Contacts of the helix formed by residues 170 - 181 (chain A) in PDB entry 1KKU
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 170 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 4.8 10.1 + - - -
168A LEU 5.6 0.7 - - - +
169A TRP* 1.3 74.6 - - - +
171A SER* 1.3 67.3 + - - +
172A GLU* 3.0 5.6 - - + +
173A ASP* 2.7 46.9 + - + +
174A ILE* 3.1 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TRP 3.6 4.0 + - - -
170A LYS* 1.3 71.5 - - - +
172A GLU* 1.3 62.0 + - - +
174A ILE* 3.4 14.9 + - - +
175A THR* 2.7 37.9 + - - -
202A VAL* 4.3 17.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LYS* 2.8 5.7 + - + -
171A SER* 1.3 83.1 - - - +
173A ASP* 1.3 58.6 + - - +
175A THR* 3.2 8.8 + - - -
176A GLN* 2.7 45.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 4.0 16.6 - - - +
96A LEU* 3.8 19.6 - - + +
169A TRP* 4.7 15.2 - - + -
170A LYS* 2.7 39.1 + - + +
172A GLU* 1.3 75.9 - - - +
174A ILE* 1.3 66.5 + - - +
175A THR 3.0 1.2 + - - -
176A GLN* 3.1 17.8 + - - +
177A ILE* 3.1 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A PHE* 3.4 56.4 - - + +
169A TRP* 3.7 22.9 - - + +
170A LYS 3.1 6.8 + - - +
171A SER* 3.5 14.1 - - - +
173A ASP* 1.3 76.3 - - - +
175A THR* 1.3 63.5 + - - +
177A ILE* 3.5 8.1 + - - +
178A VAL* 3.0 21.5 + - - +
202A VAL* 3.7 24.5 - - + -
203A LEU* 4.1 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A SER* 2.7 21.8 + - - -
172A GLU* 3.4 13.8 - - - -
173A ASP 3.0 0.6 - - - -
174A ILE* 1.3 77.9 - - - +
176A GLN* 1.3 62.7 + - + +
178A VAL* 3.8 2.0 - - - +
179A ALA* 2.8 37.5 + - + +
202A VAL* 3.4 18.8 - - + +
206A HIS* 3.8 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.7 25.4 - - + +
172A GLU* 2.7 39.1 + - - +
173A ASP* 3.1 19.0 + - - +
175A THR* 1.3 80.5 - - + +
177A ILE* 1.3 55.3 + - - +
179A ALA* 4.9 0.4 - - - -
180A ASN* 2.7 59.0 + - - +
181A TYR* 3.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 4.9 6.1 - - + -
96A LEU* 4.0 29.4 - - + +
99A LEU* 4.1 21.1 - - + -
153A LEU* 4.5 7.0 - - + -
163A PHE* 4.4 15.9 - - + -
169A TRP* 4.2 26.0 - - + -
173A ASP* 3.1 17.8 + - + +
174A ILE* 3.8 2.9 - - - +
176A GLN* 1.3 75.8 - - - +
178A VAL* 1.3 70.0 + - - +
181A TYR* 3.2 23.2 + - + +
182A GLY 3.2 8.6 + - - +
183A LEU* 3.9 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A PHE* 6.1 0.6 - - + -
174A ILE* 3.0 15.0 + - + +
175A THR* 3.8 1.6 - - - +
177A ILE* 1.3 86.8 - - - +
179A ALA* 1.3 70.0 + - + +
182A GLY* 3.3 8.7 + - - +
183A LEU* 4.9 9.2 - - + -
202A VAL* 5.4 1.1 - - + +
203A LEU* 4.4 15.0 - - + -
206A HIS* 3.0 38.4 - - + +
209A ASN* 2.6 29.5 + - - +
210A ILE* 4.1 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A THR* 2.8 21.0 + - + +
176A GLN* 4.9 0.7 - - - -
178A VAL* 1.3 93.4 - - + +
180A ASN* 1.3 66.2 + - - +
181A TYR 3.5 0.2 - - - -
206A HIS* 3.6 26.2 - - + +
209A ASN* 3.5 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLN* 5.6 0.7 - - - +
150A LYS* 5.1 11.3 + - - +
176A GLN* 2.7 48.9 + - - +
179A ALA* 1.3 79.8 - - - +
181A TYR* 1.3 80.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.9 21.5 - - + +
99A LEU* 3.9 40.4 - - + -
100A ARG* 3.6 25.2 - - - +
103A GLN* 3.9 21.5 - - + +
150A LYS* 5.1 3.9 - - - +
151A VAL* 3.2 35.9 - - + +
152A LYS* 2.9 26.1 - - - -
176A GLN 3.7 7.2 - - - -
177A ILE* 3.2 12.5 + - + +
180A ASN* 1.3 101.6 + - + +
182A GLY* 1.3 64.7 + - - +
209A ASN* 3.9 6.2 + - - -
----------------------------------------------------------
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