Contacts of the helix formed by residues 154 - 164 (chain C) in PDB entry 2OX6
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 SER 154 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLU* 5.4 2.5 - - - -
142C TYR* 3.6 0.4 + - - -
152C SER* 3.4 6.7 + - - -
153C GLU* 1.3 83.1 + - - +
155C ARG* 1.3 64.0 + - - +
156C GLU* 3.4 17.4 + - - +
157C SER* 3.0 25.3 + - - -
158C ARG* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASN* 4.1 19.0 + - - +
32B HIS* 4.0 9.2 + - - +
33B SER* 3.8 27.0 - - - +
88C VAL* 5.6 0.2 - - - +
90C TYR* 5.3 1.3 - - - +
99C TYR 5.9 0.4 + - - -
100C ASN* 5.0 4.6 + - - +
102C GLU* 3.6 26.5 + - - +
103C PHE* 3.3 43.4 - - - -
154C SER* 1.3 73.4 - - - +
156C GLU* 1.3 65.3 + - - +
158C ARG* 3.2 33.8 + - - +
159C ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASN 5.1 0.3 - - - +
32B HIS* 3.2 34.3 + - - -
36B GLU* 3.4 20.7 - - - +
48B PRO* 5.6 0.2 - - - +
154C SER* 3.6 16.9 + - - +
155C ARG* 1.3 85.8 + - - +
157C SER* 1.3 56.9 + - - +
159C ALA* 3.2 8.7 + - - +
160C LYS* 2.9 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C TYR* 3.4 23.3 - - - -
145C TYR* 4.5 2.3 - - - -
146C ARG* 4.4 2.9 - - - -
151C LEU* 3.7 21.3 - - - +
152C SER* 2.7 29.9 + - - -
154C SER* 3.0 12.7 + - - -
156C GLU* 1.3 72.0 - - - +
158C ARG* 1.3 66.0 + - - +
160C LYS* 3.3 12.2 + - - +
161C TRP* 3.0 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C VAL* 3.6 16.8 - - + +
90C TYR* 2.9 36.6 + - - -
99C TYR* 2.9 43.0 + - - +
100C ASN* 3.5 8.3 + - - -
137C LEU* 4.3 10.5 - - + -
142C TYR* 3.4 26.2 + - + +
153C GLU* 2.7 33.5 + - - +
154C SER* 3.0 10.0 + - - +
155C ARG* 3.5 34.0 - - - +
157C SER* 1.3 74.8 - - - +
159C ALA* 1.3 56.4 + - - +
161C TRP* 3.4 5.9 + - - +
162C ALA* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA* 5.1 4.7 - - - +
88C VAL* 4.2 10.7 - - + +
155C ARG 2.9 13.1 + - - +
156C GLU* 3.2 12.1 + - - +
158C ARG* 1.3 73.8 - - - +
160C LYS* 1.3 65.9 + - - +
162C ALA* 3.3 3.8 + - - +
163C ALA* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C TYR* 3.8 18.9 + - + +
151C LEU* 4.1 32.8 - - + +
156C GLU* 2.9 24.9 + - - +
157C SER* 3.5 11.7 - - - +
159C ALA* 1.3 76.9 - - - +
161C TRP* 1.3 63.2 + - - +
163C ALA* 3.3 18.7 + - - +
164C THR* 3.6 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C VAL* 5.3 1.6 - - + -
135C ILE* 3.7 20.4 - - + -
136C ASN 3.4 18.4 - - - -
137C LEU* 3.9 18.6 - - + -
138C ASN* 3.4 40.6 - - + -
141C ALA* 3.9 21.1 + - + +
142C TYR* 3.8 17.7 - + + -
145C TYR* 3.6 46.1 - + + -
157C SER 3.0 14.2 + - - +
158C ARG 3.6 10.8 - - - +
160C LYS* 1.3 76.1 - - - +
162C ALA* 1.3 75.5 + - + +
164C THR* 2.6 31.2 + - - -
165C GLN* 3.6 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA* 3.6 24.6 - - + +
88C VAL* 3.6 21.3 - - + +
135C ILE* 4.1 12.9 - - + +
158C ARG 2.9 18.3 + - - +
159C ALA* 3.3 6.5 + - - +
161C TRP* 1.3 85.6 - - + +
163C ALA* 1.3 56.5 + - - +
165C GLN* 2.9 29.3 + - - +
166C LEU 3.9 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA* 3.9 11.4 - - + +
159C ALA 3.0 12.5 + - - +
160C LYS* 3.5 13.5 - - - +
161C TRP 3.2 0.4 - - - -
162C ALA* 1.3 77.3 - - - +
164C THR* 1.3 60.2 + - + +
165C GLN 3.1 0.9 + - - -
166C LEU* 3.6 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C TYR* 3.8 26.6 - - + +
160C LYS 3.6 15.5 - - - +
161C TRP* 2.6 21.1 + - - +
163C ALA* 1.3 76.6 - - + +
165C GLN* 1.3 76.9 + - - +
166C LEU 3.4 6.6 + - - +
----------------------------------------------------------
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