Contacts of the helix formed by residues 166 - 180 (chain E) in PDB entry 3KZ1
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 166 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E GLU 4.3 8.6 - - - +
159E CYS* 4.0 4.0 - - - +
164E LYS 3.9 2.4 + - - -
165E ASP* 1.3 75.3 + - - +
167E VAL* 1.3 63.4 + - - +
168E ARG 3.3 3.1 - - - -
169E GLU* 3.0 42.0 + - - +
170E VAL* 3.2 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 4.0 18.8 - - + +
24E VAL* 4.5 15.0 - - + -
25E PHE* 4.4 23.1 - - + +
159E CYS* 4.0 10.3 - - + -
160E SER 3.4 29.4 - - - +
161E ALA* 4.2 6.7 - - - -
164E LYS* 3.5 28.9 - - + -
165E ASP 3.1 3.1 - - - +
166E GLY* 1.3 76.9 - - - +
168E ARG* 1.3 61.1 + - - +
170E VAL* 3.2 20.0 + - - +
171E PHE* 3.5 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 4.8 18.6 - - + -
46E ILE* 4.0 23.8 - - - +
47E GLU* 4.2 15.4 + - - +
166E GLY 3.3 0.4 - - - -
167E VAL* 1.3 76.6 - - - +
169E GLU* 1.3 74.0 + - - +
170E VAL 3.2 0.4 - - - -
171E PHE* 3.3 2.5 + - - +
172E GLU* 2.7 75.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157E MET* 4.0 27.9 - - + +
166E GLY* 3.0 32.6 + - - +
168E ARG* 1.3 89.6 - - - +
170E VAL* 1.3 58.6 + - - +
172E GLU* 3.2 19.1 + - - +
173E MET* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 4.2 15.7 - - + -
81E LEU* 3.9 24.0 - - + +
113E ILE* 5.1 2.8 - - + +
115E VAL* 3.9 19.1 - - + -
157E MET* 3.9 21.1 - - + -
159E CYS* 3.7 28.5 - - + -
166E GLY 3.5 13.7 - - - +
167E VAL 3.3 9.9 - - - +
168E ARG 3.2 0.2 - - - -
169E GLU* 1.3 79.7 - - - +
171E PHE* 1.3 64.3 + - + +
173E MET* 3.4 4.0 + - - +
174E ALA* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 171 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 4.0 8.3 - - + -
21E LEU* 4.0 21.8 - - + -
22E LEU* 4.2 18.4 - - + -
25E PHE* 3.5 57.4 - + + -
46E ILE* 4.2 4.5 - - + -
55E LEU* 3.8 19.3 - - + -
57E LEU* 4.0 20.0 - - + -
81E LEU* 3.7 28.3 - - + -
167E VAL* 3.5 15.9 - - + -
168E ARG 3.3 4.2 + - - +
169E GLU 3.2 0.2 - - - -
170E VAL* 1.3 81.2 - - + +
172E GLU* 1.3 60.9 + - - +
174E ALA* 3.7 2.4 - - + +
175E THR* 2.6 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E ILE* 4.2 6.7 - - + +
48E VAL* 4.3 15.4 - - + +
168E ARG* 2.7 60.2 + - - +
169E GLU* 3.5 22.8 - - - +
171E PHE* 1.3 77.0 - - - +
173E MET* 1.3 61.7 + - - +
175E THR* 3.8 2.1 - - - -
176E ARG* 3.0 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 173 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E ILE* 3.8 16.4 - - + -
154E PHE* 4.3 17.3 - - + +
155E GLY* 3.9 28.5 - - - -
156E TYR 4.0 13.7 - - - +
157E MET* 3.7 29.6 - - + -
169E GLU 2.9 16.7 + - - +
170E VAL* 3.6 5.6 - - - +
172E GLU* 1.3 74.9 - - - +
174E ALA* 1.3 66.0 + - - +
176E ARG* 3.3 10.2 + - + +
177E ALA* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 4.0 26.0 - - + -
79E VAL* 3.6 17.2 - - + +
81E LEU* 4.1 15.3 - - + -
113E ILE* 4.3 5.8 - - - +
170E VAL 2.9 17.4 + - - +
171E PHE* 3.7 9.0 - - + +
172E GLU 3.3 0.2 - - - -
173E MET* 1.3 76.6 - - - +
175E THR* 1.3 58.4 + - - +
177E ALA* 3.1 6.6 + - - +
178E ALA* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 175 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E ILE* 3.7 16.0 - - + +
48E VAL* 3.6 20.0 - - + -
53E VAL* 3.6 40.4 - - + -
55E LEU* 3.8 13.2 - - + +
171E PHE 2.6 22.4 + - - -
172E GLU* 3.8 3.6 - - - -
174E ALA* 1.3 73.1 - - - +
176E ARG* 1.3 57.8 + - - +
178E ALA* 4.1 6.5 - - + -
179E LEU* 2.7 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E VAL* 3.4 21.8 - - + +
49E ASP* 2.4 58.7 + - - +
154E PHE* 4.6 12.3 - - + -
172E GLU* 3.0 47.1 + - - +
173E MET* 3.5 8.7 - - + +
175E THR* 1.3 76.5 - - - +
177E ALA* 1.3 61.9 + - - +
179E LEU* 3.5 6.3 + - - +
180E GLN* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E VAL* 4.1 2.2 - - + -
111E PRO* 3.9 26.5 - - + +
113E ILE* 3.8 22.0 - - + -
154E PHE* 3.8 23.5 - - + -
173E MET 2.9 13.3 + - - +
174E ALA 3.2 9.4 - - - +
176E ARG* 1.3 76.7 - - - +
178E ALA* 1.3 63.2 + - - +
180E GLN* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LYS* 3.6 44.0 + - + +
55E LEU* 6.4 0.4 - - + -
78E ASP* 4.2 18.8 - - + +
79E VAL* 4.0 18.6 - - + -
174E ALA 2.9 16.2 + - - +
175E THR* 3.0 8.0 + - - +
177E ALA* 1.3 74.4 - - - +
179E LEU* 1.3 65.3 + - - +
180E GLN 3.6 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E ILE* 4.7 11.7 - - + -
6E LYS* 4.1 24.8 + - + +
48E VAL* 4.2 19.7 - - + +
49E ASP* 5.8 2.7 - - + +
51E LYS* 4.0 30.7 - - + -
53E VAL* 3.9 19.7 - - + -
175E THR* 2.7 26.0 + - + +
176E ARG* 3.9 4.7 - - - +
178E ALA* 1.3 73.8 - - - +
180E GLN* 1.3 65.4 + - - +
181E ALA* 3.1 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 180 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E PRO* 5.2 6.2 - - - +
154E PHE* 3.1 37.7 - - - -
176E ARG 3.1 13.4 + - - +
177E ALA 3.3 17.0 + - - +
178E ALA 4.1 4.0 - - - +
179E LEU* 1.3 74.9 - - - +
181E ALA* 1.3 72.2 + - - +
----------------------------------------------------------
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