Contacts of the helix formed by residues 75 - 89 (chain E) in PDB entry 1KXT
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 ASN 75 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E TRP* 3.6 3.5 - - - -
69E LEU 3.2 8.5 - - - -
70E CYS* 3.9 23.0 - - + +
71E THR 4.7 3.8 + - - -
74E GLY* 1.3 77.3 + - - -
76E GLU* 1.3 68.0 + - - +
77E ASN* 3.4 17.6 - - - +
78E GLU* 2.8 14.9 + - - +
79E PHE* 3.0 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E LEU* 2.9 47.8 + - + +
70E CYS* 5.2 0.2 - - - +
75E ASN* 1.3 77.4 - - - +
77E ASN* 1.3 56.7 + - - +
79E PHE* 3.2 3.5 + - - +
80E ARG* 2.7 70.1 + - - +
185E LYS* 4.9 7.0 - - - +
189E ILE* 4.6 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E ASN* 3.5 18.7 - - - +
76E GLU* 1.3 76.5 - - - +
78E GLU* 1.3 75.0 + - - +
80E ARG* 3.2 14.3 + - - +
81E ASP* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ARG* 5.6 2.9 + - - -
21E TRP* 3.9 17.5 - - + +
22E VAL* 4.0 25.3 - - + +
73E SER 4.4 1.1 - - - +
74E GLY* 2.9 15.0 - - - -
75E ASN* 2.8 33.2 + - - +
76E GLU 3.2 0.6 - - - -
77E ASN* 1.3 95.2 + - - +
79E PHE* 1.3 66.8 + - - +
81E ASP* 3.2 7.2 + - - +
82E MET* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E TRP* 3.4 34.2 - + + +
42E VAL* 4.6 3.4 - - + -
45E PRO* 3.9 17.3 - - + -
69E LEU* 3.9 19.5 - - + -
75E ASN 3.0 9.8 + - - +
76E GLU* 3.2 11.2 + - - +
78E GLU* 1.3 76.4 - - - +
80E ARG* 1.3 64.7 + - - +
82E MET* 3.3 26.5 + - + +
83E VAL* 3.0 44.9 + - + +
93E ILE* 4.3 3.4 - - + -
95E VAL* 3.8 12.3 - - + -
186E LEU* 3.5 28.5 - - + -
189E ILE* 4.2 11.7 - - + -
191E VAL* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E GLU* 2.7 51.9 + - - +
77E ASN* 3.4 14.6 - - - +
79E PHE* 1.3 77.1 - - - +
81E ASP* 1.3 63.9 + - - +
83E VAL* 3.2 3.1 + - - +
84E THR* 2.9 30.3 + - - +
185E LYS* 5.1 5.7 - - - +
189E ILE* 3.9 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E VAL* 6.1 0.5 - - - +
25E ALA* 4.7 0.9 - - - +
77E ASN 2.8 20.6 + - - +
78E GLU* 3.6 7.9 - - - +
80E ARG* 1.3 72.1 - - - +
82E MET* 1.3 57.5 + - - +
84E THR* 3.8 5.7 - - - -
85E ARG* 2.7 79.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E TRP* 3.7 39.5 - - + +
24E ILE* 3.5 42.8 - - + -
25E ALA* 3.9 13.8 - - - +
42E VAL* 4.1 11.2 - - + -
78E GLU 2.9 13.4 + - - +
79E PHE* 3.4 45.5 - - + +
80E ARG 3.2 0.2 - - - -
81E ASP* 1.3 77.1 + - - +
83E VAL* 1.3 57.7 + - + +
85E ARG* 3.7 0.7 - - - +
86E CYS* 2.7 45.2 + - - -
93E ILE* 4.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E PHE* 3.0 47.2 + - + +
80E ARG 3.6 3.8 - - - +
82E MET* 1.3 78.4 - - + +
84E THR* 1.3 62.5 + - - +
87E ASN* 3.0 47.7 + - - +
93E ILE* 3.7 25.4 - - + +
189E ILE* 3.5 26.0 - - + +
190E GLY* 3.5 14.8 - - - -
191E VAL* 3.9 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E ARG* 2.9 20.8 + - - +
81E ASP* 3.8 6.0 - - - -
83E VAL* 1.3 76.2 - - - +
85E ARG* 1.3 60.3 + - + +
87E ASN* 4.0 1.2 - - - +
88E ASN* 2.9 47.5 + - - +
189E ILE* 4.8 4.2 + - - +
221E TRP* 3.9 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E VAL* 5.1 4.4 + - - +
25E ALA* 3.5 25.6 - - - +
26E LEU* 3.7 22.2 - - - +
28E CYS* 5.1 1.1 - - - -
29E GLU* 2.9 49.2 + - + +
81E ASP* 2.7 62.7 + - - +
82E MET* 3.8 3.4 - - - +
84E THR* 1.3 77.3 - - + +
86E CYS* 1.3 65.4 + - - +
88E ASN* 3.4 17.3 + - - +
89E VAL* 3.6 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ILE* 3.8 10.8 - - - -
25E ALA* 4.3 2.7 - - - -
28E CYS* 2.0 51.4 - - - -
82E MET* 2.7 33.3 + - - +
85E ARG* 1.3 70.6 - - - +
87E ASN* 1.3 66.0 + - - +
89E VAL* 3.1 10.7 + - - +
90E GLY 3.3 0.2 + - - -
91E VAL 2.9 25.1 + - - +
93E ILE* 3.2 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E VAL* 3.0 34.6 + - - +
84E THR 4.0 0.2 - - - +
86E CYS* 1.3 77.1 - - - +
88E ASN* 1.3 58.6 + - - +
90E GLY* 3.0 18.2 + - - -
91E VAL 3.7 7.1 - - - +
92E ARG* 2.8 41.0 + - - +
93E ILE* 4.7 3.7 + - - +
190E GLY* 3.1 28.5 + - - +
221E TRP* 3.5 40.8 - - + +
222E PHE* 3.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E THR* 2.9 39.0 + - - +
85E ARG* 3.6 12.8 - - - +
86E CYS 3.1 1.2 - - - -
87E ASN* 1.3 76.6 - - - +
89E VAL* 1.3 62.2 + - + +
90E GLY 3.4 0.7 - - - -
221E TRP* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLN* 5.1 1.6 - - - -
10E ARG* 3.6 15.6 + - - -
28E CYS* 3.7 29.6 - - + +
29E GLU* 4.3 17.7 - - + +
33E GLY* 3.9 8.6 - - - -
34E PRO* 6.0 0.7 - - + -
85E ARG 3.6 11.4 + - - +
86E CYS 3.4 12.1 - - - +
88E ASN* 1.3 82.2 - - + +
90E GLY* 1.3 59.2 + - - +
91E VAL* 4.0 8.1 - - + -
----------------------------------------------------------
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