Contacts of the helix formed by residues 184 - 190 (chain F) in PDB entry 6K71
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 GLY 184 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F ILE 3.4 0.8 + - - -
183F LYS* 1.3 68.8 - - - +
185F SER* 1.3 60.1 + - - +
186F ILE 3.1 0.7 + - - -
187F LEU* 3.2 5.5 + - - +
188F GLN* 3.0 37.2 + - - +
221I LEU 5.1 1.1 - - - -
222I ARG* 2.8 26.7 + - - +
224I PHE* 3.6 26.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 185 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F GLY* 1.3 73.4 - - - +
186F ILE* 1.3 66.1 + - - +
188F GLN* 3.3 22.4 - - - +
189F LYS* 3.0 24.9 + - - +
222I ARG* 3.1 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F LEU* 3.7 21.8 - - + -
183F LYS* 3.6 26.2 - - + +
184F GLY 3.1 0.8 - - - -
185F SER* 1.3 91.0 - - - +
187F LEU* 1.3 63.7 + - - +
189F LYS* 3.1 14.2 + - + +
190F HIS* 3.2 23.9 + - + -
234F ARG* 3.4 59.9 - - + +
236F GLN* 5.5 1.1 - - - +
222I ARG* 4.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 187 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F LEU* 4.8 6.1 - - + +
182F ILE* 4.0 38.6 - - + +
183F LYS 3.4 3.4 + - - +
184F GLY 3.2 7.8 + - - +
186F ILE* 1.3 75.2 - - - +
188F GLN* 1.3 64.2 + - - +
190F HIS* 3.0 30.5 - - - +
191F PRO* 3.4 19.0 - - - +
193F ILE* 4.3 16.4 - - + -
202I VAL* 5.5 1.3 - - + -
224I PHE* 4.0 20.9 - - + -
240I VAL* 4.7 11.9 - - + -
241I ARG 5.2 2.7 - - - +
242I TYR* 3.7 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 188 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F GLY* 3.0 24.2 + - - +
185F SER* 3.3 22.4 - - - +
187F LEU* 1.3 77.6 - - - +
189F LYS* 1.3 60.5 + - - +
191F PRO* 4.5 1.6 - - - +
190I PRO* 3.4 28.9 - - + +
200I ASN* 5.9 0.2 - - - +
218I THR* 5.5 6.7 - - - +
221I LEU 5.8 2.0 + - - -
224I PHE* 5.8 2.2 - - + -
242I TYR* 3.2 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 189 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F SER 3.0 13.5 + - - +
186F ILE* 3.1 16.8 + - + +
188F GLN* 1.3 77.4 - - - +
190F HIS* 1.3 85.4 + - + +
191F PRO* 3.5 8.4 - - - +
234F ARG* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 190 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F ASP* 3.5 30.2 + - - +
166F ARG* 4.9 16.1 + - + -
168F LEU* 4.2 15.6 - - + +
186F ILE 3.2 22.7 + - - +
187F LEU* 3.0 12.3 + - - +
189F LYS* 1.3 107.2 + - + +
191F PRO* 1.3 68.5 - - - +
192F ARG 3.6 8.3 - - - +
193F ILE* 3.8 13.2 - - + +
234F ARG* 3.7 24.8 + - - -
----------------------------------------------------------
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