Contacts of the helix formed by residues 69 - 78 (chain A) in PDB entry 3K8G
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 69 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 5.1 3.7 - - + +
64A GLU* 5.8 7.1 + - + +
67A GLU* 2.7 73.4 + - - +
70A ALA* 1.3 69.7 + - - +
71A ASP* 3.3 10.9 + - - -
72A ILE* 3.6 16.1 + - - +
73A LYS* 3.6 14.4 + - - +
114A ASP* 6.1 3.6 - - - +
116A TRP* 5.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 1.3 80.0 - - - +
71A ASP* 1.3 55.8 + - - +
73A LYS* 3.2 8.8 + - - +
74A LYS* 2.8 64.1 + - + +
114A ASP* 5.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS 3.3 6.1 + - - -
70A ALA* 1.3 82.5 + - - +
72A ILE* 1.3 58.6 + - + +
74A LYS* 3.3 7.5 + - - +
75A ILE* 2.8 36.1 + - - +
109A ILE* 3.3 21.1 - - + +
110A PHE* 2.7 37.2 + - + +
111A SER 4.2 1.6 + - - -
114A ASP* 4.3 13.9 - - - +
116A TRP* 2.8 39.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.8 21.1 - - + -
67A GLU 5.3 6.3 - - - +
69A LYS* 3.6 11.4 + - - +
70A ALA 3.3 0.6 - - - -
71A ASP* 1.3 78.8 - - + +
73A LYS* 1.3 61.6 + - - +
75A ILE* 3.2 9.6 + - + +
76A VAL* 2.9 27.5 + - - +
116A TRP* 4.5 10.8 - - + -
133A THR* 4.0 26.2 - - + +
135A VAL* 4.2 15.9 - - + -
145A VAL* 4.7 1.1 - - + -
300A MPD 3.6 27.8 - - + +
301A MPD 3.3 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 4.1 27.6 + - - +
63A ILE* 4.3 17.3 - - + -
64A GLU* 3.8 36.7 + - - +
69A LYS 3.6 10.6 + - - +
70A ALA* 3.2 10.2 + - - +
72A ILE* 1.3 76.2 - - - +
74A LYS* 1.3 63.3 + - + +
76A VAL* 3.1 8.6 + - - +
77A ASP* 3.0 35.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
70A ALA* 2.8 44.7 + - + +
71A ASP* 3.5 5.6 - - - +
72A ILE 3.3 0.2 - - - -
73A LYS* 1.3 74.1 - - + +
75A ILE* 1.3 61.2 - - - +
77A ASP* 3.4 18.2 + - - +
78A ARG* 3.5 10.6 + - - +
105A PHE* 3.6 26.4 - - + -
108A LEU 5.8 1.3 - - - -
109A ILE* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASP 2.8 21.4 + - - +
72A ILE* 3.2 16.3 + - + +
74A LYS* 1.3 74.3 - - - +
76A VAL* 1.3 59.1 + - - +
78A ARG* 3.0 13.5 + - - +
79A THR* 2.6 22.5 + - - -
101A TYR* 3.7 17.0 - - + -
105A PHE* 3.9 11.4 - - + -
109A ILE* 3.9 15.0 - - + -
110A PHE* 3.9 28.9 - - + -
135A VAL* 4.0 16.2 - - + -
137A ILE* 4.6 4.9 - - + -
143A SER* 4.1 7.6 - - - +
301A MPD 3.7 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.9 26.4 - - + +
56A GLU* 6.4 1.1 - - - -
59A ILE* 3.8 22.9 - - + -
63A ILE* 3.5 24.5 - - + -
72A ILE 2.9 18.0 + - - +
73A LYS* 3.1 7.4 + - - +
75A ILE* 1.3 74.5 - - - +
77A ASP* 1.3 62.2 + - - +
79A THR* 3.0 30.7 + - - +
82A VAL* 5.4 0.7 - - + -
301A MPD 2.9 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 5.8 1.3 - - - -
73A LYS* 3.0 25.0 + - - +
74A LYS* 3.7 12.8 - - - +
75A ILE 3.2 0.6 - - - -
76A VAL* 1.3 78.3 - - - +
78A ARG* 1.3 62.8 + - + +
79A THR 3.5 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS 3.5 10.1 + - - +
75A ILE 3.0 10.9 + - - +
77A ASP* 1.3 82.8 - - + +
79A THR* 1.3 55.7 + - - +
80A THR* 5.4 1.5 - - - +
99A GLY* 3.3 2.4 - - - -
100A SER* 2.7 62.2 + - - +
101A TYR* 3.8 6.5 - - + -
102A PRO* 3.7 26.1 - - - +
105A PHE* 3.5 38.2 - - + +
----------------------------------------------------------
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