Contacts of the helix formed by residues 150 - 157 (chain M) 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 M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M ARG* 3.4 33.4 - - + +
32M ILE* 4.0 26.9 - - + +
71M GLN 4.4 12.6 + - - +
72M LEU* 3.7 29.7 - - - +
149M ILE* 1.3 86.2 + - - +
151M PHE* 1.3 67.5 + - - +
152M VAL* 3.2 3.8 - - + +
153M ASP* 2.9 26.9 + - - +
154M THR* 3.1 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M ILE 5.4 4.7 - - - +
33M ASP* 6.2 1.6 - - - -
35M ALA* 4.0 27.6 - - + -
39M TYR* 4.5 11.7 - + - -
63M LEU* 3.5 25.4 - - + -
72M LEU* 3.9 27.3 + - + +
74M VAL* 3.8 32.5 - - + -
76M GLN* 4.7 6.1 - - + -
77M PRO 3.9 22.2 - - - -
78M ASP* 4.0 2.0 - - - -
150M GLN* 1.3 75.9 - - - +
152M VAL* 1.3 73.9 + - + +
154M THR* 3.3 7.0 + - - -
155M VAL* 3.1 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M ARG* 3.8 24.5 - - + +
30M ILE* 3.5 27.5 - - + +
31M GLY 3.9 7.4 - - - +
32M ILE 3.8 20.4 + - - +
33M ASP 4.6 0.2 - - - -
34M ASN 3.3 35.0 - - - +
35M ALA* 4.2 3.4 - - - +
38M ALA* 3.4 19.4 - - + +
150M GLN* 3.2 2.4 - - + +
151M PHE* 1.3 84.0 - - + +
153M ASP* 1.3 62.8 + - - +
156M ALA* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M PRO* 3.8 4.9 - - - +
26M LEU* 2.8 35.2 + - - +
27M ARG* 2.9 44.2 + - - +
144M ILE* 3.7 18.3 - - + +
148M SER 4.7 0.4 - - - -
149M ILE* 3.6 15.5 - - + -
150M GLN* 2.9 18.8 + - - +
152M VAL* 1.3 76.8 - - - +
154M THR* 1.3 65.0 + - - +
156M ALA* 3.8 4.0 - - - +
157M ASP* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M LEU* 5.1 7.3 - - + +
72M LEU* 4.7 4.3 - - - +
78M ASP* 4.2 13.5 - - - +
147M TRP* 5.7 0.7 - - + -
149M ILE* 3.8 20.5 - - + +
150M GLN 3.1 15.1 + - - -
151M PHE* 3.5 6.5 + - - -
153M ASP* 1.3 74.1 - - - +
155M VAL* 1.3 61.4 + - - +
157M ASP* 2.9 13.7 + - - -
159M ALA* 2.7 40.8 + - - +
160M SER* 2.5 32.1 - - - +
1262M PO4 4.8 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M ALA* 3.7 8.5 - - + -
39M TYR* 3.4 56.5 - - + +
42M GLN* 3.2 20.3 + - - +
78M ASP* 3.1 24.5 - - - +
151M PHE* 3.1 40.9 + - + +
154M THR* 1.3 77.6 - - - +
156M ALA* 1.3 64.2 + - - +
158M ASN 3.0 11.6 + - - -
159M ALA* 4.0 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M LEU* 3.6 12.1 - - - +
26M LEU* 4.1 19.3 - - + -
30M ILE* 5.0 1.1 - - + -
38M ALA* 3.4 20.1 + - + +
41M ILE* 3.9 29.6 - - + +
42M GLN* 3.9 8.5 - - - +
45M ASN* 4.8 3.6 + - - -
152M VAL 3.3 17.7 + - - +
153M ASP 3.8 3.8 - - - +
154M THR 3.2 0.4 - - - -
155M VAL* 1.3 77.6 - - - +
157M ASP* 1.3 57.8 + - - +
158M ASN 3.0 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13M LEU* 4.0 14.5 - - + +
141M GLY 4.2 0.7 - - - +
142M SER* 3.7 8.8 + - - -
143M ARG* 2.7 80.7 + - - +
144M ILE* 4.1 9.0 + - + +
149M ILE* 5.4 0.8 - - + +
153M ASP 3.1 17.9 + - - +
154M THR* 2.9 10.5 + - - +
156M ALA* 1.3 73.6 - - - +
158M ASN* 1.3 64.6 + - - +
160M SER* 3.1 7.5 + - - +
----------------------------------------------------------
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