Contacts of the helix formed by residues 72 - 88 (chain A) in PDB entry 2WQN
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 ASP 72 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET* 1.3 75.9 - - - +
73A ALA* 1.3 70.6 + - - +
74A LYS* 2.9 31.8 + - - +
75A ALA* 2.9 26.7 + - - +
76A ARG* 2.9 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 1.3 73.9 - - - +
74A LYS* 1.3 63.4 + - - +
76A ARG* 3.2 26.1 + - - +
77A ALA* 3.1 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 2.9 16.6 + - - +
73A ALA* 1.3 75.7 - - - +
75A ALA* 1.3 63.9 + - - +
77A ALA* 3.1 10.6 + - - +
78A ASP* 3.1 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET* 3.5 18.2 - - + -
72A ASP* 2.9 32.8 + - - +
74A LYS* 1.3 74.1 - - - +
76A ARG* 1.3 55.1 + - - +
78A ASP* 3.1 10.2 + - - +
79A CYS* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.7 21.6 + - + -
68A PHE* 3.1 48.5 + - - +
71A MET* 3.3 39.2 + - + +
72A ASP* 2.9 12.9 + - - +
73A ALA* 3.4 40.2 - - - +
75A ALA* 1.3 76.0 - - - +
77A ALA* 1.3 57.5 + - - +
79A CYS* 4.6 0.2 - - - -
80A ILE* 3.0 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA 3.1 10.6 + - - +
74A LYS* 3.1 13.7 + - - +
76A ARG* 1.3 76.9 - - - +
78A ASP* 1.3 58.0 + - - +
80A ILE* 4.0 2.3 - - - +
81A LYS* 2.8 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS* 3.1 16.9 + - - +
75A ALA* 3.1 11.0 + - - +
77A ALA* 1.3 78.5 - - - +
79A CYS* 1.3 62.8 + - - +
81A LYS* 3.5 4.7 + - - +
82A GLU* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 5.6 0.9 - - - -
71A MET* 3.7 25.6 - - + -
75A ALA 2.8 19.7 + - - +
76A ARG 4.2 0.4 - - - +
78A ASP* 1.3 72.1 - - - +
80A ILE* 1.3 59.5 + - + +
82A GLU* 3.1 7.3 + - - +
83A ILE* 2.8 47.4 + - - +
107A LEU* 4.8 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 6.4 2.7 - - + -
71A MET* 6.4 0.2 - - + -
76A ARG* 3.0 31.4 + - + +
77A ALA* 4.0 2.5 - - - +
79A CYS* 1.3 76.9 - - + +
81A LYS* 1.3 67.9 + - - +
83A ILE* 3.4 7.7 + - + +
84A ASP* 3.0 38.8 + - - +
102A ILE* 6.3 2.9 - - + -
107A LEU* 5.0 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA 2.8 23.9 + - - +
78A ASP* 3.8 5.2 - - - +
80A ILE* 1.3 75.0 - - - +
82A GLU* 1.3 62.5 + - - +
84A ASP* 3.3 7.5 + - - +
85A LEU* 3.1 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP 2.9 19.9 + - - +
79A CYS* 3.1 6.5 + - - +
81A LYS* 1.3 74.7 - - - +
83A ILE* 1.3 67.1 + - + +
85A LEU* 3.1 21.5 + - - +
86A LEU* 2.9 37.0 + - + +
157A VAL* 4.5 8.3 - - - +
158A MET 4.3 4.9 + - - +
160A ARG* 3.6 33.0 + - - +
180A LEU* 4.2 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A CYS* 2.8 40.2 + - - +
80A ILE* 3.8 8.1 - - + +
82A GLU* 1.3 71.8 - - + +
84A ASP* 1.3 58.6 + - - +
86A LEU* 3.0 19.7 + - + +
87A LYS* 3.0 31.7 + - + +
97A TYR* 4.6 15.5 - - + -
100A SER* 3.3 34.8 - - - +
107A LEU* 4.8 6.1 - - + -
109A ILE* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.0 32.5 + - - +
81A LYS* 3.7 7.6 - - - +
82A GLU 3.2 0.2 - - - -
83A ILE* 1.3 75.4 - - - +
85A LEU* 1.3 65.9 + - - +
87A LYS* 3.3 36.8 + - - +
88A GLN* 3.8 14.4 + - - +
100A SER* 3.9 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 3.1 18.1 + - + +
82A GLU* 3.1 26.2 + - - +
84A ASP* 1.3 74.8 - - - +
86A LEU* 1.3 64.7 + - + +
88A GLN* 3.2 36.5 + - - +
89A LEU* 4.0 5.5 + - - +
156A ARG 5.6 3.4 - - - +
157A VAL* 4.6 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 2.9 29.4 + - + +
83A ILE* 3.0 22.2 + - + +
85A LEU* 1.3 77.7 - - + +
87A LYS* 1.3 60.5 + - - +
89A LEU* 3.1 42.5 + - + +
97A TYR* 4.0 43.9 + - + +
157A VAL* 3.9 12.6 - - + -
180A LEU* 3.5 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN* 5.0 4.6 - - - +
83A ILE* 3.0 15.9 + - + +
84A ASP* 3.3 29.9 + - - +
85A LEU 3.3 0.8 - - - -
86A LEU* 1.3 75.8 - - - +
88A GLN* 1.3 60.1 + - + +
89A LEU 3.3 6.6 + - - +
96A LYS* 3.9 11.8 + - - -
97A TYR* 3.6 30.8 - - + +
98A TYR 4.5 2.2 - - - +
99A ALA* 3.8 22.5 - - - +
100A SER* 3.3 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASP 3.8 14.4 - - - +
85A LEU* 3.4 27.8 - - - +
86A LEU 3.1 0.4 - - - -
87A LYS* 1.3 77.8 - - + +
89A LEU* 1.3 64.4 + - + +
90A ASN* 3.6 4.2 + - - +
96A LYS* 5.2 0.6 + - - -
155A ARG* 3.1 27.1 + - - +
----------------------------------------------------------
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