Contacts of the helix formed by residues 217 - 234 (chain F) in PDB entry 3E8C
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 LYS 217 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F HIS* 3.4 41.3 - - + +
161F ASP* 3.1 37.6 + - - +
162F LEU 3.6 15.9 - - - +
163F ILE* 3.4 27.4 - - + +
191F VAL* 2.6 30.5 + - - +
193F GLY 5.5 0.8 + - - -
216F ASN* 1.3 79.8 - - + +
218F ALA* 1.3 61.2 + - - +
219F VAL 3.1 0.2 - - - -
220F ASP* 3.0 25.2 + - - +
221F TRP* 3.9 2.9 + - + +
283F ASN* 5.5 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 218 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216F ASN* 3.1 11.5 + - - +
217F LYS* 1.3 77.4 - - - +
219F VAL* 1.3 59.7 + - - +
221F TRP* 3.2 14.1 + - - +
222F TRP 3.1 17.8 + - - -
277F LEU* 3.0 35.7 - - + -
280F ARG* 3.2 14.2 + - - +
283F ASN* 3.6 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F ILE* 4.0 14.6 - - + -
165F ARG* 4.6 6.3 - - + -
204F TYR 4.9 1.4 - - - +
206F ALA* 3.8 23.4 + - + +
208F GLU* 3.0 22.9 - - - +
209F ILE* 4.1 15.0 - - + -
215F TYR* 3.6 38.1 - - + -
216F ASN 3.3 16.2 - - - +
217F LYS 3.1 0.4 + - - -
218F ALA* 1.3 74.4 - - - +
220F ASP* 1.3 69.2 + - - +
222F TRP* 3.7 3.1 + - - +
223F ALA* 3.2 21.7 + - - +
280F ARG* 4.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 220 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F PHE* 3.2 30.4 - - + -
158F HIS* 2.8 29.0 + - + +
163F ILE* 3.5 12.1 - - - +
164F TYR* 3.0 29.0 + - - +
165F ARG* 3.0 27.1 + - - -
167F LEU* 6.1 0.3 - - - +
217F LYS 3.0 9.2 + - - +
219F VAL* 1.3 80.0 - - - +
221F TRP* 1.3 58.1 + - - +
223F ALA* 3.4 6.8 + - - +
224F LEU 3.0 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 221 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F VAL* 3.8 20.2 - - + -
154F PHE* 3.5 30.3 - + + -
155F GLU* 4.2 5.6 - - - -
158F HIS* 3.5 33.8 + + - -
217F LYS* 4.1 7.1 - - + +
218F ALA* 3.2 14.8 + - - +
220F ASP* 1.3 73.8 - - - +
222F TRP* 1.3 66.0 + - - +
224F LEU* 3.4 26.3 + - + +
225F GLY 3.3 15.1 + - - -
272F LEU* 3.9 15.0 - - + +
280F ARG* 4.6 2.7 - - - -
281F PHE 3.6 18.2 - - - +
282F GLY* 3.5 32.0 + - - -
283F ASN* 4.5 0.9 - - - -
288F VAL* 3.9 26.5 - - + -
291F ILE* 3.4 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 222 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F GLU 5.2 0.8 + - - -
204F TYR 3.7 12.2 + - - -
205F LEU 3.4 12.5 + - - -
206F ALA* 3.6 16.4 - - + -
207F PRO* 3.7 22.0 - - + -
218F ALA 3.1 6.3 + - - -
219F VAL 3.7 7.0 - - - +
220F ASP 3.4 0.2 - - - -
221F TRP* 1.3 75.9 - - - +
223F ALA* 1.3 62.9 + - - +
225F GLY* 3.0 13.3 + - - -
226F VAL* 3.2 23.4 + - + +
238F PHE* 3.7 24.8 - + - -
250F ILE* 3.7 30.7 - - + +
272F LEU 3.6 10.3 - - - -
273F LEU* 3.4 47.9 - - + +
274F GLN 3.7 9.4 - - - -
275F VAL* 3.8 6.1 - - + -
280F ARG* 3.5 38.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F LEU* 3.4 30.2 - - + +
204F TYR* 3.7 22.7 - - + +
219F VAL 3.2 12.4 + - - +
220F ASP* 3.5 11.2 - - - +
221F TRP 3.3 0.2 - - - -
222F TRP* 1.3 81.4 - - - +
224F LEU* 1.3 60.7 + - - +
226F VAL* 3.2 7.6 + - - +
227F LEU* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F ALA* 4.4 7.0 - - - +
150F ILE* 3.5 34.8 - - + -
151F VAL* 3.5 26.7 - - + -
154F PHE* 4.5 1.6 - - + -
167F LEU* 3.3 10.9 - - + +
220F ASP 3.0 13.8 + - - +
221F TRP* 3.4 31.6 - - + +
222F TRP 3.2 0.2 - - - -
223F ALA* 1.3 77.2 - - - +
225F GLY* 1.3 56.0 + - - +
227F LEU* 3.2 5.6 + - + +
228F ILE* 2.8 55.9 + - + +
272F LEU* 4.3 13.0 - - + -
291F ILE* 4.4 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 225 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F TRP 3.3 4.0 + - - -
222F TRP 3.0 9.3 + - - -
224F LEU* 1.3 79.3 - - - +
226F VAL* 1.3 56.0 + - - +
228F ILE* 3.9 4.2 - - - +
