Contacts of the strand formed by residues 67 - 72 (chain H) in PDB entry 2OK0
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 ALA 67 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H ILE* 3.8 26.0 - - + -
59H TYR* 3.1 23.7 - - + -
63H PHE* 3.0 13.3 + - + +
64H LYS 3.7 12.1 - - - +
65H ASP 5.0 0.2 - - - -
66H LYS* 1.3 80.0 - - - +
68H THR* 1.3 64.4 + - - +
69H LEU* 4.7 1.1 - - + -
80H MET* 4.2 6.7 - - + -
81H HIS 3.1 5.8 - - - +
82H LEU* 3.8 17.0 - - + -
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Residues in contact with THR 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H TYR* 3.4 8.7 - - - +
66H LYS 5.2 0.3 + - - -
67H ALA* 1.3 76.5 + - - +
69H LEU* 1.3 70.2 + - - +
70H THR* 4.1 13.8 + - + +
79H TYR 3.7 0.7 - - - +
80H MET* 3.4 1.9 - - - -
81H HIS* 2.7 56.7 + - + +
82H SER* 5.7 0.9 - - - +
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Residues in contact with LEU 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H TRP* 3.4 23.3 - - + +
48H ILE* 4.8 1.3 - - + -
49H GLY* 3.7 28.0 - - - +
50H TRP 3.6 24.2 - - - +
51H VAL* 3.7 16.8 - - + -
57H ILE* 3.4 23.6 - - + +
58H LYS 4.3 0.7 - - - +
59H TYR* 2.9 27.7 + - + -
67H ALA* 4.7 3.1 - - + -
68H THR* 1.3 73.3 - - - +
70H THR* 1.3 69.7 + - - +
79H TYR 3.3 2.2 - - - +
80H MET* 3.4 37.5 - - + -
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Residues in contact with THR 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H LYS* 4.5 7.5 + - - -
51H VAL* 3.7 5.7 - - - +
57H ILE* 4.9 3.1 - - + -
68H THR* 4.4 15.8 + - + +
69H LEU* 1.3 81.2 - - - +
71H ALA* 1.3 62.8 + - - +
78H VAL* 3.2 6.8 - - - +
79H TYR* 2.8 53.9 + - - +
81H HIS* 6.6 0.2 - - + -
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Residues in contact with ALA 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H PHE* 4.5 10.3 - - + -
51H VAL* 3.7 13.9 - - + +
52H PRO* 4.7 20.4 - - + +
57H ILE* 5.6 0.6 - - - +
70H THR* 1.3 77.5 - - - +
72H ASP* 1.3 61.9 + - - +
73H THR* 3.7 6.5 + - + +
77H ILE 3.6 4.5 - - - -
78H VAL* 3.7 17.7 - - + -
79H TYR* 5.3 0.7 - - - -
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Residues in contact with ASP 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H PHE* 4.5 1.3 - - - -
71H ALA* 1.3 73.6 - - - +
73H THR* 1.3 56.7 + - - +
74H SER* 3.3 22.5 + - - -
75H SER* 2.7 26.1 + - - +
76H SER 2.8 23.0 + - - -
77H ILE* 2.6 27.3 + - + +
79H TYR* 4.2 13.6 + - + -
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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