Contacts of the helix formed by residues 72 - 82 (chain A) in PDB entry 2HNK
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 GLY 72 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.0 3.5 - - - +
69A THR* 3.1 17.3 + - - -
71A THR* 1.3 81.0 + - - +
73A TYR* 1.3 65.1 + - - +
74A SER 3.5 1.8 - - - -
75A SER* 2.7 29.4 + - - -
76A LEU* 3.0 11.6 + - - +
101A ALA* 3.7 12.6 - - - -
105A TRP* 4.3 2.0 + - - -
2001A SAH 4.5 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 2.8 33.8 + - - +
27A PHE* 3.5 34.4 - + + -
30A LEU* 3.6 18.1 - - + +
31A ARG* 3.5 22.7 - - + -
43A GLN* 3.8 18.6 - - - +
44A ILE* 3.5 27.8 - - + -
45A SER 4.1 10.8 - - - -
46A PRO* 3.4 15.0 + - + +
49A GLY* 4.1 2.4 - - - -
71A THR* 3.7 1.6 + - - -
72A GLY* 1.3 77.0 - - - +
74A SER* 1.3 61.6 + - - +
76A LEU* 3.3 6.0 + - + +
77A CYS* 3.2 34.6 + - - -
2001A SAH 4.1 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.9 9.6 - - - -
52A LEU* 3.8 15.3 - - - -
66A GLU* 2.8 23.6 + - - -
69A THR 5.1 0.2 + - - -
73A TYR* 1.3 75.1 - - - +
75A SER* 1.3 60.5 + - - +
77A CYS* 3.0 8.2 + - - +
78A PHE* 2.9 32.3 + - - -
152A PHE* 3.4 17.6 - - - -
2001A SAH 2.9 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 3.2 26.4 + - - -
69A THR* 4.5 1.3 - - - -
72A GLY* 2.7 19.9 + - - -
74A SER* 1.3 76.4 + - - +
76A LEU* 1.3 55.5 + - - +
78A PHE* 3.8 4.7 - - - +
79A ALA* 2.8 33.9 + - - +
88A ILE* 4.3 5.4 - - - +
90A CYS* 3.7 22.7 - - - -
105A TRP* 2.7 32.3 + - - -
114A ILE* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.8 43.5 - - + -
30A LEU* 3.8 25.6 - - + -
72A GLY 3.0 9.7 + - - +
73A TYR* 3.4 10.3 - - - +
75A SER* 1.3 77.7 + - - +
77A CYS* 1.3 52.3 + - - +
79A ALA* 4.2 2.6 - - - +
80A SER* 2.7 38.5 + - - -
104A TYR* 3.7 34.1 - - + +
105A TRP* 3.8 17.7 - - + -
108A ASN* 3.8 9.2 - - - +
110A LEU* 3.8 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 4.0 14.8 - - - -
49A GLY* 3.5 32.8 - - - +
52A LEU* 4.9 3.8 - - + -
53A ASN* 3.6 12.4 + - + +
73A TYR* 3.3 40.8 - - - -
74A SER* 3.0 9.5 + - - +
76A LEU* 1.3 74.3 - - - +
78A PHE* 1.3 60.4 + - - +
80A SER* 3.6 4.5 + - - -
81A ALA* 3.0 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.9 32.5 - - + -
56A THR* 3.2 23.7 - - - +
64A ILE* 3.9 15.9 - - + -
66A GLU* 3.4 22.4 - - - -
74A SER* 2.9 27.7 + - - +
75A SER 3.8 0.2 - - - +
77A CYS* 1.3 76.4 - - + +
79A ALA* 1.3 56.9 + - - +
81A ALA* 3.2 4.2 + - - +
82A LEU* 2.9 36.9 + - - +
88A ILE* 3.6 25.6 - - + -
150A LEU* 3.9 17.3 - - + -
152A PHE* 3.5 37.7 - + + -
178A ILE* 4.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER 2.8 22.2 + - - +
76A LEU* 4.6 0.2 - - - -
78A PHE* 1.3 75.1 - - - +
80A SER* 1.3 54.4 + - - +
82A LEU* 3.7 11.1 + - - +
88A ILE* 4.2 4.0 - - + -
110A LEU* 4.0 18.2 - - + +
113A LYS* 2.7 38.9 + - + +
114A ILE* 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 3.6 17.2 - - - -
53A ASN* 4.4 6.4 + - - -
57A LYS* 5.1 2.3 + - - -
76A LEU 2.7 25.1 + - - -
77A CYS* 3.6 4.9 + - - -
79A ALA* 1.3 75.6 - - - +
81A ALA* 1.3 65.6 + - - +
82A LEU 3.6 5.4 + - - +
110A LEU* 4.2 18.1 - - - +
113A LYS* 4.6 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASN* 3.4 40.6 - - - +
56A THR* 3.8 14.3 - - - +
57A LYS* 3.6 27.3 - - - +
77A CYS 3.0 20.9 + - - +
78A PHE 3.2 4.2 + - - +
80A SER* 1.3 74.7 + - - +
82A LEU* 1.3 65.5 + - - +
83A PRO* 3.7 2.1 - - - +
1003C SO4 5.4 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 4.1 4.9 - - + -
61A ALA 3.3 26.9 - - - +
62A LYS* 4.1 2.2 - - - -
64A ILE* 3.5 29.6 - - + -
78A PHE 2.9 23.6 + - - +
79A ALA* 3.8 17.3 - - - +
80A SER 3.3 4.8 - - - +
81A ALA* 1.3 80.6 - - - +
83A PRO* 1.3 72.9 - - + +
86A GLY* 3.9 11.2 - - - +
87A LYS* 3.6 32.5 - - - +
88A ILE* 3.9 6.1 - - + +
113A LYS* 2.9 21.5 + - - +
----------------------------------------------------------
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