Contacts of the helix formed by residues 79 - 90 (chain E) in PDB entry 2XQL
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 ILE 79 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ASN* 5.7 4.3 - - - +
75E LYS* 4.1 25.4 - - + +
77E ARG* 4.4 13.5 - - + +
78E ILE* 1.3 77.2 - - - +
80E PRO* 1.3 66.7 - - + +
81E ARG* 4.2 18.2 - - + +
82E HIS* 2.7 53.1 + - + +
83E LEU 3.5 2.4 + - - -
55F SER* 3.7 20.4 - - - +
58F ALA* 4.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ILE* 1.3 90.0 - - + -
81E ARG* 1.3 62.9 + - - +
83E LEU* 2.8 11.4 + - + +
84E GLN* 2.8 23.0 + - - +
102E ILE* 4.1 1.4 - - - +
103E ALA 3.5 14.6 - - - +
104E GLN* 3.6 14.4 - - + +
105E GLY* 4.2 3.8 - - - +
55F SER* 3.7 4.5 - - - +
57F LYS* 4.1 17.3 - - + -
58F ALA* 3.7 21.0 - - + +
61F ILE* 3.4 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C LEU* 5.8 3.0 - - - +
68C ASN* 5.6 10.6 - - - +
72C ASP* 5.6 5.3 + - - -
89C ASN* 4.4 32.5 + - - +
73E ASN* 5.7 3.4 - - - +
79E ILE* 2.9 20.9 + - + +
80E PRO* 1.3 77.0 - - - +
82E HIS* 1.3 62.9 + - + +
84E GLN* 3.4 9.0 + - - +
85E LEU* 2.8 63.4 + - + +
104E GLN 3.9 6.8 + - - +
105E GLY 3.3 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E ALA* 3.7 19.0 - - - +
69E ALA* 3.9 16.9 + - + +
70E ALA* 3.7 29.1 + - + -
73E ASN* 4.2 22.4 - - + -
75E LYS* 4.6 10.8 - - + +
77E ARG 3.9 6.1 + - - -
78E ILE* 3.6 17.0 - - + -
79E ILE* 2.7 54.1 + - + +
81E ARG* 1.3 76.0 - - + +
83E LEU* 1.3 66.0 + - - +
85E LEU* 3.8 6.2 - - - +
86E ALA* 2.7 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ILE* 4.6 10.8 - - + +
63E LEU* 4.8 3.4 - - + -
66E ALA* 3.7 21.8 - - + -
78E ILE* 4.3 11.2 - - + -
79E ILE 3.5 0.2 + - - -
80E PRO* 2.8 8.6 + - + +
82E HIS* 1.3 75.9 - - - +
84E GLN* 1.3 54.2 + - - +
86E ALA* 3.2 4.0 - - - +
87E ILE* 2.7 49.9 + - + +
102E ILE* 4.7 2.2 - - + -
54F ILE* 5.3 0.7 - - + -
58F ALA* 3.6 27.1 - - + +
61F ILE* 3.5 39.3 - - + -
62F MET* 4.0 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ASN 3.8 20.1 + - - +
90C ASP* 3.8 11.9 + - - +
91C GLU 3.8 14.8 - - - +
80E PRO 2.8 10.7 + - - +
81E ARG* 3.4 11.4 - - - +
83E LEU* 1.3 76.9 - - - +
85E LEU* 1.3 67.1 + - - +
86E ALA 2.9 1.0 + - - -
87E ILE* 2.9 1.7 + - - +
88E ARG* 2.8 68.6 + - + +
102E ILE* 3.5 16.6 + - + +
105E GLY* 3.1 36.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ALA* 4.6 12.1 - - + -
73E ASN* 4.6 13.5 - - - +
81E ARG* 2.8 64.9 + - + +
82E HIS* 3.8 13.7 - - + +
84E GLN* 1.3 74.4 - - - +
86E ALA* 1.3 60.9 + - - +
88E ARG* 4.1 3.8 - - - -
89E ASN* 3.1 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ILE* 4.5 3.6 - - + +
65E LEU* 3.8 19.4 - - + +
66E ALA* 3.7 29.4 - - + +
69E ALA* 5.0 2.9 - - + +
82E HIS 2.7 23.2 + - - +
83E LEU* 3.2 5.4 - - - +
84E GLN 2.9 0.2 + - - -
85E LEU* 1.3 71.0 - - - +
87E ILE* 1.3 68.0 + - + +
89E ASN* 3.3 4.4 + - - +
90E ASP* 3.2 23.2 + - - +
93E LEU* 5.3 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ILE* 4.9 20.4 - - + -
83E LEU* 2.7 31.4 + - + +
84E GLN 3.6 2.7 - - - +
86E ALA* 1.3 75.3 - - + +
88E ARG* 1.3 74.6 + - - +
90E ASP 3.0 22.3 - - - +
93E LEU* 3.9 20.3 - - + +
94E ASN* 3.3 8.6 + - - -
97E LEU* 3.6 43.1 - - + -
102E ILE* 3.9 29.2 - - + -
61F ILE* 5.9 1.1 - - + -
65F PHE* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ASN 5.4 3.8 - - - +
91C GLU* 2.6 44.1 + - + +
84E GLN* 2.8 63.8 + - + +
85E LEU* 4.4 4.3 - - - +
87E ILE* 1.3 86.1 - - - +
89E ASN* 1.3 66.1 + - - +
90E ASP 3.7 4.3 + - - +
91E GLU* 4.9 0.7 + - - -
94E ASN* 3.0 33.0 - - - +
97E LEU 2.5 31.9 + - - -
100E VAL* 3.5 16.2 + - - +
102E ILE* 3.9 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E LEU* 3.1 32.6 + - - +
86E ALA* 3.3 2.9 + - - +
88E ARG* 1.3 82.1 + - - +
90E ASP* 1.3 63.6 + - - +
91E GLU* 3.3 4.6 + - - +
81G ARG* 4.4 30.1 + - - +
84G GLN* 3.8 10.6 + - - +
88G ARG* 5.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLU* 5.3 2.1 - - - +
65E LEU* 4.9 12.3 - - + +
86E ALA 3.2 12.5 + - - +
87E ILE 3.0 14.6 - - - +
88E ARG 4.3 0.2 - - - -
89E ASN* 1.3 72.8 - - - +
91E GLU* 1.3 64.7 + - - +
92E GLU* 2.9 20.7 + - - +
93E LEU* 3.2 45.7 + - + +
94E ASN* 3.1 10.9 + - - +
106F LEU* 5.0 1.6 - - - +
84G GLN* 3.8 13.7 + - - +
88G ARG* 5.8 0.2 + - - -
101G THR* 4.4 10.8 - - - +
102G ILE 4.9 9.0 + - - +
105G GLY 5.4 6.5 - - - -
----------------------------------------------------------
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