Contacts of the helix formed by residues 187 - 204 (chain F) in PDB entry 3TKR
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 SER 187 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D GLU* 3.6 20.6 + - - -
193D ARG* 3.6 22.4 - - - +
211D GLY* 4.4 7.8 - - - +
94F PHE* 4.8 2.2 - - - -
186F ARG* 1.3 78.7 - - - +
188F VAL* 1.3 62.8 + - - +
189F ASP* 3.3 8.5 + - - +
190F GLU* 3.0 22.4 + - - +
191F THR* 2.9 27.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D ALA* 5.6 2.6 - - + +
211D GLY* 5.3 2.8 - - - +
93F ALA* 3.7 39.9 - - + -
94F PHE* 3.8 26.2 - - + +
97F ARG* 3.6 37.9 - - + +
101F PHE* 3.8 26.5 - - + -
186F ARG 4.3 0.8 + - - -
187F SER* 1.3 69.4 - - - +
189F ASP* 1.3 66.4 + - - +
191F THR* 3.3 0.9 + - - -
192F LEU* 2.9 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 189 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D LYS* 4.9 11.1 + - - -
97F ARG* 2.8 35.9 + - - +
187F SER* 3.3 7.2 + - - +
188F VAL* 1.3 78.0 - - - +
190F GLU* 1.3 62.8 + - - +
192F LEU* 3.4 5.0 + - - +
193F ARG* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D ARG* 5.3 0.5 - - - -
187D SER* 3.6 14.2 + - - -
190D GLU* 3.8 38.6 - - + +
187F SER* 3.0 20.7 + - - +
189F ASP* 1.3 76.3 - - - +
191F THR* 1.3 62.8 + - - +
193F ARG* 2.9 47.5 + - - +
194F LEU* 3.0 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F VAL* 3.9 30.7 - - + -
94F PHE* 3.5 31.6 - - + -
101F PHE* 4.1 2.9 - - + -
165F LEU* 3.7 20.4 - - + +
167F ILE* 4.5 3.6 - - + -
186F ARG* 5.6 0.5 - - - +
187F SER 2.9 20.1 + - - -
188F VAL 3.7 4.3 - - - -
190F GLU* 1.3 76.7 - - - +
192F LEU* 1.3 55.4 + - - +
194F LEU* 3.3 11.1 + - - +
195F VAL* 3.0 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F ARG* 4.4 7.9 - - - +
100F GLU* 3.7 47.8 - - + +
101F PHE* 3.6 33.8 - - + -
104F ILE* 4.0 11.2 - - + -
188F VAL* 2.9 17.8 + - + +
189F ASP* 3.6 5.4 - - - +
191F THR* 1.3 78.6 - - - +
193F ARG* 1.3 62.9 + - - +
195F VAL* 3.4 2.6 + - - +
196F GLN* 3.0 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 193 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D VAL* 5.1 4.8 - - - +
185D GLY 3.2 25.7 + - - -
186D ARG* 3.6 12.9 - - - +
187D SER* 3.6 9.9 - - - -
189F ASP 3.0 14.3 + - - +
190F GLU* 2.9 45.8 + - - +
192F LEU* 1.3 76.1 - - - +
194F LEU* 1.3 71.2 + - - +
196F GLN* 3.4 12.8 + - - +
197F ALA* 2.9 28.1 + - - +
209F PRO 4.7 0.2 + - - -
211F GLY* 3.6 7.0 - - - -
212F TRP* 2.9 56.1 + - - +
213F LYS* 4.1 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D THR* 6.0 1.1 - - + -
180D ASN* 3.7 28.5 - - - +
184D VAL* 4.0 11.9 - - + -
165F LEU* 6.1 0.7 - - + -
167F ILE* 3.6 17.7 - - + -
176F GLN* 3.8 32.5 - - + +
178F THR* 4.8 3.1 - - - +
190F GLU* 3.0 41.9 + - + +
191F THR* 3.7 2.7 - - - +
192F LEU 3.2 0.2 - - - -
193F ARG* 1.3 92.0 - - - +
195F VAL* 1.3 65.9 + - - +
197F ALA* 3.2 3.9 + - - +
198F PHE* 2.9 34.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F TYR* 4.3 7.8 - - + -
75F VAL* 3.8 28.0 - - + -
101F PHE* 4.4 5.8 - - + -
104F ILE* 3.9 15.9 - - + -
106F THR* 3.4 28.3 - - + +
167F ILE* 4.2 20.6 - - + -
