Contacts of the strand formed by residues 62 - 67 (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 GLU 62 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49I LYS* 3.8 29.8 + - - +
209I TYR* 4.7 9.0 - - - -
32J ASN* 5.0 2.5 - - - +
33J VAL 3.3 4.8 + - - -
34J LYS* 3.3 31.8 + - + +
35J LEU 2.9 23.9 + - - -
51J LYS* 4.2 7.4 - - - +
55J GLU* 2.9 10.1 - - - +
61J VAL* 1.3 76.7 - - - +
63J VAL* 1.3 64.8 + - - +
64J GLN* 3.6 21.3 + - - +
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Residues in contact with VAL 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209I TYR* 5.5 0.2 + - - -
35J LEU* 3.6 18.6 - - + +
37J VAL* 4.2 18.4 - - + -
47J MET* 6.2 0.2 - - - -
51J LYS* 2.5 40.6 + - + +
54J PHE* 3.5 40.4 - - + -
55J GLU* 2.8 21.0 + - + -
61J VAL* 4.9 0.9 - - + +
62J GLU* 1.3 73.4 - - - +
64J GLN* 1.3 61.6 + - - +
65J THR* 3.6 16.5 + - + +
302J PHE* 4.5 12.8 - - + -
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Residues in contact with GLN 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209I TYR* 3.5 52.6 - - + +
34J LYS* 3.0 42.8 + - + +
35J LEU 2.7 15.2 + - - +
36J LYS* 3.2 31.3 - - + +
37J VAL* 2.9 28.8 + - - +
38J PHE* 5.0 2.4 - - - -
62J GLU* 3.9 19.3 - - - +
63J VAL* 1.3 70.1 - - - +
65J THR* 1.3 63.5 + - - +
66J GLU* 5.0 0.7 - - - +
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Residues in contact with THR 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209I TYR* 3.2 19.7 + - - -
219I GLU* 4.2 13.9 + - - +
37J VAL* 3.4 7.4 - - + -
39J HIS* 3.9 14.9 + - + -
47J MET* 4.7 24.0 - - + +
48J LYS* 6.0 0.7 - - - -
51J LYS* 4.5 15.9 - - + -
63J VAL* 3.6 19.6 + - + +
64J GLN* 1.3 73.6 - - - +
66J GLU* 1.3 73.8 + - - +
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Residues in contact with GLU 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208I TYR* 4.7 17.3 - - + +
209I TYR* 3.6 18.6 - - + -
219I GLU* 4.9 5.6 - - - +
36J LYS* 5.7 0.3 - - - +
37J VAL 3.2 6.9 + - - -
38J PHE* 3.1 29.1 - - + -
39J HIS* 3.1 26.2 + - - +
64J GLN* 5.0 0.9 - - - +
65J THR* 1.3 85.0 - - - +
67J ALA* 1.3 66.6 + - - +
73J THR* 3.8 3.8 + - - -
76J LYS* 3.0 27.2 + - - +
82J ARG* 2.5 45.7 + - - -
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Residues in contact with ALA 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I GLU* 5.3 6.2 + - + +
223I SER* 3.4 21.3 + - - +
39J HIS* 3.6 13.7 + - + -
40J ALA 4.5 0.2 - - - -
41J GLY* 4.2 1.1 - - - -
44J THR* 3.9 15.9 - - + +
65J THR* 5.5 0.2 + - - -
66J GLU* 1.3 70.0 - - - +
68J ALA* 1.3 67.7 + - - +
76J LYS* 3.9 4.0 + - - -
217J MET* 3.2 29.3 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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