Contacts of the helix formed by residues 150 - 157 (chain F) in PDB entry 2WQT
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 GLN 150 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ARG* 3.4 33.9 - - + +
32F ILE* 4.0 25.4 - - + +
71F GLN 4.4 12.4 + - - +
72F LEU* 3.7 28.7 - - - +
149F ILE* 1.3 85.2 + - - +
151F PHE* 1.3 68.3 + - - +
152F VAL* 3.2 4.0 - - + +
153F ASP* 3.0 26.5 + - - +
154F THR* 3.0 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F ILE 5.4 4.9 - - - +
33F ASP* 6.2 1.3 - - + -
35F ALA* 4.0 27.1 - - + -
39F TYR* 4.4 11.4 - + - -
63F LEU* 3.5 25.6 - - + -
72F LEU* 3.9 27.3 + - + +
74F VAL* 3.8 31.0 - - + -
76F GLN* 4.7 6.3 - - + -
77F PRO 3.8 23.6 - - - -
78F ASP* 4.0 1.8 - - - -
150F GLN* 1.3 75.7 - - - +
152F VAL* 1.3 73.3 + - + +
154F THR* 3.3 6.5 + - - -
155F VAL* 3.1 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ARG* 3.8 24.0 - - + +
30F ILE* 3.5 28.4 - - + +
31F GLY 3.9 8.1 - - - +
32F ILE 3.8 20.8 + - - +
33F ASP 4.6 0.2 - - - -
34F ASN 3.3 34.8 - - - +
35F ALA* 4.2 3.6 - - - +
38F ALA* 3.4 19.0 - - + +
150F GLN* 3.2 2.5 - - + +
151F PHE* 1.3 83.4 - - + +
153F ASP* 1.3 64.5 + - - +
156F ALA* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F PRO* 3.8 4.9 - - - +
26F LEU* 2.8 34.2 + - - +
27F ARG* 2.9 43.5 + - - +
144F ILE* 3.7 17.4 - - + +
148F SER 4.7 0.7 - - - -
149F ILE* 3.6 15.9 - - + -
150F GLN* 3.0 19.9 + - - +
152F VAL* 1.3 76.0 - - - +
154F THR* 1.3 63.9 + - - +
156F ALA* 3.8 3.6 - - - +
157F ASP* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LEU* 5.1 7.4 - - + +
72F LEU* 4.7 4.2 - - - +
78F ASP* 4.2 13.0 - - - +
147F TRP* 5.7 0.9 - - + -
149F ILE* 3.8 20.8 - - + +
150F GLN 3.0 15.1 + - - -
151F PHE* 3.4 6.4 + - - -
153F ASP* 1.3 74.7 - - - +
155F VAL* 1.3 61.4 + - - +
157F ASP* 2.9 13.9 + - - -
159F ALA* 2.7 40.0 + - - +
160F SER* 2.5 32.0 + - - +
1264F PO4 4.6 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ALA* 3.7 8.3 - - + -
39F TYR* 3.5 57.0 - - + +
42F GLN* 3.1 20.5 + - - +
78F ASP* 3.1 25.4 - - - +
151F PHE* 3.1 41.2 + - + +
154F THR* 1.3 76.9 - - - +
156F ALA* 1.3 64.7 + - - +
158F ASN 3.1 10.4 + - - -
159F ALA* 4.0 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LEU* 3.7 11.4 - - - +
26F LEU* 4.0 18.8 - - + -
30F ILE* 5.0 1.6 - - + -
38F ALA* 3.4 19.9 + - - +
41F ILE* 3.9 24.6 - - + +
42F GLN* 3.8 14.4 + - - +
45F ASN* 4.8 3.5 + - - -
152F VAL 3.3 16.9 + - - +
153F ASP 3.8 3.8 - - - +
154F THR 3.3 0.2 - - - -
155F VAL* 1.3 79.2 - - - +
157F ASP* 1.3 57.8 + - - +
158F ASN 3.0 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F LEU* 4.0 15.4 - - + +
141F GLY 4.2 0.9 - - - +
142F SER* 3.6 8.7 + - - -
143F ARG* 2.7 79.7 + - - +
144F ILE* 4.1 8.7 + - + +
149F ILE* 5.4 1.0 - - + +
153F ASP 3.1 17.7 + - - +
154F THR* 2.9 10.0 + - - +
156F ALA* 1.3 74.3 - - - +
158F ASN* 1.3 64.3 + - - +
160F SER* 3.1 7.6 + - - +
----------------------------------------------------------
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