Contacts of the helix formed by residues 224 - 235 (chain F) in PDB entry 1R4N
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 LEU 224 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331E ASP* 3.7 31.2 - - + +
339E TYR* 4.5 13.7 - - + +
343E GLN* 5.1 5.8 - - - +
213F PHE* 5.7 3.1 - - + -
223F ARG* 1.3 86.9 - - + +
225F PRO* 1.3 75.6 - - + +
226F GLU* 2.9 23.1 - - + +
227F HIS* 2.8 49.7 + - + +
228F CYS 3.5 2.4 + - - -
273F ILE* 3.8 7.2 - - - +
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Residues in contact with PRO 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F ARG 4.6 0.2 - - - +
224F LEU* 1.3 84.2 - - + +
226F GLU* 1.3 70.6 + - - +
228F CYS* 3.1 14.9 + - + +
229F ILE* 3.2 19.2 + - - +
273F ILE* 3.7 10.7 - - + -
274F ARG 3.1 26.9 - - - +
275F GLY* 3.2 30.7 - - - +
276F VAL* 3.7 12.6 - - + +
280F LEU* 3.7 12.3 - - + -
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Residues in contact with GLU 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213F PHE* 3.8 26.5 - - + -
224F LEU* 3.8 15.9 - - + +
225F PRO* 1.3 99.1 - - - +
227F HIS* 1.3 57.9 + - - +
228F CYS 3.1 0.3 + - - -
229F ILE* 3.2 2.5 + - - +
230F GLU* 2.8 32.1 + - - +
280F LEU* 4.0 17.0 - - + +
284F VAL* 4.2 24.3 - - + +
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Residues in contact with HIS 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E ASP* 3.8 7.1 + - - -
213F PHE* 3.5 40.0 - + + +
214F PRO* 6.3 0.2 - - - +
217F THR* 4.7 9.2 + - - -
218F ILE* 3.7 15.6 - - + +
221F MET 4.7 0.4 + - - -
222F PRO* 4.0 18.7 - - + +
223F ARG* 3.1 45.3 + - - -
224F LEU* 2.8 46.3 + - + +
226F GLU* 1.3 72.8 - - - +
228F CYS* 1.3 62.9 + - - +
230F GLU* 4.1 4.5 - - - -
231F TYR* 3.5 18.2 + - - +
267F ARG* 3.9 3.3 + - - -
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Residues in contact with CYS 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F PRO* 4.5 5.8 - - - -
224F LEU 3.5 3.3 + - - -
225F PRO* 3.1 9.1 + - - +
226F GLU 3.1 0.8 - - - -
227F HIS* 1.3 78.3 - - - +
229F ILE* 1.3 69.0 + - - +
231F TYR* 2.9 13.7 + - - +
232F VAL* 3.0 14.4 + - - +
264F SER* 3.8 19.7 - - - +
267F ARG* 3.9 18.6 + - + +
268F ALA* 3.4 35.7 - - + +
271F TYR* 5.7 0.7 - - - -
273F ILE* 4.0 24.5 - - - -
276F VAL* 4.8 0.9 - - + -
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Residues in contact with ILE 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F PRO 3.2 12.1 + - - +
226F GLU 3.7 4.3 - - - +
228F CYS* 1.3 75.8 - - - +
230F GLU* 1.3 54.6 + - - +
231F TYR 2.7 12.6 + - - -
232F VAL* 2.8 14.4 + - - +
233F ARG* 3.0 10.1 + - + +
260F ILE* 4.2 1.6 - - + -
264F SER* 3.0 27.1 + - - +
276F VAL* 4.5 6.7 - - + -
280F LEU* 3.5 14.4 - - + +
281F THR* 3.2 50.9 - - + +
284F VAL* 3.4 36.6 - - + -
285F VAL* 4.2 9.0 - - + -
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Residues in contact with GLU 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F ASN* 5.4 2.1 + - - -
213F PHE* 3.8 22.6 - - + +
218F ILE* 3.8 26.2 - - + +
226F GLU 2.8 21.1 + - - +
227F HIS* 4.2 4.0 - - - +
229F ILE* 1.3 71.9 - - - +
231F TYR* 1.3 56.7 + - - +
233F ARG* 2.9 34.1 + - - -
234F MET* 2.9 48.8 + - + +
284F VAL* 3.8 10.0 - - + +
287F ARG* 2.9 33.3 + - - -
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Residues in contact with TYR 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F ILE* 3.4 23.1 - - + +
219F ALA* 4.4 7.9 - - + -
227F HIS 3.5 7.6 + - - +
228F CYS 2.9 4.6 + - - +
229F ILE 2.7 4.9 + - - -
230F GLU* 1.3 72.0 - - - +
232F VAL* 1.3 71.6 + - + +
233F ARG 2.6 16.3 + - - -
234F MET* 5.0 0.2 - - - -
235F LEU* 2.9 51.9 + - + +
236F GLN* 3.3 37.1 + - + +
267F ARG* 2.9 54.0 + - - +
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Residues in contact with VAL 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228F CYS 3.8 4.7 - - - +
229F ILE 2.8 6.1 + - - +
231F TYR* 1.3 85.1 - - + +
233F ARG* 1.3 56.5 + - - +
236F GLN* 3.6 17.7 - - - +
237F TRP* 3.6 19.8 + - - +
259F TRP* 4.0 9.1 - - + -
260F ILE* 3.5 28.5 - - + +
263F LYS* 3.3 34.8 - - + +
264F SER* 3.3 37.2 - - - +
267F ARG* 4.4 2.7 - - + -
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Residues in contact with ARG 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229F ILE 3.0 11.5 + - - +
230F GLU* 2.9 31.8 + - - +
231F TYR 2.6 5.9 + - - -
232F VAL* 1.3 75.9 - - - +
234F MET* 1.3 90.7 + - - +
235F LEU 3.1 2.6 + - - -
237F TRP* 3.9 3.0 - - - +
238F PRO* 3.2 20.4 - - - +
249F LEU* 3.7 27.6 - - + +
260F ILE* 4.7 2.7 - - + -
284F VAL* 4.6 1.6 - - - -
285F VAL* 3.9 45.7 + - + +
287F ARG* 4.4 17.0 - - - +
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Residues in contact with MET 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F ASN* 5.5 7.9 - - - +
213F PHE* 5.6 3.1 - - + +
215F MET* 5.2 14.4 - - - +
218F ILE* 4.2 23.1 - - + -
230F GLU* 2.9 46.1 + - + +
231F TYR* 5.0 0.4 - - - -
233F ARG* 1.3 90.8 - - - +
235F LEU* 1.3 74.8 + - + +
238F PRO* 4.0 11.1 - - - +
287F ARG* 5.0 3.6 - - - +
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Residues in contact with LEU 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215F MET* 4.4 28.9 - - + -
218F ILE* 5.0 6.1 - - + -
219F ALA* 4.3 14.8 - - + -
231F TYR* 2.9 39.5 + - + +
233F ARG 3.1 0.8 + - - -
234F MET* 1.3 95.8 - - + +
236F GLN* 1.3 64.6 + - - +
237F TRP 3.2 2.2 - - - -
238F PRO* 3.0 15.5 - - + +
239F LYS* 3.1 16.5 + - - +
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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