Contacts of the helix formed by residues 150 - 157 (chain N) 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 N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N ARG* 3.4 33.7 - - + +
32N ILE* 4.0 24.8 - - + +
71N GLN 4.3 12.6 + - - +
72N LEU* 3.8 28.6 - - - +
149N ILE* 1.3 86.4 + - - +
151N PHE* 1.3 67.0 + - - +
152N VAL* 3.2 4.3 - - + +
153N ASP* 2.9 26.3 + - - +
154N THR* 3.1 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N ILE 5.4 4.7 - - - +
33N ASP* 6.2 1.8 - - - -
35N ALA* 4.0 28.3 - - + -
39N TYR* 4.5 12.1 - + - -
63N LEU* 3.5 25.6 - - + -
72N LEU* 3.9 28.2 + - + +
74N VAL* 3.7 30.7 - - + -
76N GLN* 4.7 6.1 - - + -
77N PRO 3.8 23.1 - - - -
78N ASP* 4.0 7.9 - - - -
150N GLN* 1.3 75.6 - - - +
152N VAL* 1.3 73.1 + - + +
154N THR* 3.3 6.4 + - - -
155N VAL* 3.1 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27N ARG* 3.9 23.3 - - + +
30N ILE* 3.5 28.3 - - + +
31N GLY 3.9 8.3 - - - +
32N ILE 3.8 20.1 + - - +
33N ASP 4.7 0.2 - - - -
34N ASN 3.3 34.5 - - - +
35N ALA* 4.2 3.8 - - - +
38N ALA* 3.4 18.7 - - + +
150N GLN* 3.2 2.3 - - + +
151N PHE* 1.3 83.4 - - + +
153N ASP* 1.3 63.7 + - - +
156N ALA* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N PRO* 4.3 4.9 - - - -
26N LEU* 2.8 35.0 + - - +
27N ARG* 2.9 44.2 + - - +
144N ILE* 3.6 17.2 - - + +
148N SER 4.7 0.4 - - - -
149N ILE* 3.6 15.5 - - + -
150N GLN* 2.9 20.0 + - - +
152N VAL* 1.3 75.6 - - - +
154N THR* 1.3 65.2 + - - +
156N ALA* 3.6 4.6 + - - +
157N ASP* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 154 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N LEU* 5.0 7.1 - - + +
72N LEU* 4.7 4.0 - - - +
78N ASP* 4.2 12.8 - - - +
147N TRP* 5.7 0.7 - - + -
149N ILE* 3.8 19.9 - - + +
150N GLN 3.1 14.6 + - - -
151N PHE* 3.5 7.0 + - - -
153N ASP* 1.3 74.2 - - - +
155N VAL* 1.3 62.0 + - - +
157N ASP* 2.9 13.9 + - - -
159N ALA* 2.7 42.6 + - - +
160N SER* 2.5 35.0 - - - +
1262N PO4 4.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N ALA* 3.8 8.5 - - + -
39N TYR* 3.4 56.1 - - + +
42N GLN* 3.1 20.9 + - - +
78N ASP* 3.1 24.9 - - - +
151N PHE* 3.1 41.5 + - + +
154N THR* 1.3 78.0 - - - +
156N ALA* 1.3 64.8 + - - +
158N ASN 3.0 12.0 + - - -
159N ALA* 4.0 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N LEU* 3.6 11.5 - - - +
26N LEU* 4.1 18.2 - - + -
30N ILE* 5.0 1.8 - - + -
38N ALA* 3.4 21.0 + - + +
41N ILE* 3.9 25.3 - - + +
42N GLN* 3.8 12.8 - - - -
45N ASN* 4.8 3.6 + - - -
152N VAL 3.3 16.7 + - - +
153N ASP 3.8 4.0 - - - +
154N THR 3.2 0.2 - - - -
155N VAL* 1.3 80.1 - - - +
157N ASP* 1.3 56.7 + - - +
158N ASN 3.0 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13N LEU* 4.0 15.8 - - + +
141N GLY 4.2 0.9 - - - +
142N SER* 3.7 9.0 + - - -
143N ARG* 2.7 78.9 + - - +
144N ILE* 4.1 9.3 + - + +
149N ILE* 5.4 1.2 - - + +
153N ASP 3.1 17.3 + - - +
154N THR* 2.9 9.4 + - - +
156N ALA* 1.3 73.2 - - - +
158N ASN* 1.3 65.0 + - - +
160N 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