191F THR 3.0 22.6 + - - +
192F LEU* 3.8 4.9 - - - +
194F LEU* 1.3 75.9 - - - +
196F GLN* 1.3 64.4 + - - +
198F PHE* 3.3 3.2 + - - +
199F GLN* 2.9 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 196 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F ILE* 4.2 21.9 - - + +
192F LEU* 3.0 43.9 + - - +
193F ARG* 3.6 12.6 - - - +
195F VAL* 1.3 75.3 - - - +
197F ALA* 1.3 58.6 + - - +
199F GLN* 3.4 10.1 + - - +
200F TYR* 2.8 30.1 + - - +
212F TRP* 3.8 11.3 - - + -
214F PRO* 3.2 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D VAL* 3.6 31.4 - - + -
193F ARG* 2.9 21.5 + - - +
194F LEU* 3.2 3.3 + - - +
196F GLN* 1.3 77.6 - - - +
198F PHE* 1.3 57.9 + - - +
200F TYR* 3.2 1.4 + - - +
201F THR* 2.9 34.1 + - - +
208F CYS* 4.1 6.7 - - + -
212F TRP* 3.5 25.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 198 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D ASN* 4.6 1.8 - - + -
181D ASP* 3.6 32.1 - - + -
183D PRO* 4.4 2.2 - - + -
184D VAL* 3.4 35.0 - - + -
73F TYR* 3.4 23.8 - - + +
167F ILE* 4.9 5.6 - - + -
175F ARG* 3.3 54.1 - - + -
176F GLN* 3.9 22.4 - - + -
194F LEU* 2.9 31.8 + - + +
195F VAL 4.0 0.2 - - - +
197F ALA* 1.3 73.4 - - - +
199F GLN* 1.3 60.7 + - - +
201F THR* 3.2 4.5 + - - -
202F ASP* 2.9 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 199 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F TYR* 3.7 33.0 - - + +
104F ILE* 2.7 44.1 + - - +
105F ASN* 4.4 6.3 + - - +
106F THR* 3.3 12.9 + - - -
195F VAL* 2.9 25.8 + - - +
196F GLN* 3.7 7.6 - - - +
198F PHE* 1.3 75.6 - - - +
200F TYR* 1.3 62.8 + - - +
202F ASP* 3.4 6.8 + - - +
203F LYS* 3.2 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196F GLN 2.8 19.4 + - - +
197F ALA* 3.5 4.3 - - - +
199F GLN* 1.3 77.3 - - - +
201F THR* 1.3 62.7 + - + +
203F LYS* 3.2 2.3 + - - +
204F HIS* 2.9 60.8 + + + +
206F GLU* 2.6 39.4 + - + -
208F CYS* 4.2 12.6 - - - -
212F TRP* 4.0 24.9 - + + -
218F THR* 3.8 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D PRO* 3.6 38.9 - - - +
184D VAL* 3.9 3.2 - - + +
175F ARG* 4.7 0.3 + - - -
197F ALA 2.9 19.8 + - - +
198F PHE* 3.2 17.0 + - - -
200F TYR* 1.3 74.1 - - + +
202F ASP* 1.3 67.0 + - - +
204F HIS 3.1 14.9 - - - +
206F GLU 3.3 25.4 - - - +
207F VAL* 3.9 0.9 - - - -
208F CYS* 3.5 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F TYR* 2.5 33.8 + - - -
169F ASP* 4.3 2.8 - - - +
170F ASP* 4.1 6.4 - - - +
175F ARG* 2.9 28.5 + - - -
198F PHE 2.9 21.1 + - - +
199F GLN* 3.5 6.5 - - - +
201F THR* 1.3 78.7 - - - +
203F LYS* 1.3 61.6 + - - +
204F HIS 4.6 0.9 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
199F GLN 3.2 14.8 + - - +
200F TYR* 3.2 4.0 + - - +
202F ASP* 1.3 84.4 - - + +
204F HIS* 1.3 88.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 204 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200F TYR* 2.9 61.1 + + + +
201F THR 3.1 18.0 - - - +
202F ASP 4.6 0.7 - - - +
203F LYS* 1.3 111.3 + - + +
205F GLY* 1.3 58.4 + - - +
206F GLU* 3.0 32.5 + - + +
----------------------------------------------------------
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