Contacts of the strand formed by residues 33 - 39 (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 TYR 33 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C SER* 5.8 3.1 - - - -
90C PRO* 3.5 31.6 - - + +
91C TYR 4.8 3.8 - - - -
92C THR 4.7 5.6 - - - -
94C TYR* 3.3 37.7 - + + -
96C VAL* 5.8 5.1 - - + +
31R GLY 5.2 1.1 - - - -
32R THR* 1.3 81.0 - - - +
34R ILE* 1.3 62.4 + - - +
35R HIS* 3.7 20.3 - - + +
51R ILE 3.5 6.7 - - - +
52R TYR* 3.5 41.8 + + + -
58R TYR* 5.7 6.7 - + - -
94R LYS* 3.4 4.5 - - - +
95R TRP* 2.9 60.4 + + + +
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Residues in contact with ILE 34 (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* 5.2 4.7 - - + -
22R CYS* 4.1 19.5 - - - -
27R PHE* 4.3 11.2 - - + -
29R ILE* 3.8 31.4 - - + +
32R THR* 3.1 30.3 + - - +
33R TYR* 1.3 76.9 - - - +
35R HIS* 1.3 65.9 + - - +
36R TRP* 5.0 5.5 - - - +
50R GLY* 3.2 1.4 - - - -
51R ILE* 2.7 46.6 + - + +
52R PRO* 5.8 1.8 - - + -
78R ALA* 3.7 26.0 - - + -
92R CYS* 4.6 1.3 - - + -
93R ALA 3.6 6.7 - - - +
94R LYS* 5.0 4.0 - - + -
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Residues in contact with HIS 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C THR* 4.4 23.2 + - + -
93C LEU* 6.2 0.9 - - + -
33R TYR* 3.7 27.7 - - + +
34R ILE* 1.3 79.8 + - - +
36R TRP* 1.3 65.4 + - - +
37R VAL* 5.3 0.4 - - + -
47R TRP* 3.0 33.3 + + + +
49R GLY 3.3 4.3 - - - +
50R GLY* 3.4 19.1 - - - -
51R ILE 4.9 0.4 + - - -
58R TYR* 5.0 6.1 - + - -
92R CYS* 3.0 9.4 - - - +
93R ALA 2.8 33.6 + - - +
95R TRP* 3.8 19.9 - + + +
100R PHE* 3.8 24.2 - - - -
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Residues in contact with TRP 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R GLU* 4.1 13.9 - - + -
20R LEU* 3.6 36.6 - - + -
21R SER 3.9 15.7 - - - -
22R CYS* 3.9 20.2 - - + -
34R ILE* 5.0 3.3 - - + +
35R HIS* 1.3 77.6 - - - +
37R VAL* 1.3 57.3 + - - +
47R TRP* 3.6 4.7 - - - -
48R VAL* 2.7 47.5 + - + +
49R GLY 2.7 12.5 + - - +
69R ILE* 3.8 28.1 - - + +
78R ALA* 4.5 7.2 - - - +
79R TYR 4.1 10.3 + - - -
80R LEU* 3.4 44.2 - - + +
90R TYR* 4.2 12.3 - - + -
91R TYR 3.3 20.4 - - - -
92R CYS* 3.9 12.5 - - + +
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Residues in contact with VAL 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98Q PHE* 4.2 3.4 - - + -
35R HIS* 5.3 0.9 - - + -
36R TRP* 1.3 81.6 - - - +
38R ARG* 1.3 72.7 + - - +
45R LEU* 3.8 19.3 - - + -
46R GLU 3.4 13.0 - - - +
47R TRP* 4.2 7.2 - - - -
48R VAL* 4.1 1.3 - - - -
90R TYR* 4.8 0.9 - - - -
91R TYR* 2.8 34.9 + - - +
92R CYS* 4.8 0.2 - - - +
93R ALA* 5.6 2.7 - - + -
100R PHE* 4.1 31.6 - - - +
103R TRP* 3.6 36.6 - - + -
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Residues in contact with ARG 38 (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* 1.3 78.3 - - - +
39R GLN* 1.3 63.8 + - - +
40R ALA 5.2 1.1 - - - +
45R LEU* 3.3 6.9 - - - +
46R GLU* 2.5 73.4 + - + +
48R VAL* 3.6 9.2 - - + +
62R SER* 4.5 6.9 + - - -
63R VAL* 3.9 24.3 - - - +
66R ARG* 5.0 1.0 - - - +
67R PHE* 4.0 2.4 - - - -
85R GLU* 4.2 14.8 + - - +
86R ASP* 3.3 27.1 + - - +
88R ALA* 4.1 9.0 - - + -
89R VAL 3.2 10.5 - - - +
90R TYR* 2.6 57.0 + - + +
91R TYR* 4.9 0.4 - - - -
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Residues in contact with GLN 39 (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* 3.1 39.6 + - - +
87Q TYR* 3.5 11.1 + - - -
38R ARG* 1.3 80.6 - - - +
40R ALA* 1.3 70.3 + - - +
41R PRO* 3.7 1.0 - - - +
42R GLY 5.8 0.4 - - - +
43R LYS 3.3 26.2 + - - +
44R GLY 3.4 8.7 - - - +
45R LEU* 3.8 23.1 - - + +
46R GLU* 6.1 0.2 - - - -
88R ALA* 3.5 2.2 - - - -
89R VAL* 3.0 28.2 + - + +
91R TYR* 3.4 18.6 + - + -
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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