Contacts of the helix formed by residues 214 - 232 (chain F) in PDB entry 4R8A
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 214 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40F LEU* 3.7 8.6 - - - +
212F PHE* 3.5 1.6 - - - +
213F ARG* 1.3 100.1 - - + +
215F ARG* 1.3 73.7 + - + +
216F ALA* 3.6 26.2 - - + +
217F ASP* 3.1 34.1 + - - +
218F VAL* 3.8 5.9 + - - +
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Residues in contact with ARG 215 (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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39F ASP 5.2 1.3 - - - +
40F LEU* 3.4 39.9 + - - +
41F LEU 5.4 0.7 - - - -
42F ASP* 3.5 24.1 + - - +
44F GLN* 5.2 1.8 - - - +
45F GLU* 3.0 40.0 + - - -
174F ARG* 3.4 34.4 - - - +
214F LEU* 1.3 79.3 - - + +
216F ALA* 1.3 58.2 + - - +
218F VAL* 2.8 31.8 + - - +
219F ASP* 3.3 17.1 + - - +
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Residues in contact with ALA 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214F LEU* 3.2 24.2 + - + +
215F ARG* 1.3 78.5 - - - +
217F ASP* 1.3 63.3 + - - +
219F ASP* 3.7 13.9 + - - +
220F ALA* 3.4 18.4 + - - +
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Residues in contact with ASP 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F PHE* 3.7 16.4 - - + -
213F ARG 5.8 0.8 + - - +
214F LEU* 3.1 28.4 + - - +
215F ARG 2.9 1.2 + - - -
216F ALA* 1.3 78.5 - - - +
218F VAL* 1.3 64.1 + - - +
220F ALA* 3.3 3.7 + - - +
221F TYR* 3.1 21.3 + - - +
249F TYR* 6.0 0.3 - - - -
251F ASN* 3.2 32.1 - - - +
254F LEU* 3.5 24.5 - - + +
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Residues in contact with VAL 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F LEU* 4.4 1.3 - - + -
174F ARG* 3.4 30.7 - - + +
177F LEU* 4.0 19.3 - - + -
178F MET* 3.8 27.8 - - + -
212F PHE* 3.5 40.2 - - + -
214F LEU 4.1 4.0 - - - +
215F ARG* 2.8 13.3 + - - +
217F ASP* 1.3 76.4 - - - +
219F ASP* 1.3 63.4 + - - +
221F TYR* 3.2 4.4 + - - +
222F LEU* 3.1 22.4 + - + +
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Residues in contact with ASP 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F ARG* 2.4 43.0 + - - +
215F ARG* 3.3 26.4 + - - +
216F ALA* 3.8 14.3 - - - +
217F ASP 3.3 0.2 - - - -
218F VAL* 1.3 76.3 - - - +
220F ALA* 1.3 58.4 + - - +
222F LEU* 3.5 5.5 + - - +
223F HIS* 3.0 27.9 + - - +
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Residues in contact with ALA 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216F ALA 3.4 11.2 + - - +
217F ASP* 3.3 10.3 + - - +
218F VAL 3.2 0.6 - - - -
219F ASP* 1.3 77.1 - - - +
221F TYR* 1.3 63.9 + - - +
223F HIS* 3.3 5.3 + - - +
224F LEU* 3.1 28.8 + - - +
249F TYR* 3.5 33.3 + - + -
254F LEU* 3.7 16.4 - - + -
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Residues in contact with TYR 221 (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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177F LEU* 3.5 24.9 - - + -
181F GLY 4.0 12.9 + - - -
182F ASN* 3.6 12.2 - - - +
183F LEU* 4.7 2.5 - - + -
212F PHE* 3.6 26.7 - + + -
217F ASP 3.1 12.7 + - - +
218F VAL 3.2 8.9 + - - +
220F ALA* 1.3 77.0 - - - +
222F LEU* 1.3 56.8 + - - +
224F LEU* 3.4 4.7 + - - +
225F PHE* 3.0 33.9 + + + +
253F TRP* 5.7 6.1 - + + -
254F LEU* 3.6 12.0 - - + +
257F ARG* 3.5 37.1 + - - +
-1G C 4.0 8.0 - + - +
0G C 3.0 46.4 + + - -
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Residues in contact with LEU 222 (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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170F ALA 6.0 1.1 - - - +
173F ASP* 5.3 5.4 - - + -
174F ARG* 3.5 48.5 - - + +
177F LEU* 3.6 21.5 - - + -
183F LEU* 4.2 16.4 - - + -
218F VAL* 3.1 19.5 + - + +
219F ASP* 3.8 7.4 - - - +
221F TYR* 1.3 79.0 - - - +
223F HIS* 1.3 58.7 + - - +
225F PHE* 3.4 8.6 - - + +
226F ASP* 3.0 28.1 + - - +
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Residues in contact with HIS 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F ASP 3.0 17.5 + - - +
