Contacts of the helix formed by residues 201 - 213 (chain F) in PDB entry 3HYW
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 ALA 201 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ASP* 4.0 27.1 - - - +
211B ALA* 4.0 13.8 - - + +
212B GLU* 4.6 11.4 - - + +
199F ILE 3.4 0.6 + - - -
200F GLY* 1.3 68.2 - - - -
202F SER* 1.3 62.5 + - - +
203F LYS* 3.3 3.5 + - - +
204F ARG* 3.5 10.3 + - + +
205F LEU* 3.1 22.5 + - - +
372F THR* 4.3 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192F GLY* 2.6 28.4 + - - -
194F PHE* 3.9 7.8 - - - -
198F GLY* 3.5 2.1 - - - -
199F ILE 3.0 31.4 + - - -
200F GLY 3.1 2.4 + - - -
201F ALA* 1.3 74.4 - - - +
203F LYS* 1.3 60.6 + - - +
205F LEU* 4.0 7.6 - - - -
206F VAL* 2.9 35.5 + - - +
358F PHE* 3.7 23.8 - - - -
372F THR* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 203 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F TYR* 3.6 42.2 - - + -
191F LEU 3.2 23.6 - - - +
198F GLY* 5.7 0.2 - - - -
200F GLY 4.9 0.4 + - - -
201F ALA* 3.3 1.7 - - - +
202F SER* 1.3 82.0 + - - +
204F ARG* 1.3 57.4 + - - +
206F VAL* 3.9 1.0 - - - +
207F GLU* 2.9 63.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 204 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ARG* 3.1 47.9 + - - +
207B GLU* 2.9 38.8 + - - +
208B ASP* 2.6 36.9 + - - -
204D ARG* 3.4 31.3 - - - +
201F ALA* 3.5 14.1 + - + +
202F SER 3.4 0.2 - - - -
203F LYS* 1.3 78.4 - - - +
205F LEU* 1.3 54.6 + - - +
207F GLU* 3.7 8.6 - - - +
208F ASP* 2.8 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F ALA 3.1 17.2 + - - +
202F SER* 3.5 6.3 - - - +
204F ARG* 1.3 76.5 - - - +
206F VAL* 1.3 68.7 + - + +
208F ASP* 3.6 7.3 - - - +
209F LEU* 2.9 36.0 + - + +
351F PHE* 5.3 3.6 - - + -
356F GLY* 5.6 1.6 - - - -
358F PHE* 4.3 25.8 - - + -
372F THR* 4.3 22.2 - - - +
373F LYS* 4.6 16.6 - - - +
374F MET* 4.4 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F TYR* 3.6 33.4 - - + -
165F LEU* 5.9 0.4 - - + -
191F LEU* 4.1 15.7 - - + -
192F GLY* 4.1 14.8 - - - +
194F PHE* 4.2 13.7 - - + -
202F SER 2.9 24.6 + - - +
203F LYS 4.1 1.6 - - - +
205F LEU* 1.3 80.1 - - + +
207F GLU* 1.3 60.8 + - - +
209F LEU* 3.1 9.6 + - + +
210F PHE* 2.8 42.7 + - + +
351F PHE* 6.2 2.2 - - + -
358F PHE* 4.9 4.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
204D ARG* 3.4 25.8 + - - +
190F TYR* 5.3 0.5 - - - +
191F LEU* 3.9 26.8 + - + +
203F LYS* 2.9 54.7 + - - +
204F ARG* 3.7 7.6 - - - +
206F VAL* 1.3 76.4 - - - +
208F ASP* 1.3 56.3 + - - +
210F PHE* 3.4 2.4 + - - +
211F ALA* 2.9 30.9 + - - +
217F TRP* 3.8 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 208 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D ALA* 4.3 11.4 - - - +
204D ARG* 2.5 37.7 + - - -
204F ARG* 2.8 34.5 + - - +
205F LEU* 3.6 7.6 + - - +
207F GLU* 1.3 71.6 - - - +
209F LEU* 1.3 58.1 + - - +
211F ALA* 3.3 6.8 + - - +
212F GLU* 2.9 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F LEU* 4.1 15.5 - - + -
205F LEU* 2.9 23.3 + - + +
206F VAL* 3.5 9.9 - - + +
208F ASP* 1.3 77.2 - - - +
210F PHE* 1.3 59.2 + - + +
212F GLU* 3.5 9.5 + - - +
213F ARG* 3.0 73.2 + - - +
351F PHE* 3.3 38.8 - - + -
374F MET* 3.6 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 210 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F TYR* 3.6 22.4 - + - -
164F ALA* 4.8 3.6 - - + -
165F LEU* 3.7 29.2 - - + -
184F PHE* 3.5 41.3 - + + -
191F LEU* 3.7 21.1 - - + -
206F VAL* 2.8 29.3 + - + +
207F GLU 3.9 3.4 - - - +
209F LEU* 1.3 72.9 - - + +
211F ALA* 1.3 60.7 + - - +
213F ARG* 4.9 0.9 - - - -
214F ASN* 2.9 25.6 + - - -
215F ILE* 2.9 51.3 + - + +
217F TRP* 3.9 16.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D GLY* 3.6 35.7 + - - +
201D ALA* 4.5 3.6 - - + +
370D VAL* 4.6 1.7 - - - +
207F GLU 2.9 18.8 + - - +
208F ASP* 3.5 7.9 - - - +
210F PHE* 1.3 77.2 - - - +
212F GLU* 1.3 63.0 + - - +
213F ARG 3.3 0.7 + - - -
214F ASN* 3.4 11.1 + - - +
217F TRP* 5.6 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 212 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D GLY* 4.2 13.5 - - - -
201D ALA* 4.3 16.9 - - - +
369D ARG* 5.6 0.7 - - - -
370D VAL* 3.3 26.2 + - + +
208F ASP* 2.9 35.3 + - - +
209F LEU* 3.8 14.2 - - - +
211F ALA* 1.3 76.4 - - - +
213F ARG* 1.3 64.2 - - + +
214F ASN* 3.9 0.7 + - - +
374F MET* 5.3 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 213 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D ARG 5.0 0.6 - - - +
165F LEU* 3.7 21.6 + - - +
168F HIS* 3.3 38.2 + - + +
177F ARG* 2.9 24.6 + - - -
209F LEU* 3.0 41.2 + - - +
210F PHE 4.4 1.1 - - - +
211F ALA 3.2 0.2 - - - -
212F GLU* 1.3 83.6 - - + +
214F ASN* 1.3 62.3 + - - +
215F ILE* 3.3 12.2 + - + +
351F PHE* 3.9 18.4 + - - +
354F ASP* 2.9 40.6 + - - -
374F MET* 4.8 4.9 - - - +
----------------------------------------------------------
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