Contacts of the helix formed by residues 155 - 168 (chain A) in PDB entry 1OKC
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 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 3.9 13.1 - - - +
153A PHE 3.5 2.0 - - - -
154A THR* 1.3 83.9 + - - +
156A LEU* 1.3 60.3 + - - -
157A GLY 3.4 0.2 - - - -
158A ASN* 3.3 2.1 + - - +
159A CYS* 2.9 31.4 + - - +
800A CDL 3.8 14.1 - - - -
980A PC1 3.1 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 3.7 32.8 - - + -
75A ALA* 4.1 21.1 - - + +
78A ILE* 4.0 14.6 - - + -
133A LEU* 4.3 16.4 - - + -
136A ALA* 3.5 28.3 - - + -
140A LEU* 3.7 14.8 - - + +
155A GLY* 1.3 72.2 - - - +
157A GLY* 1.3 63.9 + - - +
159A CYS* 3.6 1.5 - - - +
160A ILE* 3.1 37.0 + - + +
800A CDL 3.8 5.0 - - - -
980A PC1 2.8 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 1.3 80.2 - - - +
158A ASN* 1.3 56.7 + - - +
160A ILE* 3.4 4.9 + - - +
161A THR* 2.9 41.1 + - - +
980A PC1 3.0 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLU 4.4 2.0 + - - -
153A PHE* 3.2 17.6 - - - +
154A THR* 2.9 46.9 + - - +
155A GLY 3.3 6.0 + - - +
156A LEU 3.3 0.2 - - - -
157A GLY* 1.3 72.0 - - - +
159A CYS* 1.3 58.8 - - - +
161A THR* 3.0 7.2 + - - -
162A LYS* 2.8 45.3 + - - +
980A PC1 3.6 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE* 4.0 11.7 - - - -
136A ALA* 3.7 32.1 - - + -
139A ARG* 3.8 21.3 - - - -
140A LEU* 4.5 4.7 - - + -
153A PHE* 3.4 31.4 - - + -
155A GLY 2.9 18.8 + - - +
156A LEU 3.6 4.7 - - - +
158A ASN* 1.3 75.6 - - - +
160A ILE* 1.3 63.8 + - - +
162A LYS* 3.8 0.7 - - - +
163A ILE* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PRO* 4.2 25.4 - - + +
133A LEU* 4.6 9.2 - - + -
136A ALA* 4.1 12.6 - - + -
156A LEU* 3.1 34.3 + - + +
157A GLY* 3.8 4.5 - - - +
159A CYS* 1.3 79.6 - - - +
161A THR* 1.3 64.3 + - + +
164A PHE* 3.0 28.4 + - + +
172A LEU* 3.6 31.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLY* 2.9 25.3 + - - +
158A ASN* 3.0 12.3 + - - -
160A ILE* 1.3 78.7 - - + +
162A LYS* 1.3 73.0 + - - +
164A PHE* 3.2 7.3 + - - +
165A LYS* 2.9 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLU* 2.8 35.2 + - - +
153A PHE* 3.8 21.0 - - + -
158A ASN* 2.8 34.0 + - - +
159A CYS 3.8 1.8 - - - +
161A THR* 1.3 75.4 + - - +
163A ILE* 1.3 64.7 + - + +
165A LYS* 3.4 9.1 + - - +
166A SER* 3.3 21.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
135A PHE* 3.5 29.4 - - + -
139A ARG* 4.3 0.9 - - - +
153A PHE* 3.8 26.9 - - + -
159A CYS 2.9 20.1 + - - +
162A LYS* 1.3 74.6 - - + +
164A PHE* 1.3 67.9 + - - +
166A SER* 3.2 4.3 + - - +
167A ASP* 2.8 26.1 + - + +
171A GLY* 3.8 18.8 - - - -
172A LEU* 3.7 21.1 - - + +
241A SER* 4.0 29.4 - - - +
242A GLY* 4.1 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ILE* 3.0 22.0 + - + +
161A THR* 3.2 8.5 + - - +
163A ILE* 1.3 78.4 - - - +
165A LYS* 1.3 66.4 + - + +
168A GLY* 2.6 52.3 + - - -
169A LEU* 3.7 30.5 - - + -
172A LEU* 4.5 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR* 2.9 29.0 + - - +
162A LYS* 3.7 7.4 - - - +
163A ILE 3.2 0.2 - - - -
164A PHE* 1.3 85.5 - - + +
166A SER* 1.3 58.9 + - - +
168A GLY 4.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LYS* 3.3 9.7 + - - -
163A ILE* 3.2 10.5 + - - +
165A LYS* 1.3 79.9 - - - +
167A ASP* 1.3 82.3 + - - +
242A GLY* 3.9 11.6 - - - -
244A LYS* 3.4 23.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE* 2.8 10.1 + - - +
166A SER* 1.3 103.4 + - - +
168A GLY* 1.3 62.9 + - - +
170A ARG* 4.2 7.4 + - - +
171A GLY* 3.6 24.6 + - - +
174A GLN* 5.6 1.2 + - - -
240A GLN 4.6 0.3 - - - +
241A SER* 3.3 12.0 - - - -
242A GLY 2.7 26.4 + - - -
243A ARG 4.6 1.2 + - - +
244A LYS* 2.8 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A PHE* 2.6 49.7 + - - -
165A LYS 4.6 0.2 - - - -
166A SER 3.8 0.4 - - - -
167A ASP* 1.3 76.4 - - - +
169A LEU* 1.3 65.7 + - - +
171A GLY* 3.2 8.8 + - - -
172A LEU* 3.9 2.9 + - - +
----------------------------------------------------------
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