220F ALA* 3.6 7.9 - - - +
221F TYR 3.2 0.4 - - - -
222F LEU* 1.3 74.5 - - - +
224F LEU* 1.3 63.7 + - - +
226F ASP* 3.2 5.1 + - + +
227F CYS* 2.8 53.0 + - - -
243F GLY* 3.1 32.5 + - - -
244F LEU* 5.4 0.8 - - - +
245F PRO* 5.4 1.9 - - + +
249F TYR* 4.9 9.7 + - - +
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Residues in contact with LEU 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220F ALA 3.1 16.7 + - - +
221F TYR* 3.9 3.6 - - - +
223F HIS* 1.3 81.1 - - - +
225F PHE* 1.3 57.0 + - - +
227F CYS* 3.6 5.2 - - - +
228F ARG* 3.0 29.3 + - - +
244F LEU* 3.7 28.7 - - + -
245F PRO* 4.8 0.4 - - + -
249F TYR* 3.7 26.7 - - + +
254F LEU* 3.6 33.4 - - + +
257F ARG* 3.8 20.4 - - + +
258F ARG* 3.7 20.2 - - - +
261F LEU* 4.0 9.5 - - + +
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Residues in contact with PHE 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F LEU* 3.7 35.2 - - + -
221F TYR* 3.0 22.0 + + + +
222F LEU* 3.4 13.7 - - + +
224F LEU* 1.3 78.2 - - - +
226F ASP* 1.3 60.3 + - + +
228F ARG* 3.5 8.6 + - + +
229F GLN* 3.0 45.9 + - - +
257F ARG* 5.2 6.5 - - - +
0G C 3.2 41.7 - + - -
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Residues in contact with ASP 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222F LEU 3.0 15.7 + - - +
223F HIS* 3.9 5.4 - - + +
225F PHE* 1.3 78.6 - - + +
227F CYS* 1.3 61.0 + - - +
228F ARG 3.2 0.4 - - - -
229F GLN* 3.7 13.1 - - - +
230F ARG* 2.5 71.0 + - - +
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Residues in contact with CYS 227 (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 HIS* 2.8 52.6 + - - +
224F LEU 3.6 6.3 - - - +
225F PHE 3.3 0.2 - - - -
226F ASP* 1.3 78.3 - - - +
228F ARG* 1.3 60.5 + - - +
230F ARG* 4.1 2.1 - - - +
231F PHE* 3.2 22.0 + - - +
240F LEU* 4.0 22.3 - - + +
243F GLY* 4.7 8.1 - - - -
244F LEU* 4.2 15.7 - - + -
261F LEU* 3.7 17.9 - - + -
265F PHE* 4.5 4.7 - - + -
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Residues in contact with ARG 228 (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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224F LEU 3.0 17.9 + - - +
225F PHE* 3.6 7.9 - - + +
227F CYS* 1.3 75.1 - - - +
229F GLN* 1.3 64.8 + - - +
231F PHE* 3.3 22.0 + - - +
232F ASP* 3.1 59.5 + - - +
261F LEU* 3.8 25.2 - - + +
264F GLN* 3.0 28.1 - - - +
0G C 5.5 5.6 - - + +
1G A 3.2 31.4 + - - +
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Residues in contact with GLN 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 PHE* 3.0 44.5 + - + +
226F ASP* 3.2 21.7 + - - +
228F ARG* 1.3 78.3 - - - +
230F ARG* 1.3 62.9 + - + +
232F ASP* 3.2 11.9 + - - +
233F LEU* 3.2 38.5 - - + +
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Residues in contact with ARG 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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226F ASP* 2.5 44.2 + - - +
227F CYS* 5.3 1.1 - - - +
229F GLN* 1.3 76.6 - - + +
231F PHE* 1.3 61.8 + - - +
233F LEU* 3.1 22.0 + - + +
234F GLY 3.5 0.2 + - - -
235F GLU* 3.2 56.5 + - - +
240F LEU* 3.8 16.2 - - + -
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Residues in contact with PHE 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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227F CYS 3.2 14.9 + - - +
228F ARG* 3.4 28.7 - - - +
229F GLN 3.1 0.6 - - - -
230F ARG* 1.3 73.1 - - - +
232F ASP* 1.3 77.7 + - - +
233F LEU 3.0 5.2 + - - -
234F GLY* 3.3 12.5 + - - -
235F GLU 4.8 3.9 - - - +
237F LEU* 4.1 10.8 - - + -
240F LEU* 3.6 19.0 - - + +
264F GLN* 4.2 8.7 - - + -
265F PHE* 3.4 39.5 - + + -
268F HIS* 3.6 44.0 - + + -
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Residues in contact with ASP 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 ARG* 3.1 57.2 + - - +
229F GLN* 3.2 10.0 + - - +
231F PHE* 1.3 81.9 - - - +
233F LEU* 1.3 65.5 + - + +
234F GLY 3.3 2.3 + - - -
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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