Contacts of the helix formed by residues 79 - 88 (chain A) in PDB entry 5WN0
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 LYS 79 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE 2.8 14.6 + - - +
77A LYS* 3.0 17.2 + - - +
78A LYS* 1.3 80.6 - - - +
80A GLY* 1.3 64.5 + - - +
81A LEU 3.2 2.9 - - - -
82A ASP* 3.1 41.2 + - + +
83A TRP* 3.6 4.0 + - - +
305A LEU 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 4.1 6.4 - - - -
75A TRP* 2.8 45.0 + - - -
76A ILE 3.8 1.0 + - - -
78A LYS 3.3 2.1 - - - -
79A LYS* 1.3 77.7 - - - +
81A LEU* 1.3 62.3 + - - +
83A TRP* 3.2 15.0 + - - +
84A VAL* 3.3 16.6 + - - +
305A LEU 4.6 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TRP* 3.7 22.3 - - + -
76A ILE* 4.2 18.8 + - + +
79A LYS 3.2 1.0 - - - -
80A GLY* 1.3 73.3 - - - +
82A ASP* 1.3 68.6 + - - +
84A VAL* 3.2 9.2 + - + +
85A LYS* 3.1 37.2 + - - +
92A LEU* 5.3 1.8 - - + -
107A GLU* 3.7 50.5 - - + +
108A LEU* 3.9 23.1 - - + +
111A LEU* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LYS* 3.1 42.5 + - + +
81A LEU* 1.3 78.9 - - - +
83A TRP* 1.3 62.4 + - - +
84A VAL 3.2 0.2 + - - -
85A LYS* 3.2 15.0 + - - +
86A GLU* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A CYS* 3.7 18.2 - - - -
67A TRP* 3.7 21.3 - + + -
79A LYS 3.6 3.8 + - - +
80A GLY* 3.2 12.1 + - - +
82A ASP* 1.3 79.2 - - - +
84A VAL* 1.3 65.4 + - + +
86A GLU* 3.5 9.9 + - + +
87A GLU* 2.9 66.7 + - + -
301A ARG* 3.7 24.5 - - + +
304A ALA* 3.3 34.0 - - + +
305A LEU 5.5 1.8 - - - +
311A PRO* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 4.3 1.8 - - + -
75A TRP* 3.7 22.7 - - + -
80A GLY 3.3 14.6 - - - +
81A LEU* 3.2 10.5 + - + +
82A ASP 3.2 0.8 - - - -
83A TRP* 1.3 90.9 - - + +
85A LYS* 1.3 56.3 + - + +
87A GLU* 3.5 2.0 - - - +
88A ALA* 2.6 33.8 + - - -
89A PRO* 3.5 16.9 - - + +
92A LEU* 3.7 35.0 - - + -
111A LEU* 5.1 5.6 - - + -
114A LEU* 4.1 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.1 29.5 + - - +
82A ASP* 3.2 15.0 + - - +
84A VAL* 1.3 77.7 - - + +
86A GLU* 1.3 62.8 + - - +
88A ALA* 3.5 17.4 + - - +
107A GLU* 5.6 1.1 - - - -
110A GLU* 3.8 25.2 + - - +
111A LEU* 3.4 35.3 - - + +
112A PRO* 5.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 5.3 0.2 + - - -
82A ASP 3.1 12.2 + - - +
83A TRP* 3.6 14.4 - - + +
84A VAL 3.3 0.2 - - - -
85A LYS* 1.3 78.5 - - - +
87A GLU* 1.3 61.1 + - - +
88A ALA* 4.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 2.6 47.2 + - - +
65A CYS* 4.7 3.4 - - + -
83A TRP* 2.9 53.8 + - + +
84A VAL* 3.8 3.4 - - - +
86A GLU* 1.3 76.6 - - - +
88A ALA* 1.3 67.3 + - - +
89A PRO* 4.4 7.0 - - + -
301A ARG* 2.7 33.1 + - - -
313A THR* 2.7 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 4.1 6.6 - - - +
84A VAL 2.6 17.8 + - - -
85A LYS* 3.6 14.8 - - - +
86A GLU 4.2 3.1 - - - +
87A GLU* 1.3 74.6 - - - +
89A PRO* 1.3 67.6 - - - +
90A ASP* 5.7 0.2 - - - -
114A LEU* 6.1 0.2 - - - -
----------------------------------------------------------
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