - - +
274C TYR* 3.5 25.7 - - + +
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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
----------------------------------------------------------
78C PHE* 6.0 2.2 - + - -
157C LEU* 3.8 22.2 - - + -
159C ILE* 5.1 12.8 - - + -
194C LEU* 4.1 18.2 - - + -
196C ALA* 5.6 0.7 - - + -
219C LEU* 4.8 5.2 - - + -
223C LEU* 4.0 17.0 - - + -
230C LEU 3.8 0.4 + - - -
231C GLU* 1.3 73.0 - - - +
233C MET* 1.3 59.8 + - + +
235C ILE* 3.0 15.2 + - + -
236C LEU* 2.8 66.7 + - + +
269C LEU* 5.4 3.1 - - + -
273C LEU* 2.9 45.1 + - + +
275C PHE* 3.4 26.9 - + + -
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Residues in contact with MET 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A MET* 3.4 43.2 - - + +
234A HIS* 4.4 9.0 - - + +
237A THR* 4.9 8.3 - - - +
265A ILE* 4.8 4.9 - - + -
194C LEU* 3.9 22.7 - - - -
231C GLU* 3.0 24.3 + - - +
232C PHE* 1.3 78.0 - - - +
234C HIS* 1.3 57.4 + - + +
236C LEU* 3.4 6.2 + - - +
237C THR* 2.7 35.7 + - - -
265C ILE* 3.8 20.0 - - + +
267C SER* 3.6 28.0 - - - +
269C LEU* 5.0 7.2 - - + -
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Residues in contact with HIS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLU* 2.9 44.6 + - + +
233A MET* 4.9 1.6 - - + -
234A HIS* 3.4 38.3 + + - -
272A GLU* 3.6 34.0 + - + +
274A TYR* 4.3 3.1 - - - -
230C LEU* 4.2 14.8 - - + +
231C GLU* 3.1 13.2 + - + +
233C MET* 1.3 80.4 - - + +
235C ILE* 1.3 65.6 + - - +
237C THR* 3.3 10.1 + - - -
238C ARG* 3.1 26.2 + - - +
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Residues in contact with ILE 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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219C LEU* 5.3 0.2 - - + -
222C MET* 4.0 28.0 - - + +
223C LEU* 4.2 22.7 - - + +
226C TYR* 3.6 20.6 - - + +
227C ALA* 3.8 15.3 - - + +
230C LEU* 3.5 31.0 - - + +
231C GLU 3.1 10.4 + - - +
232C PHE* 3.0 20.8 + - + +
234C HIS* 1.3 77.0 - - - +
236C LEU* 1.3 63.1 + - + +
238C ARG* 3.1 11.8 + - - +
239C VAL* 3.0 23.5 + - + +
275C PHE* 4.7 4.3 - - + -
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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
----------------------------------------------------------
194C LEU* 3.8 20.6 - - + -
196C ALA* 4.2 17.0 - - + -
215C PHE* 5.3 3.1 - - + -
219C LEU* 3.9 29.2 - - + -
232C PHE* 2.8 54.6 + - + +
233C MET* 3.7 5.6 - - - +
235C ILE* 1.3 72.4 - - + +
237C THR* 1.3 57.0 + - - +
239C VAL* 3.2 11.7 + - + +
240C ASN* 2.9 30.7 + - - +
265C ILE* 3.6 32.5 - - + -
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Residues in contact with THR 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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233A MET* 5.1 9.0 - - - +
267A SER* 5.1 2.6 + - - -
269A LEU* 3.8 10.5 - - + +
270A THR 3.7 3.0 - - - +
271A LYS* 3.5 42.8 - - - +
272A GLU* 4.3 6.7 - - + +
233C MET 2.7 24.1 + - - -
234C HIS* 3.5 13.4 - - - -
235C ILE 3.1 0.2 - - - -
236C LEU* 1.3 77.5 - - - +
238C ARG* 1.3 61.1 + - - +
240C ASN* 3.2 8.4 + - - +
241C ARG* 3.1 20.6 + - - +
265C ILE* 4.3 8.7 - - - +
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Residues in contact with ARG 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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35A ASN* 3.3 43.6 + - - +
270A THR 5.4 0.7 - - - -
272A GLU* 4.5 10.9 + - - -
222C MET* 3.7 21.6 - - + +
226C TYR* 2.7 49.1 + - + -
230C LEU* 3.8 26.5 - - + +
234C HIS 3.1 14.4 + - - +
235C ILE* 3.3 8.7 - - - +
237C THR* 1.3 73.0 - - - +
239C VAL* 1.3 60.7 + - - +
241C ARG* 3.3 6.9 + - - +
242C LYS* 2.9 30.5 + - - +
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Residues in contact with VAL 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C PHE* 3.8 35.0 - - + -
218C SER* 4.1 5.8 - - - +
219C LEU* 3.8 37.7 - - + +
222C MET* 3.7 25.8 - - + -
235C ILE* 3.0 15.7 + - + +
