Contacts of the helix formed by residues 201 - 221 (chain F) in PDB entry 3KDO
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 ARG 201 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLU* 4.9 5.1 + - - +
98C GLU* 5.8 2.6 + - - +
196F SER* 2.8 37.4 + - - +
197F PRO* 3.5 11.2 - - - +
198F TRP* 3.7 30.9 + - - +
200F ASN* 1.3 73.6 - - - +
202F PHE* 1.3 66.1 + - - +
203F GLU* 4.4 4.0 - - + +
204F GLU* 3.0 42.4 + - + +
205F ARG* 3.0 20.6 + - - +
98J GLU* 4.0 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 202 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F THR 4.1 1.8 - - - +
196F SER* 2.8 27.4 + - - +
200F ASN 3.6 2.2 + - - -
201F ARG* 1.3 71.2 - - - +
203F GLU* 1.3 68.4 + - + +
205F ARG* 3.1 24.9 + - - +
206F ALA* 3.0 21.0 + - + +
226F TRP* 4.4 2.8 - + - -
228F ALA* 3.7 31.4 - - + -
229F ASN 3.4 32.3 - - - -
230F ILE* 4.1 5.4 - - + -
240F ARG* 3.6 51.1 - - + +
243F VAL* 4.1 15.7 - - + -
244F LEU* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 203 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196F SER* 4.7 0.4 + - - -
201F ARG* 3.3 4.6 - - + +
202F PHE* 1.3 85.2 - - + +
204F GLU* 1.3 58.5 + - + +
206F ALA* 3.5 5.9 + - - +
207F GLU* 3.1 35.3 + - + +
243F VAL* 4.5 18.3 - - + +
247F LEU* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F PRO* 3.7 28.6 - - + +
198F TRP 5.3 1.2 - - - +
199F TYR 5.8 0.3 - - - -
200F ASN* 4.9 0.3 - - - -
201F ARG* 3.0 39.2 + - + +
203F GLU* 1.3 77.0 - - + +
205F ARG* 1.3 65.4 + - - +
207F GLU* 3.6 6.6 + - - +
208F ILE* 3.2 31.5 + - + +
134J ARG* 5.2 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 205 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F PRO* 5.1 2.5 - - + -
173F PHE* 4.2 25.1 - - + -
190F ASP* 3.0 41.9 + - - -
194F LEU* 3.8 21.6 + - - +
195F THR 2.9 24.4 + - - -
200F ASN* 2.7 62.7 + - - +
201F ARG 3.0 10.5 + - - +
202F PHE* 3.5 26.2 - - - +
204F GLU* 1.3 73.5 - - - +
206F ALA* 1.3 59.5 + - - +
208F ILE* 3.2 8.1 + - - +
209F MET* 2.8 34.0 + - - +
226F TRP* 3.8 10.7 - - + -
229F ASN 4.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F PHE* 3.0 16.5 + - + +
203F GLU 3.7 4.7 - - - +
204F GLU 3.3 0.2 - - - -
205F ARG* 1.3 78.0 - - - +
207F GLU* 1.3 56.2 + - - +
209F MET* 3.8 0.3 - - - +
210F ALA* 2.9 33.6 + - - +
226F TRP* 3.4 23.7 - - + -
243F VAL* 3.8 15.9 - - + -
244F LEU* 4.5 2.9 - - + -
247F LEU* 3.4 21.1 - - + +
249F LEU* 4.1 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203F GLU* 3.1 20.8 + - + +
204F GLU* 3.8 7.4 - - - +
206F ALA* 1.3 76.3 - - - +
208F ILE* 1.3 63.7 + - + +
210F ALA* 3.9 3.4 - - - +
211F LYS* 3.2 23.4 + - - +
247F LEU* 3.8 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F PRO* 3.3 43.1 - - + +
171F GLU* 4.5 1.3 - - + +
173F PHE* 4.5 9.9 - - + -
174F GLU* 3.4 48.7 - - + +
204F GLU* 3.2 18.7 + - + +
205F ARG* 3.6 8.3 - - - +
206F ALA 3.2 0.2 - - - -
207F GLU* 1.3 79.5 - - + +
209F MET* 1.3 54.4 + - - +
211F LYS* 3.3 7.7 + - + +
212F ILE* 2.7 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 209 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F PHE* 3.5 33.0 - - + -
177F ALA* 3.8 15.5 - - + -
181F LEU* 3.9 21.8 - - + -
188F MET* 4.1 8.1 - - + -
205F ARG 2.8 22.6 + - - +
206F ALA 4.0 0.7 - - - +
208F ILE* 1.3 72.9 - - - +
210F ALA* 1.3 58.1 + - - +
212F ILE* 4.3 5.4 - - + -
213F ILE* 2.7 62.7 + - + +
225F THR 4.6 0.7 - - - +
226F TRP* 3.6 48.9 - - + -
249F LEU* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F ALA 2.9 17.0 + - - +
