Contacts of the helix formed by residues 152 - 163 (chain A) in PDB entry 1CEZ
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 152 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 2.8 37.0 + - - +
149A ALA 4.0 1.7 + - - -
150A ARG 2.7 12.5 + - - -
151A PHE* 1.3 72.8 - - - +
153A ARG* 1.3 62.2 + - - +
155A ARG* 3.0 7.3 + - - +
156A ASP* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 2.7 51.4 + - - +
149A ALA 5.0 2.8 + - - -
151A PHE* 3.3 1.4 - - - +
152A GLY* 1.3 74.7 - - - +
154A ILE* 1.3 61.5 + - + +
156A ASP* 3.3 8.0 + - + +
157A LEU* 3.3 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 3.4 33.7 - - + +
16A LEU* 4.0 25.8 - - + -
17A ALA* 4.0 16.6 - - - +
151A PHE* 3.3 19.3 + - + +
152A GLY 3.3 0.4 - - - -
153A ARG* 1.3 74.0 - - + +
155A ARG* 1.3 59.9 + - - +
157A LEU* 4.0 6.7 - - - -
158A GLU* 3.0 24.3 + - - +
289A ASN* 3.6 39.7 - - + +
290A GLY 3.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A HIS* 3.1 42.7 - - + +
44A TYR* 3.1 29.9 + - + +
45A GLU* 3.3 34.7 + - - +
110A LYS* 6.2 0.2 - - - +
113A ALA* 4.5 1.2 - - - +
148A GLU* 2.6 43.0 + - - -
151A PHE 2.9 12.9 + - - +
152A GLY* 3.0 10.8 + - - +
154A ILE* 1.3 75.5 - - - +
156A ASP* 1.3 63.5 + - - +
158A GLU* 4.2 2.2 - - - -
159A ALA* 2.9 29.5 + - - +
290A GLY* 3.2 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LYS* 5.0 11.3 + - - +
152A GLY 3.0 11.3 + - - +
153A ARG* 3.6 11.2 - - - +
155A ARG* 1.3 82.0 - - - +
157A LEU* 1.3 65.4 + - + +
159A ALA* 3.5 4.9 + - - +
160A LYS* 2.8 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 3.7 35.4 - - + +
14A ILE* 4.6 11.2 - - + +
17A ALA* 3.6 14.9 - - + +
153A ARG* 3.3 29.6 + - + +
154A ILE* 4.1 1.6 - - - +
156A ASP* 1.3 84.0 - - - +
158A GLU* 1.3 64.3 + - - +
160A LYS* 3.1 16.0 + - + +
161A HIS* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 3.2 26.7 - - - +
20A PRO* 3.7 15.6 - - - +
21A PHE* 6.0 0.7 - - + -
37A LEU* 4.0 10.6 - - + +
41A HIS* 2.7 30.0 + - + -
154A ILE 3.0 18.6 + - - +
155A ARG 3.4 4.2 + - - +
157A LEU* 1.3 76.2 - - - +
159A ALA* 1.3 62.7 + - - +
161A HIS* 3.2 4.0 + - - +
162A PHE* 3.0 33.5 + - + +
288A ALA* 3.5 9.6 - - - +
289A ASN* 2.9 25.5 + - - +
290A GLY* 2.9 20.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A HIS* 4.1 7.0 - - - +
155A ARG* 2.9 20.0 + - - +
156A ASP* 3.8 5.8 - - - +
158A GLU* 1.3 74.1 - - - +
160A LYS* 1.3 65.3 + - + +
161A HIS 3.3 0.3 + - - -
162A PHE* 3.3 29.7 + - + -
163A LYS* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ASP* 2.8 38.7 + - - +
157A LEU* 3.1 19.1 + - + +
159A ALA* 1.3 79.1 - - + +
161A HIS* 1.3 61.5 + - - +
163A LYS* 3.5 16.0 - - - +
164A LYS* 3.8 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 4.3 4.9 - - + +
18A ALA* 3.2 33.5 - - + +
21A PHE* 3.3 28.4 - + + -
22A ASN* 3.0 31.1 + - - -
157A LEU 2.9 12.9 + - - +
158A GLU* 3.4 11.9 - - - +
159A ALA 3.1 0.2 - - - -
160A LYS* 1.3 74.6 - - - +
162A PHE* 1.3 59.1 + - - +
163A LYS 3.1 6.0 + - - -
164A LYS* 3.4 21.6 + - - +
167A GLU* 5.6 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.2 38.4 - - + -
34A ARG* 2.7 51.1 + - + -
37A LEU* 4.0 25.4 - - + -
38A ALA* 4.1 25.8 - - + -
41A HIS* 3.5 24.2 - + - -
158A GLU* 3.0 20.6 + - + +
159A ALA* 3.3 32.5 + - + -
161A HIS* 1.3 75.6 - - - +
163A LYS* 1.3 62.7 + - + +
164A LYS 3.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG* 3.9 10.3 + - - +
159A ALA 3.3 16.9 + - - +
160A LYS* 3.5 11.0 - - - +
161A HIS 3.1 0.2 - - - -
162A PHE* 1.3 86.2 - - + +
164A LYS* 1.3 59.4 + - - +
165A ASN* 3.8 3.6 + - - -
----------------------------------------------------------
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