Contacts of the helix formed by residues 84 - 89 (chain E) in PDB entry 1KR2
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 THR 84 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E PRO* 5.6 0.2 - - - -
67E VAL* 3.5 35.9 - - + -
71E GLU* 4.6 6.3 - - - +
82E VAL* 5.0 2.9 - - + +
83E ASP* 1.3 72.4 + - - +
85E TRP* 1.3 68.2 + - - +
86E GLU 3.3 2.5 - - - -
87E SER* 2.7 27.9 + - - -
88E LEU* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E ASP* 2.8 21.4 + - - +
84E THR* 1.3 80.2 + - - +
86E GLU* 1.3 85.5 + - + +
88E LEU* 3.1 12.1 + - + +
89E GLN* 2.9 49.5 + - + +
93E LYS* 4.0 35.0 - - + -
97E LYS* 4.7 4.3 - - + -
98E VAL* 4.3 14.4 - - + -
101E HIS* 3.4 64.1 + + + +
102E HIS* 5.0 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E CYS* 3.8 7.1 - - - -
49E SER* 2.5 48.1 + - - +
50E PRO 4.1 7.6 - - - +
51E VAL* 4.0 21.2 - - + +
52E GLY* 4.3 6.6 + - - +
83E ASP* 4.3 1.6 + - - -
84E THR 3.3 0.8 - - - -
85E TRP* 1.3 95.2 - - + +
87E SER* 1.3 62.1 + - - +
88E LEU 3.2 0.9 + - - -
89E GLN* 3.3 18.2 + - - +
92E TRP* 5.3 0.2 - - - -
93E LYS* 4.1 18.9 + - + +
95E THR* 5.8 0.5 - - - -
98E VAL* 3.4 33.9 - - + +
102E HIS* 5.7 0.2 + - - -
813E TAD 4.1 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E PRO* 3.6 17.6 + - - -
51E VAL 4.3 0.4 - - - -
52E GLY* 3.7 25.1 - - - -
53E ASP 4.8 1.4 + - - -
63E ALA* 4.3 18.1 - - - +
67E VAL* 3.9 14.3 - - - +
83E ASP 5.1 0.2 + - - -
84E THR* 2.7 34.0 + - - +
86E GLU* 1.3 78.8 - - - +
88E LEU* 1.3 62.4 + - - +
89E GLN 3.6 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E THR* 3.0 35.6 + - - +
85E TRP* 3.1 12.2 + - - +
87E SER* 1.3 80.2 - - - +
89E GLN* 1.3 67.2 + - - +
90E LYS* 3.7 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E GLY* 5.5 2.8 - - - -
54E ALA* 5.1 3.3 - - - +
85E TRP* 2.9 65.5 + - + +
86E GLU* 3.3 14.7 + - - +
87E SER 4.0 6.2 - - - +
88E LEU* 1.3 84.8 - - - +
90E LYS* 1.3 65.2 + - - +
91E GLU 3.6 18.9 + - - +
93E LYS* 4.0 27.5 + - + +
----------------------------------------------------------
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