229F TYR* 3.0 30.1 + - - +
269F LEU* 3.9 7.6 - - - +
272F LEU* 3.8 27.0 - - - +
273F LEU* 3.9 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F GLU 3.5 21.8 - - - +
204F TYR* 3.3 31.2 - - + -
222F TRP* 3.2 26.7 + - + +
223F ALA* 3.2 8.4 + - - +
225F GLY* 1.3 74.4 - - - +
227F LEU* 1.3 58.8 + - - +
229F TYR* 3.5 2.8 + - - +
230F GLU* 3.0 27.4 + - - +
236F PRO* 4.5 3.4 - - + -
237F PRO* 3.6 27.0 - - + +
238F PHE* 4.6 2.2 - - + -
273F LEU* 3.6 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F MET* 4.5 0.9 - - - -
146F TYR* 6.5 0.2 - - + -
147F ALA* 6.1 0.2 - - - -
150F ILE* 4.1 12.1 - - + -
167F LEU* 3.6 27.1 - - + -
168F LYS* 4.2 2.0 - - - -
169F PRO* 3.7 40.2 - - + -
172F LEU* 3.5 28.3 - - + -
204F TYR* 3.5 9.6 - - + +
223F ALA 2.9 16.1 + - - +
224F LEU* 3.2 8.9 + - + +
226F VAL* 1.3 74.7 - - - +
228F ILE* 1.3 59.6 + - - +
230F GLU* 3.3 1.0 + - - +
231F MET* 2.9 55.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 228 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F ALA* 4.8 1.3 - - + +
147F ALA* 3.8 28.5 - - + -
224F LEU* 2.8 44.6 + - + +
225F GLY 3.9 3.4 - - - +
227F LEU* 1.3 71.3 - - - +
229F TYR* 1.3 62.7 + - - +
231F MET* 3.6 12.4 + - + +
232F ALA* 3.2 24.0 + - + +
265F LEU* 3.5 16.6 - - + -
268F LEU* 4.1 13.5 - - + -
269F LEU* 3.4 22.2 - - + -
272F LEU* 4.1 16.2 - - + -
296F TRP* 3.9 12.3 - - + -
297F PHE* 4.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 229 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225F GLY 3.0 19.4 + - - +
226F VAL 3.6 3.8 - - - +
228F ILE* 1.3 76.7 - - - +
230F GLU* 1.3 51.1 + - - +
232F ALA 3.3 0.7 + - - -
233F ALA* 2.7 48.9 + - + +
235F TYR* 3.3 34.1 + + - -
236F PRO 3.7 2.2 - - - -
237F PRO* 3.4 43.5 + - + +
255F VAL* 4.0 3.1 - - + -
256F ARG 2.4 33.1 + - - -
257F PHE* 3.5 20.6 - + - -
258F PRO* 3.6 15.9 - - + +
261F PHE* 3.6 6.3 - + - -
269F LEU* 3.5 25.4 - - + -
273F LEU* 4.7 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F LEU* 3.8 7.1 - - + +
133F ARG* 2.7 30.5 + - - +
169F PRO* 3.5 12.2 - - + +
204F TYR* 2.7 28.1 + - - +
226F VAL 3.0 16.5 + - - +
227F LEU 3.9 2.2 - - - +
229F TYR* 1.3 76.2 - - - +
231F MET* 1.3 56.9 + - - +
234F GLY* 2.8 28.2 + - - -
235F TYR 3.3 23.8 - - - +
236F PRO* 3.6 11.7 - - + +
19L ARG* 3.0 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 231 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F MET* 3.8 30.1 - - - +
132F LEU* 3.7 13.9 - - + +
137F ARG* 3.7 0.7 - - - -
138F PHE* 2.8 47.0 + - + +
143F ALA* 3.2 34.5 - - + +
146F TYR* 3.8 23.6 - - + -
147F ALA* 4.1 14.4 - - + +
227F LEU* 2.9 39.0 + - + +
228F ILE* 3.8 15.3 - - + +
230F GLU* 1.3 77.6 - - - +
232F ALA* 1.3 55.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F ARG* 3.6 11.1 + - - +
138F PHE 3.6 13.4 - - - +
140F GLU* 4.7 7.9 - - + -
143F ALA* 4.5 10.3 - - + -
228F ILE* 3.2 16.5 + - + +
231F MET* 1.3 79.5 - - - +
233F ALA* 1.3 59.5 + - - +
260F HIS* 3.3 18.1 - - + -
261F PHE* 3.6 20.9 - - + -
265F LEU* 3.8 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F ARG* 3.7 13.7 - - - +
229F TYR* 2.7 30.5 + - + +
232F ALA* 1.3 74.3 - - - +
234F GLY* 1.3 56.2 + - - +
235F TYR* 3.3 35.8 - - + +
258F PRO* 3.7 24.9 - - + -
260F HIS* 4.3 6.3 + - - -
261F PHE* 3.8 5.4 - - + -
7L TYR* 4.6 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 234 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F LEU* 4.7 2.2 - - - -
133F ARG* 3.5 19.5 + - - -
136F GLY 3.1 27.9 - - - +
137F ARG* 3.6 5.3 - - - +
230F GLU 2.8 20.5 + - - -
233F ALA* 1.3 72.7 - - - +
235F TYR* 1.3 61.6 + - - +
7L TYR* 4.5 7.2 - - - -
10L PHE* 3.6 10.6 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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