Contacts of the helix formed by residues 69 - 79 (chain J) 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 GLY 69 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J ALA* 1.3 68.2 - - - +
70J SER* 1.3 67.4 + - - -
71J ALA 3.2 2.5 - - - -
72J ALA* 2.7 21.4 + - - +
73J THR 2.7 9.2 + - - -
152J ASP* 3.3 10.8 - - - -
153J ASP* 3.5 13.9 - - - -
216J SER* 5.2 2.0 + - - -
217J MET* 3.9 10.6 - - - +
702J WO4 3.1 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 70 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40J ALA* 3.6 2.0 - - - +
68J ALA 3.1 4.9 + - - -
69J GLY* 1.3 68.5 - - - -
71J ALA* 1.3 64.5 + - - +
73J THR* 3.1 6.8 + - - -
74J ILE* 2.7 31.1 + - - +
89J THR* 3.0 23.3 - - - -
90J ALA 2.9 24.3 + - - -
94J LEU* 3.5 5.4 - - - -
154J PRO* 3.5 19.0 - - - +
702J WO4 2.6 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J GLY 2.9 1.6 + - - -
70J SER* 1.3 75.0 - - - +
72J ALA* 1.3 55.1 + - - +
74J ILE* 3.1 3.8 + - - +
75J ARG* 2.9 40.8 + - - +
94J LEU* 3.8 14.0 - - + +
98J MET* 3.9 17.8 - - + +
150J PRO 5.2 0.2 - - - +
151J ASN 3.4 20.6 - - - +
152J ASP 2.9 19.1 + - - +
153J ASP* 5.2 0.7 - - - -
154J PRO* 5.5 0.2 - - + -
157J TYR* 5.9 0.2 - - + -
272J LEU* 4.7 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J ALA* 4.6 6.7 - - + -
69J GLY 2.7 19.4 + - - +
71J ALA* 1.3 71.8 - - - +
73J THR* 1.3 57.8 + - - +
75J ARG* 2.7 37.5 + - - +
76J LYS* 3.1 13.9 + - - +
152J ASP* 3.2 25.0 + - + +
216J SER* 5.0 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J PHE* 3.9 35.3 - - + +
39J HIS* 3.2 18.4 + - - +
66J GLU 3.8 1.7 + - - -
68J ALA* 2.5 41.5 + - - +
69J GLY 2.7 9.3 + - - -
70J SER* 3.5 11.0 - - - +
72J ALA* 1.3 72.3 - - - +
74J ILE* 1.3 64.7 + - + +
76J LYS* 3.3 23.6 + - - +
77J VAL 4.1 0.7 + - - -
87J ILE* 4.2 15.1 - - + +
88J ALA 4.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J SER 2.7 24.4 + - - +
71J ALA 3.5 4.5 - - - +
73J THR* 1.3 70.1 - - + +
75J ARG* 1.3 57.7 + - - +
76J LYS 3.0 5.4 - - - -
77J VAL* 3.0 22.3 + - + +
78J THR* 3.2 11.6 + - - +
87J ILE* 4.2 20.4 - - + -
89J THR* 4.0 11.4 - - + -
94J LEU* 3.8 41.5 - - + +
95J ILE* 3.9 7.2 - - + +
98J MET* 4.1 19.7 - - + +
99J MET* 3.4 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H LEU 4.7 6.0 + - - +
223H SER* 3.6 29.8 + - - +
71J ALA* 2.9 20.9 + - - +
72J ALA* 2.7 25.9 + - - +
74J ILE* 1.3 69.7 - - - +
76J LYS* 1.3 59.0 + - - -
77J VAL 3.1 0.2 - - - -
78J THR* 3.4 9.4 - - + +
79J GLU* 2.6 42.4 + - + +
80J LEU* 3.2 6.5 + - - +
98J MET* 3.5 27.9 - - + +
151J ASN* 2.4 32.3 + - - +
152J ASP* 3.1 19.2 + - - +
274J ASN* 3.8 22.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H LEU* 6.1 2.7 - - - -
208I TYR* 5.9 3.1 - - - -
38J PHE* 3.5 31.8 - - + -
66J GLU* 3.0 41.4 + - - +
67J ALA 3.9 3.6 + - - -
68J ALA* 3.6 30.4 - - - +
72J ALA 3.1 7.0 + - - +
73J THR* 3.4 13.1 + - - +
74J ILE 3.0 1.0 - - - -
75J ARG* 1.3 77.4 - - - +
77J VAL* 1.3 58.8 + - - +
80J LEU* 3.2 33.2 - - + +
81J GLY 3.0 24.4 + - - -
82J ARG* 3.3 16.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J PHE* 4.4 5.4 - - + -
73J THR 4.9 0.2 - - - +
74J ILE* 3.0 11.0 + - + +
76J LYS* 1.3 79.6 - - - +
78J THR* 1.3 58.6 + - - +
81J GLY* 3.9 9.9 - - - +
82J ARG 3.6 16.8 - - - +
83J LYS* 5.8 0.9 - - - -
84J ALA* 4.2 16.8 - - + +
87J ILE* 4.0 29.4 - - + -
99J MET* 4.7 9.2 - - + -
103J PHE* 3.4 47.9 - - + -
290J PRO* 4.9 8.7 - - + -
292J ASN* 4.7 5.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 78 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J ILE* 3.2 10.4 + - - +
75J ARG* 3.0 17.0 + - + -
77J VAL* 1.3 80.4 - - - +
79J GLU* 1.3 86.5 + - + +
81J GLY* 3.9 6.0 + - - -
98J MET* 4.1 13.1 + - - +
99J MET* 5.6 0.2 - - - +
103J PHE* 3.7 31.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222H LEU 4.3 6.1 - - - +
223H SER 3.5 20.0 - - - +
224H GLU* 3.4 28.4 - - - +
225H GLY* 3.3 18.9 - - - +
226H LEU 4.4 1.9 + - - -
75J ARG* 2.6 27.6 + - - +
78J THR* 1.3 92.4 - - + +
80J LEU* 1.3 61.2 + - - +
81J GLY 3.3 1.5 + - - -
----------------------------------------------------------
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