Contacts of the strand formed by residues 88 - 95 (chain R) 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 ALA 88 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38R ARG* 4.1 13.0 - - + -
39R GLN 3.5 10.3 - - - +
40R ALA* 3.4 26.9 - - + +
41R PRO* 4.2 5.6 - - - -
85R GLU 5.5 0.4 - - - +
86R ASP 3.2 8.5 + - - +
87R THR* 1.3 78.7 - - - +
89R VAL* 1.3 63.4 + - - +
90R TYR* 3.3 10.1 - - + -
108R LEU* 3.8 9.0 - - - -
109R VAL 2.8 30.2 + - - +
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Residues in contact with VAL 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37R VAL 4.0 0.2 - - - +
38R ARG* 3.2 3.3 - - - -
39R GLN* 3.0 37.3 + - + +
41R PRO* 6.4 1.1 - - + -
88R ALA* 1.3 73.7 - - - +
90R TYR* 1.3 63.0 + - - +
91R TYR* 3.8 38.1 + - + +
105R GLN 4.7 1.6 - - - +
106R GLY* 4.3 2.9 - - - -
107R THR 3.6 18.6 - - - +
108R LEU* 3.6 25.4 - - + +
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Residues in contact with TYR 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6R GLU* 3.7 4.9 - - - +
20R LEU* 3.6 21.3 - - + -
36R TRP* 4.2 7.2 - + + -
37R VAL 3.9 1.8 - - - -
38R ARG* 2.6 52.8 + - + -
48R VAL* 4.0 11.9 - - + -
67R PHE* 4.4 2.9 - + - -
80R LEU* 3.9 22.2 - - + -
82R MET* 3.3 28.4 - - + +
86R ASP* 2.6 24.4 + - - -
88R ALA* 3.3 20.9 - - + -
89R VAL* 1.3 73.8 - - - +
91R TYR* 1.3 61.4 + - - +
106R GLY* 3.3 1.9 - - - -
107R THR* 2.9 36.8 + - - +
109R VAL* 3.5 15.0 - - + -
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Residues in contact with TYR 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Q GLN* 3.2 23.2 + - - -
41Q GLY* 5.5 1.6 - - - -
42Q LYS 3.6 6.1 + - - -
43Q ALA* 3.9 14.6 - - + -
44Q PRO* 4.3 2.2 - - + -
6R GLU* 3.0 6.5 - - - +
36R TRP* 3.3 9.4 - - - -
37R VAL* 2.8 41.9 + - - +
39R GLN* 3.4 27.0 + - + -
45R LEU* 4.3 9.6 - - + -
89R VAL* 3.8 23.3 - - + +
90R TYR* 1.3 73.4 - - - +
92R CYS* 1.3 61.2 + - - +
103R TRP* 3.6 30.1 - + + -
104R GLY 3.3 20.6 - - - +
105R GLN 3.4 21.0 + - - -
106R GLY* 3.6 10.3 - - - -
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Residues in contact with CYS 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4R LEU* 3.4 16.1 - - - +
6R GLU* 3.0 26.6 + - - -
22R CYS* 2.0 53.4 - - + -
34R ILE* 4.6 2.5 - - + -
35R HIS 3.0 12.1 - - - +
36R TRP* 3.9 14.6 - - + -
91R TYR* 1.3 75.5 - - - +
93R ALA* 1.3 61.6 + - - +
103R TRP* 4.6 0.4 - - - -
104R GLY 3.4 14.9 + - - -
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Residues in contact with ALA 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4R LEU* 3.9 5.2 - - - -
34R ILE* 3.6 4.7 - - - +
35R HIS* 2.8 35.0 + - - +
37R VAL* 5.5 2.1 - - + +
91R TYR 4.2 0.4 - - - -
92R CYS* 1.3 75.6 - - - +
94R LYS* 1.3 61.4 + - - +
100R PHE* 3.6 32.5 - - + -
102R TYR 2.8 19.5 - - - +
103R TRP* 3.9 15.7 - - + -
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Residues in contact with LYS 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2R VAL* 3.8 16.8 - - - +
4R LEU* 4.7 5.6 - - + -
27R PHE* 3.8 38.1 - - + -
32R THR* 4.2 18.4 - - + -
33R TYR 3.4 8.1 - - - +
34R ILE* 4.7 4.3 - - + +
93R ALA* 1.3 76.5 - - - +
95R TRP* 1.3 67.7 + - - +
97R ALA* 4.3 8.7 - - + +
100R PHE* 3.3 6.7 - - - -
101R ASP* 3.1 44.5 + - - +
102R TYR* 3.0 44.3 + - + +
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Residues in contact with TRP 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C THR 4.7 3.1 - - - -
93C LEU* 3.4 46.5 + - + +
94C TYR 3.3 26.4 + - - -
95C SER* 4.2 2.2 - - - +
89Q GLN* 4.2 7.2 - - - -
91Q SER* 3.4 26.5 - - - -
96Q ALA* 4.9 0.7 - - + -
32R THR* 5.5 0.5 - - - -
33R TYR* 2.9 41.9 + + + +
35R HIS* 3.8 23.3 - + + -
93R ALA 4.3 0.2 + - - -
94R LYS* 1.3 74.3 - - - +
97R ALA* 1.3 62.0 + - - +
98R TRP 3.7 12.4 + - - -
99R PRO* 3.5 14.6 - - + -
100R ALA* 3.6 62.4 - - - -
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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