Contacts of the helix formed by residues 85 - 93 (chain E) in PDB entry 2X86
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 ASP 85 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 3.1 39.1 + - + +
83E GLU* 2.9 22.0 + - - +
84E TRP* 1.3 75.7 - - - +
86E GLY* 1.3 57.0 + - - +
87E LYS* 2.9 12.4 + - - +
88E TYR* 2.7 34.0 + - + +
89E MET* 2.9 27.9 + - - +
139E VAL* 5.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 2.8 28.5 + - - -
34A LYS 3.2 0.8 + - - -
36A GLY* 4.0 9.2 - - - -
84E TRP 3.0 6.9 + - - -
85E ASP* 1.3 70.8 + - - +
87E LYS* 1.3 59.9 + - - +
89E MET* 4.1 1.6 - - - -
90E MET* 2.8 36.0 + - - +
139E VAL* 4.1 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASN* 4.2 11.7 - - - +
33A LEU* 3.2 10.4 + - - +
34A LYS* 3.8 24.0 - - + +
50A TYR* 6.5 0.2 - - - -
52A ASP* 3.7 33.6 + - + +
54A GLU* 5.5 4.1 - - - +
55A ASP* 5.7 0.6 + - - -
85E ASP* 2.9 8.5 + - - +
86E GLY* 1.3 77.3 - - - +
88E TYR* 1.3 63.8 + - - +
90E MET* 3.9 2.7 - - - +
91E ASP* 3.0 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E LYS* 3.0 25.7 + - - -
78E CYS* 3.6 29.8 - - + -
83E GLU* 4.6 15.0 - - + -
85E ASP* 2.7 29.7 + - + +
87E LYS* 1.3 75.0 - - - +
89E MET* 1.3 66.1 + - - +
91E ASP* 3.1 6.8 + - + -
92E ASN* 2.8 52.1 + - + +
400E NAP 3.2 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E CYS* 3.9 16.2 - - - +
80E SER 3.9 11.0 - - - +
83E GLU* 3.4 48.5 - - + +
85E ASP 2.9 15.5 + - - +
86E GLY* 3.7 8.5 - - - +
88E TYR* 1.3 80.4 - - - +
90E MET* 1.3 56.6 + - + +
92E ASN* 5.0 0.4 - - - -
93E ASN* 2.9 61.8 + - - +
139E VAL* 3.8 14.8 - - + +
140E PHE* 3.9 16.6 - - - +
143E SER* 3.6 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.7 20.2 - - + -
50A TYR* 4.2 27.8 - - + -
86E GLY* 2.8 24.1 + - - +
87E LYS* 4.1 3.1 - - - +
89E MET* 1.3 72.7 - - - +
91E ASP* 1.3 58.1 + - - +
94E TYR* 3.2 29.1 + - + +
95E GLN* 2.8 29.6 + - - +
139E VAL* 5.0 4.3 - - - -
142E TYR* 4.1 21.5 - - + -
143E SER* 3.9 23.3 - - - -
146E LEU* 3.7 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 5.2 4.6 - - - +
55A ASP* 4.2 14.5 - - - +
87E LYS* 3.0 40.8 + - - +
88E TYR* 3.1 6.8 + - + +
90E MET* 1.3 76.6 - - - +
92E ASN* 1.3 60.2 - - + +
95E GLN* 3.3 17.9 - - - +
96E TYR* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E LYS* 2.7 29.5 + - - +
74E HIS* 5.7 0.5 + - - -
76E GLY 5.0 1.0 - - - +
77E ALA* 4.9 1.2 - - - -
78E CYS* 3.2 8.7 - - - +
88E TYR* 2.8 47.4 + - + +
89E MET* 4.4 0.7 - - - +
91E ASP* 1.3 75.7 - - + +
93E ASN* 1.3 71.4 + - - +
96E TYR* 3.0 24.1 - - - +
400E NAP 2.9 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E HIS* 4.9 0.2 + - - -
77E ALA* 3.4 13.3 - - + +
78E CYS* 2.8 46.2 + - - +
89E MET* 2.9 29.0 + - - +
92E ASN* 1.3 83.5 + - - +
94E TYR* 1.3 63.8 + - - +
95E GLN 3.7 0.2 - - - -
97E SER* 2.8 32.3 + - - -
140E PHE* 4.0 8.3 - - - -
143E SER* 3.2 28.7 + - - +
144E LYS* 4.6 6.7 - - + +
147E PHE* 6.0 0.4 - - - -
----------------------------------------------------------
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