Contacts of the helix formed by residues 85 - 93 (chain R) 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 R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R GLU* 2.9 22.5 + - - +
84R TRP* 1.3 74.2 - - - +
86R GLY* 1.3 57.2 + - - +
87R LYS* 2.9 12.1 + - - +
88R TYR* 2.7 32.7 + - + +
89R MET* 2.9 28.7 + - - +
34S LYS* 3.2 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84R TRP 3.0 8.5 + - - -
85R ASP* 1.3 70.9 + - - +
87R LYS* 1.3 60.8 + - - +
89R MET* 4.1 1.6 - - - -
90R MET* 2.8 36.0 + - - +
139R VAL* 4.1 24.5 - - - -
33S LEU* 2.9 25.1 + - - -
34S LYS 3.3 1.0 + - - -
36S GLY* 4.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85R ASP* 2.9 8.4 + - - +
86R GLY* 1.3 77.3 - - - +
88R TYR* 1.3 63.3 + - - +
90R MET* 4.0 2.7 - - - +
91R ASP* 3.0 45.3 + - - +
32S ASN* 4.2 10.3 - - - +
33S LEU* 3.3 11.1 + - - +
34S LYS* 3.9 22.7 - - + +
50S TYR* 6.5 0.4 - - - -
52S ASP* 3.6 37.4 + - + +
54S GLU* 5.4 5.3 - - - +
55S ASP* 5.6 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R LYS* 3.0 25.9 + - - -
78R CYS* 3.6 30.3 - - + -
83R GLU* 4.6 14.4 - - + -
85R ASP* 2.7 30.1 + - + +
87R LYS* 1.3 73.9 - - - +
89R MET* 1.3 67.4 + - - +
91R ASP* 3.1 6.5 + - + +
92R ASN* 2.8 52.3 + - + +
400R NAP 3.3 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78R CYS* 3.9 16.2 - - - +
80R SER 3.9 10.1 - - - +
83R GLU* 3.4 48.7 - - + +
85R ASP 2.9 15.1 + - - +
86R GLY* 3.3 8.7 + - - +
88R TYR* 1.3 80.4 - - - +
90R MET* 1.3 58.4 + - - +
92R ASN* 5.0 0.4 - - - -
93R ASN* 2.9 60.5 + - - +
139R VAL* 3.8 13.9 - - + +
140R PHE* 3.9 15.9 - - - +
143R SER* 3.6 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 90 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R GLY* 2.8 24.7 + - - +
87R LYS* 4.1 2.9 - - - +
89R MET* 1.3 73.4 - - + +
91R ASP* 1.3 58.4 + - - +
94R TYR* 3.2 28.0 + - + +
95R GLN* 2.8 29.2 + - - +
139R VAL* 5.0 4.3 - - - -
142R TYR* 4.1 20.9 - - + -
143R SER* 3.9 23.1 - - - -
146R LEU* 3.6 32.5 - - + -
33S LEU* 3.7 19.7 - - + -
50S TYR* 4.1 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 91 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57R LEU* 6.2 0.2 - - - +
87R LYS* 3.0 42.1 + - - +
88R TYR* 3.7 6.6 - - + +
90R MET* 1.3 77.0 - - - +
92R ASN* 1.3 60.3 + - + +
95R GLN* 3.3 18.7 - - - +
96R TYR* 2.9 31.4 + - - +
52S ASP* 5.2 4.3 - - - +
55S ASP* 4.1 16.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R LYS* 2.8 30.0 + - - +
74R HIS* 5.7 0.3 + - - -
76R GLY 5.1 0.7 - - - +
77R ALA* 4.9 0.9 - - - -
78R CYS* 3.2 7.9 - - - +
88R TYR* 2.8 46.6 + - + +
89R MET 4.4 0.2 - - - +
91R ASP* 1.3 75.6 - - + +
93R ASN* 1.3 72.8 + - - +
96R TYR* 3.0 23.4 - - - +
400R NAP 2.9 35.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77R ALA* 3.4 13.2 - - + +
78R CYS* 2.8 46.8 + - - -
89R MET* 2.9 29.6 + - - +
92R ASN* 1.3 84.6 + - - +
94R TYR* 1.3 63.9 + - - +
97R SER* 2.8 33.5 + - - -
140R PHE* 4.0 7.9 - - - -
143R SER* 3.2 29.0 + - - +
144R LYS* 4.6 7.0 - - + +
147R PHE* 6.0 0.7 - - - -
----------------------------------------------------------
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