Contacts of the helix formed by residues 99 - 113 (chain A) in PDB entry 2ONK
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 GLU 99 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASN 4.5 0.2 + - - -
98A VAL* 1.3 78.9 - - + +
100A ARG* 1.3 75.5 + - - +
101A VAL* 2.7 32.6 + - - +
102A GLU* 2.7 34.7 + - + +
103A ARG* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL 3.5 1.9 + - - -
99A GLU* 1.3 80.6 + - - +
101A VAL* 1.3 68.8 + - + +
103A ARG* 2.8 35.9 + - - +
104A ASP* 2.9 14.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 2.7 21.6 + - - +
100A ARG* 1.3 82.5 - - + +
102A GLU* 1.3 56.0 + - - +
104A ASP* 3.3 9.2 + - + +
105A ARG* 2.9 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 3.4 10.5 - - + -
99A GLU* 2.7 31.8 + - + +
100A ARG 3.1 0.2 - - - -
101A VAL* 1.3 73.2 - - - +
103A ARG* 1.3 57.5 + - - +
105A ARG* 2.8 47.4 + - - +
106A ARG* 2.9 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 5.9 0.2 - - - +
92A ALA* 4.4 15.1 + - + +
95A LEU* 2.9 42.1 - - + +
96A ARG* 3.2 62.1 + - - +
98A VAL* 3.3 27.5 + - + -
99A GLU 2.8 8.3 + - - +
100A ARG* 2.8 20.9 + - - +
102A GLU* 1.3 75.9 - - - +
104A ASP* 1.3 58.1 + - - +
105A ARG 3.2 0.3 + - - -
106A ARG* 3.2 6.3 + - - +
107A VAL* 2.8 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 2.7 29.0 + - - +
100A ARG* 2.9 12.7 + - + +
101A VAL* 3.6 13.2 - - + +
103A ARG* 1.3 76.2 - - - +
105A ARG* 1.3 66.6 + - - +
107A VAL* 3.6 2.6 - - - +
108A ARG* 2.7 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 2.9 16.0 + - + +
102A GLU* 2.8 47.6 + - - +
104A ASP* 1.3 79.3 - - - +
106A ARG* 1.3 63.9 + - - +
108A ARG* 3.7 3.0 - - - +
109A GLU* 2.7 68.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 4.3 13.7 - - + +
98A VAL* 3.6 37.1 - - - +
102A GLU* 2.9 50.1 + - - +
103A ARG 3.6 5.2 - - - +
105A ARG* 1.3 82.2 - - - +
107A VAL* 1.3 57.3 + - - +
109A GLU* 3.4 11.9 - - - +
110A MET* 2.9 33.6 + - - +
142A VAL* 3.7 23.5 + - + +
144A GLN* 3.0 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 3.7 34.5 - - + +
91A ILE* 4.0 28.0 - - + +
92A ALA* 3.9 30.5 - - + +
95A LEU* 4.0 9.9 - - + -
103A ARG* 2.8 33.6 + - + +
104A ASP* 3.6 7.2 - - - +
105A ARG 3.0 0.2 + - - -
106A ARG* 1.3 72.4 - - - +
108A ARG* 1.3 53.9 + - - +
110A MET* 3.1 4.7 + - - +
111A ALA* 2.7 34.7 + - - +
120A LEU* 4.6 7.0 - - + -
142A VAL* 4.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 4.0 18.5 - - + -
104A ASP* 2.7 50.4 + - - +
105A ARG* 3.9 2.2 - - - +
107A VAL* 1.3 79.2 - - - +
109A GLU* 1.3 63.8 + - - +
111A ALA* 3.5 8.0 - - - +
112A GLU* 2.9 26.8 + - - +
117A ALA* 4.7 4.1 - - + +
120A LEU* 3.9 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 2.7 57.1 + - + +
106A ARG* 3.4 10.9 - - - +
108A ARG* 1.3 74.2 - - - +
110A MET* 1.3 62.0 + - - +
112A GLU* 3.2 7.0 + - - +
113A LYS* 2.9 57.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 5.0 2.2 - - + -
106A ARG 2.9 17.2 + - - +
107A VAL 3.7 2.7 - - - +
109A GLU* 1.3 75.5 - - - +
111A ALA* 1.3 65.6 + - - +
112A GLU 3.0 2.0 - - - -
113A LYS* 3.6 19.5 - - + -
114A LEU* 3.1 44.6 + - + +
116A ILE* 4.8 0.3 - - - +
138A ALA* 4.1 10.5 - - + +
141A LEU* 3.6 32.3 - - - -
142A VAL* 3.6 28.0 - - + -
176A PHE* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ILE* 4.5 5.3 - - + +
107A VAL 2.7 20.4 + - - +
108A ARG* 3.2 9.2 + - - +
110A MET* 1.3 72.7 - - - +
112A GLU* 1.3 57.0 + - - +
115A GLY 3.3 2.9 + - - -
116A ILE* 2.8 46.0 + - + +
117A ALA* 2.9 23.5 + - + +
120A LEU* 3.7 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG 2.9 16.4 + - - +
109A GLU* 3.5 5.6 - - - +
111A ALA* 1.3 75.7 - - - +
113A LYS* 1.3 58.2 + - + +
114A LEU 2.8 11.2 + - - -
115A GLY* 3.0 13.0 + - - +
117A ALA* 4.1 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A GLU* 2.9 49.4 + - + +
110A MET* 3.3 21.0 + - + +
112A GLU* 1.3 75.4 - - + +
114A LEU* 1.3 66.3 + - - +
171A PHE* 5.7 5.4 - - - -
175A GLU* 5.4 6.6 + - + +
176A PHE* 4.0 31.3 - - + -
----------------------------------------------------------
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