Contacts of the helix formed by residues 158 - 171 (chain A) in PDB entry 4ZCU
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 ASP 158 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LYS 5.8 1.1 - - - -
91A MET* 4.4 3.5 - - - +
94A ALA* 5.3 2.9 - - - -
156A VAL 3.7 0.6 - - - -
157A THR* 1.3 88.3 + - - +
159A ILE* 1.3 59.7 + - - +
160A GLU* 3.0 26.3 - - - +
161A GLU* 3.1 24.1 + - - +
162A ILE* 2.9 35.0 + - - +
116C GLN 5.3 0.9 - - - +
117C THR 3.7 12.8 - - - +
118C LEU 3.3 10.7 - - - +
119C GLY* 3.3 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ALA* 5.0 11.1 - - + +
97A SER* 5.2 7.2 - - - +
98A LEU* 4.0 33.4 - - + -
114A SER* 6.0 1.6 - - - -
115A LEU* 5.3 2.5 - - + -
118A LEU* 4.0 22.4 - - + -
158A ASP* 1.3 75.6 - - - +
160A GLU* 1.3 60.5 + - - +
162A ILE* 3.4 23.9 + - + +
163A ILE* 2.9 43.2 + - + +
166A TRP* 4.7 4.3 - - + -
117C THR* 3.5 21.5 + - - +
118C LEU* 3.7 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 5.4 2.9 - - + -
158A ASP* 3.0 28.3 - - - +
159A ILE* 1.3 78.3 - - + +
161A GLU* 1.3 58.6 + - + +
163A ILE* 3.1 12.2 + - - +
164A ARG* 2.9 40.1 + - - +
118C LEU* 3.0 54.5 - - + +
160C GLU* 4.8 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 3.0 28.5 + - - -
156A VAL* 3.4 20.6 - - + +
157A THR* 2.8 36.1 + - - +
158A ASP* 3.1 19.0 + - - +
160A GLU* 1.3 73.8 - - + +
162A ILE* 1.3 61.8 + - - +
164A ARG* 3.3 27.6 + - - +
165A PHE* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 4.2 14.6 - - - -
94A ALA* 4.0 17.7 - - + -
147A TRP* 3.8 25.4 - - + -
151A PHE* 3.9 12.3 - - + -
156A VAL* 3.7 24.5 - - + -
158A ASP 2.9 20.5 + - - +
159A ILE* 3.5 15.0 - - + +
161A GLU* 1.3 77.2 - - - +
163A ILE* 1.3 56.7 + - - +
165A PHE* 3.4 4.1 + - - +
166A TRP* 2.9 64.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.9 27.4 - - + -
118A LEU* 3.7 31.2 - - + -
120A LEU* 3.9 20.0 - - + -
159A ILE* 2.9 24.1 + - + +
160A GLU* 3.1 10.0 + - + +
162A ILE* 1.3 74.6 - - - +
164A ARG* 1.3 60.0 + - - +
166A TRP* 3.2 15.7 + - + +
167A LYS* 2.9 26.0 + - - +
174A ILE* 3.8 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 2.9 24.2 + - - +
161A GLU* 3.3 32.7 + - - +
163A ILE* 1.3 77.8 - - - +
165A PHE* 1.3 62.5 + - - +
167A LYS* 3.0 12.6 + - + +
168A HIS* 3.0 43.7 + - + +
174A ILE 5.1 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TYR* 3.6 36.1 - + - -
151A PHE* 4.3 7.9 - + - -
154A ASN* 3.3 32.8 - - - -
156A VAL* 4.0 11.4 - - + -
161A GLU 2.9 18.0 + - - +
162A ILE 3.6 3.4 - - - +
164A ARG* 1.3 73.5 - - - +
166A TRP* 1.3 75.1 + + - +
168A HIS* 3.2 5.0 + - + +
169A SER* 2.9 41.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.1 23.6 - - + -
111A ILE* 4.3 12.1 - - + -
115A LEU* 4.4 20.4 - - + -
130A ILE* 3.4 42.8 - - + +
133A SER* 4.9 7.0 - - - -
134A ILE* 3.7 29.3 - - + +
147A TRP* 4.0 8.3 - + - -
150A TYR* 5.5 0.4 - + - -
151A PHE* 3.9 9.8 - + - -
159A ILE* 4.7 3.8 - - + -
162A ILE* 2.9 39.1 + - + -
163A ILE* 3.4 21.1 - - + +
165A PHE* 1.3 90.7 - + - +
167A LYS* 1.3 58.3 + - - +
169A SER* 4.3 4.5 - - - -
170A THR* 2.8 38.6 + - + +
174A ILE* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE 2.9 14.4 + - - +
164A ARG* 3.0 14.3 + - + +
166A TRP* 1.3 76.3 - - - +
168A HIS* 1.3 85.8 + - + +
171A GLY* 3.1 24.2 + - - -
172A ILE 3.4 20.9 - - - +
173A ASP* 2.9 30.2 + - - +
174A ILE* 3.6 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ARG* 3.0 30.9 + - + +
165A PHE* 3.2 6.4 + - + +
167A LYS* 1.3 107.9 + - + +
169A SER* 1.3 60.9 + - - +
171A GLY* 4.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER* 4.7 7.3 - - - -
150A TYR* 4.2 12.3 + - - -
165A PHE* 2.9 39.3 + - - -
166A TRP* 3.9 6.0 - - - -
168A HIS* 1.3 80.9 - - - +
170A THR* 1.3 67.6 + - - +
171A GLY 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 4.6 14.7 - - + +
130A ILE* 4.3 23.0 - - + +
133A SER* 4.0 27.4 - - - +
166A TRP* 2.8 26.0 + - + +
169A SER* 1.3 81.8 - - - +
171A GLY* 1.3 59.5 + - - +
172A ILE* 3.2 34.5 + - - +
174A ILE* 5.5 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LYS* 3.1 14.8 + - - +
168A HIS 4.4 1.5 - - - -
169A SER 3.5 1.6 - - - -
170A THR* 1.3 76.1 - - - +
172A ILE* 1.3 64.2 + - - +
173A ASP* 3.6 3.1 + - - +
----------------------------------------------------------
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