Contacts of the strand formed by residues 81 - 90 (chain C) in PDB entry 2WUB
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 GLN 81 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C VAL* 3.4 0.8 - - - -
68C LEU* 2.8 36.1 + - + +
79C VAL 4.0 7.0 + - - +
80C THR* 1.3 76.7 - - - +
82C THR* 1.3 61.2 + - - +
83C PHE* 3.1 27.9 - - + -
111C LYS* 4.3 4.2 + - - +
112C ALA* 3.6 6.8 - - - -
113C THR* 2.9 58.0 + - - +
115C SER* 4.8 5.3 - - - -
118C VAL* 3.2 26.1 - - + +
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Residues in contact with THR 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C SER* 3.6 21.5 - - - +
66C VAL 3.5 3.6 - - - -
67C VAL* 3.2 23.9 - - + +
76C THR* 5.4 5.7 - - - -
80C THR* 4.0 5.1 + - - -
81C GLN* 1.3 72.5 - - - +
83C PHE* 1.3 64.6 + - - +
111C LYS* 3.1 22.8 + - - +
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Residues in contact with PHE 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C SER* 3.4 9.7 + - - -
66C VAL* 2.6 40.3 + - - +
68C LEU* 3.9 18.6 - - + -
81C GLN* 3.1 44.2 - - + -
82C THR* 1.3 76.9 - - - +
84C GLY* 1.3 65.3 + - - +
108C LEU* 4.3 19.7 - - + -
109C LYS* 3.6 17.7 - - + -
111C LYS* 3.4 67.5 - - + -
112C ALA* 3.6 11.9 - - + -
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C VAL 4.0 7.2 - - - -
65C SER* 5.0 0.2 - - - -
83C PHE* 1.3 76.5 - - - +
85C ILE* 1.3 62.2 + - - -
108C LEU* 3.7 2.6 - - - -
109C LYS* 2.8 44.9 + - - +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C PHE* 5.4 0.4 - - + -
61C ARG* 3.4 49.6 + - + +
64C VAL* 3.6 41.6 + - + +
66C VAL* 3.8 14.6 - - + -
84C GLY* 1.3 76.6 - - - -
86C GLU* 1.3 60.0 + - - +
87C LYS 4.0 7.2 - - - +
88C TYR* 3.8 19.3 - - + -
106C ILE* 3.6 23.8 - - + -
107C ARG 3.6 8.3 - - - +
108C LEU* 4.4 2.0 - - + +
109C LYS* 3.6 15.2 - - - -
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Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ARG* 3.6 18.8 + - - -
84C GLY 4.0 0.4 + - - -
85C ILE* 1.3 73.2 - - - +
87C LYS* 1.3 76.7 - - + +
107C ARG* 2.7 33.7 + - - +
108C LEU 3.8 15.7 - - - +
109C LYS* 3.2 33.8 - - + +
110C LYS 5.2 0.7 - - - +
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Residues in contact with LYS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ARG* 3.6 11.0 - - - +
85C ILE* 3.4 5.1 - - - -
86C GLU* 1.3 94.6 - - + +
88C TYR* 1.3 59.4 + - - +
89C ILE* 4.1 22.2 - - + -
105C LEU 3.9 0.4 - - - +
106C ILE* 3.6 6.6 - - - +
107C ARG* 3.0 52.8 + - + +
54R GLY 2.8 20.0 - - - +
55R GLY* 3.1 22.1 + - - +
56R ALA* 5.0 0.6 - - - +
57R THR* 5.4 6.1 + - - -
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Residues in contact with TYR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C PHE* 3.5 40.2 - + + -
60C PRO* 2.8 51.5 - + - +
61C ARG* 3.8 9.4 - - + -
64C VAL* 5.2 0.9 - - + -
85C ILE* 3.8 18.4 - - + -
87C LYS* 1.3 73.0 - - - +
89C ILE* 1.3 62.0 + - - +
90C PRO* 3.4 6.7 - - + +
104C VAL* 4.0 14.6 - - + -
105C LEU 3.6 3.6 - - - -
106C ILE* 4.4 10.1 - - + +
52R TYR* 3.5 28.5 - + - -
53R ALA* 3.4 16.5 - - - +
54R GLY* 2.9 37.6 + - - +
56R ALA* 3.8 2.3 - - - +
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TRP* 4.0 28.9 - - + -
87C LYS* 4.1 21.1 - - + -
88C TYR* 1.3 78.6 - - - +
90C PRO* 1.3 67.8 - - - +
104C VAL* 3.4 4.0 - - - +
105C LEU* 2.8 39.7 + - + +
107C ARG* 5.4 1.3 - - - +
237C TRP* 3.9 7.5 - - + -
241C ARG* 4.1 34.1 - - - +
56R ALA* 3.6 15.7 - - + -
58R TYR* 3.3 28.3 - - + +
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Residues in contact with PRO 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 4.4 12.1 - - + +
59C PHE* 5.8 2.0 - - + -
88C TYR* 3.4 13.2 - - + +
89C ILE* 1.3 86.9 - - - +
91C TYR* 1.3 67.5 + - - +
92C THR 3.4 1.2 + - - -
94C TYR* 4.4 7.4 - - + -
103C LEU 3.7 6.7 - - - +
104C VAL* 3.9 10.8 - - + -
237C TRP* 3.5 7.3 - - - -
33R TYR* 3.5 27.4 - - + +
52R TYR* 3.6 26.0 - - + -
56R ALA* 4.4 0.2 - - + -
58R TYR* 2.7 30.8 + - - +
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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