207F GLU 3.9 4.3 - - - +
209F MET* 1.3 76.1 - - - +
211F LYS* 1.3 62.2 + - - +
213F ILE* 4.0 2.1 - - - +
214F ASP* 3.3 30.5 + - - +
247F LEU* 4.2 30.7 - - + +
249F LEU* 3.8 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F GLU* 3.4 29.8 + - - +
207F GLU 3.2 16.3 + - - +
208F ILE* 3.5 6.3 - - + +
210F ALA* 1.3 77.9 - - - +
212F ILE* 1.3 74.9 + - + +
214F ASP* 3.4 7.2 + - - +
215F LYS* 3.2 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 212 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F GLU* 3.7 34.1 - - + +
177F ALA* 4.4 9.9 - - + -
178F TYR* 4.1 32.5 - - + +
181F LEU* 4.4 8.5 - - + -
208F ILE* 2.7 41.1 + - + +
209F MET* 4.1 7.4 - - + +
211F LYS* 1.3 79.8 - - + +
213F ILE* 1.3 65.6 + - - +
215F LYS* 3.2 11.6 + - - +
216F VAL* 3.0 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F LEU* 4.8 1.8 - - + -
209F MET* 2.7 46.1 + - + +
210F ALA* 4.0 3.6 - - - +
212F ILE* 1.3 73.9 - - - +
214F ASP* 1.3 67.1 + - - +
216F VAL* 4.2 2.1 - - - +
217F GLU* 3.0 40.1 + - + +
224F LYS* 3.6 28.4 - - + +
225F THR* 3.7 30.3 - - - -
226F TRP* 4.2 3.6 - - + +
249F LEU* 3.9 23.1 - - + -
250F LYS* 4.6 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 214 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210F ALA* 3.3 17.5 + - - +
211F LYS* 3.7 6.1 - - - +
212F ILE 3.2 0.6 - - - -
213F ILE* 1.3 83.7 - - - +
215F LYS* 1.3 62.1 + - - +
217F GLU* 3.8 12.1 - - - +
218F ASN* 3.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F TYR* 3.0 36.3 - - + -
211F LYS* 3.2 22.2 + - - +
212F ILE* 3.2 17.8 + - + +
214F ASP* 1.3 79.6 - - - +
216F VAL* 1.3 56.7 + - - +
218F ASN* 3.3 5.7 + - - +
219F GLU* 2.9 56.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 216 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F TYR* 3.9 19.3 - - + +
181F LEU* 3.7 30.5 - - + +
182F SER* 3.7 17.3 - - - +
212F ILE* 3.0 27.6 + - + +
213F ILE* 4.2 2.7 - - - +
215F LYS* 1.3 72.1 - - - +
217F GLU* 1.3 56.2 + - - +
219F GLU* 4.4 3.8 - - - +
220F THR* 2.6 61.2 + - + +
224F LYS* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213F ILE* 3.0 32.3 + - - +
214F ASP* 3.8 11.9 - - - +
216F VAL* 1.3 75.8 - - - +
218F ASN* 1.3 55.7 + - - +
221F GLY* 2.6 34.4 + - - -
222F GLU 3.2 23.8 - - - +
223F LYS* 3.4 23.7 + - + +
224F LYS* 3.0 19.8 + - + +
250F LYS* 2.8 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 218 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214F ASP 3.0 19.3 + - - +
215F LYS* 3.5 5.8 - - - +
217F GLU* 1.3 80.6 - - - +
219F GLU* 1.3 64.8 + - - +
220F THR 3.6 0.2 + - - -
221F GLY* 4.1 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F TYR* 2.5 34.2 + - - -
182F SER* 5.1 1.6 + - - -
215F LYS* 2.9 40.8 + - + +
216F VAL* 4.1 3.7 - - - +
218F ASN* 1.3 81.8 - - + +
220F THR* 1.3 64.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 220 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F LEU 4.9 1.3 - - - +
182F SER* 4.5 20.4 - - - +
216F VAL* 2.6 48.2 + - + +
218F ASN 4.7 0.2 - - - -
219F GLU* 1.3 80.4 - - + +
221F GLY* 1.3 56.4 + - - +
222F GLU* 3.1 39.3 + - - +
224F LYS* 4.2 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F GLU* 5.1 6.1 - - - +
217F GLU* 2.6 24.7 + - - -
218F ASN 4.1 3.6 + - - -
219F GLU 3.7 0.4 - - - -
220F THR* 1.3 72.0 - - - +
222F GLU* 1.3 61.0 + - - +
223F LYS* 4.1 4.6 + - - +
----------------------------------------------------------
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