236C LEU* 3.2 15.0 + - + +
238C ARG* 1.3 75.7 - - - +
240C ASN* 1.3 64.3 + - - +
242C LYS* 3.2 3.6 + - - +
243C VAL* 2.9 26.0 + - + +
263C PRO* 4.7 1.3 - - + -
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Residues in contact with ASN 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A SER 3.3 24.4 + - - -
268A MET* 3.7 7.5 - - - +
269A LEU 2.9 30.6 + - - +
270A THR* 4.4 0.2 - - - -
215C PHE* 5.5 0.2 - - - -
236C LEU 2.9 17.6 + - - +
237C THR 3.2 6.5 + - - +
239C VAL* 1.3 75.6 - - - +
241C ARG* 1.3 57.6 + - - +
243C VAL* 4.0 0.3 - - - -
244C ALA* 2.9 31.5 + - - +
262C ILE* 3.7 9.7 - - + +
263C PRO* 3.3 37.1 + - - +
265C ILE* 3.8 15.8 - - - +
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Residues in contact with ARG 241 (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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34A ASP* 4.1 20.3 + - - +
187A ILE* 4.6 7.3 - - - +
270A THR* 3.2 57.4 + - - +
271A LYS* 3.8 25.7 - - - +
237C THR 3.1 7.8 + - - +
238C ARG* 3.8 9.2 - - - +
239C VAL 3.2 0.2 - - - -
240C ASN* 1.3 73.0 - - - +
242C LYS* 1.3 61.9 + - - +
244C ALA* 4.3 0.7 - - - -
245C THR* 2.7 62.6 + - + +
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Residues in contact with LYS 242 (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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217C GLN* 4.8 1.3 - - - -
218C SER* 3.5 39.7 - - - +
221C ALA* 4.4 13.2 - - - +
222C MET* 3.9 26.4 - - + +
238C ARG 2.9 18.3 + - - +
239C VAL* 3.6 4.5 - - - +
241C ARG* 1.3 77.1 - - - +
243C VAL* 1.3 64.6 + - - +
245C THR* 4.1 4.0 - - - -
246C GLU* 2.9 63.9 + - - +
247C PHE* 3.7 10.1 - - + -
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Residues in contact with VAL 243 (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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214C TRP* 3.8 19.8 - - + +
215C PHE* 4.0 9.2 - - - -
218C SER* 3.6 23.3 - - - +
239C VAL* 2.9 20.6 + - + +
242C LYS* 1.3 76.8 - - - +
244C ALA* 1.3 62.5 + - - +
245C THR 3.3 0.2 + - - -
247C PHE* 3.6 26.2 + - - +
261C GLN* 3.3 43.5 + - + +
263C PRO* 3.9 23.3 - - + -
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Residues in contact with ALA 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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186A LYS 3.6 2.8 - - - +
187A ILE* 3.8 7.4 - - + +
188A PRO* 3.5 22.5 - - + +
270A THR* 4.2 12.1 - - + -
240C ASN 2.9 20.7 + - - +
241C ARG* 3.8 3.1 - - - +
243C VAL* 1.3 77.5 - - - +
245C THR* 1.3 54.5 + - + +
260C LYS* 2.7 33.4 + - - -
261C GLN 3.5 10.7 + - - -
262C ILE* 3.8 14.4 - - + -
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Residues in contact with THR 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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185A HIS* 5.6 7.4 - - - -
186A LYS 4.6 3.4 + - - +
187A ILE* 3.5 18.8 - - + -
241C ARG* 2.7 65.2 + - + +
242C LYS* 4.1 0.5 - - - -
244C ALA* 1.3 78.6 - - + +
246C GLU* 1.3 77.4 + - - +
247C PHE 3.5 1.5 + - - -
260C LYS* 4.0 7.8 + - - +
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Residues in contact with GLU 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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242C LYS* 2.9 53.5 + - - +
245C THR* 1.3 90.6 - - - +
247C PHE* 1.3 70.7 + - + +
248C GLU 4.3 0.2 + - - -
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Residues in contact with PHE 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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214C TRP* 3.3 66.1 - + + -
217C GLN* 3.8 27.8 - - + -
218C SER* 3.2 26.7 - - - -
242C LYS* 3.7 24.7 - - + -
243C VAL* 3.6 16.1 + - - +
245C THR 3.5 0.4 - - - -
246C GLU* 1.3 92.0 - - + +
248C GLU* 1.3 59.9 + - - +
260C LYS* 2.8 29.3 + - - +
261C GLN 5.2 0.3 + - - -
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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