Contacts of the strand formed by residues 32 - 38 (chain A) in PDB entry 2WSK
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 ARG 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ALA 3.5 0.8 - - - -
31A GLU* 1.3 81.0 - - - +
33A VAL* 1.3 71.5 + - - +
34A GLU* 3.4 19.6 + - - -
48A ASP* 2.7 54.0 + - + +
57A TRP* 4.1 8.9 - - + -
74A VAL* 3.7 1.9 - - - +
75A HIS* 3.0 71.7 + - + +
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.7 26.0 - - + -
27A SER* 5.2 0.7 - - - -
30A ALA* 4.2 10.3 - - + -
32A ARG* 1.3 81.9 - - - +
34A GLU* 1.3 62.6 + - - +
48A ASP* 3.4 5.4 - - - +
49A LEU* 2.9 56.0 + - + -
57A TRP* 3.6 42.1 - - + -
72A TYR* 4.0 10.5 - - + -
73A ARG 3.7 4.7 - - - +
74A VAL* 4.4 7.0 - - + -
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG* 3.4 21.6 + - + +
33A VAL* 1.3 73.9 - - - +
35A LEU* 1.3 66.3 + - - +
36A CYS* 3.4 6.4 + - - -
46A ARG* 3.1 45.4 + - + +
47A TYR 3.4 6.7 - - - +
48A ASP* 3.3 20.4 - - - +
72A TYR* 3.5 5.1 - - - -
73A ARG* 2.8 42.3 + - + +
75A HIS* 2.8 25.7 + - + -
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.2 22.9 - - + -
23A PHE* 3.6 58.8 - - + -
33A VAL 4.0 1.6 + - - -
34A GLU* 1.3 72.0 - - - +
36A CYS* 1.3 62.7 + - - +
37A VAL* 4.0 16.8 + - + -
45A HIS 3.7 1.0 - - - +
46A ARG* 3.4 4.0 - - - -
47A TYR* 2.7 40.8 + - + +
49A LEU* 4.1 14.6 - - + +
61A LEU* 4.6 3.4 - - + -
70A TYR* 3.9 16.4 - - + -
71A GLY 4.0 0.4 - - - +
72A TYR* 3.7 19.0 - - + -
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Residues in contact with CYS 36 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLU 3.5 15.3 - - - -
35A LEU* 1.3 71.8 - - - +
37A VAL* 1.3 62.2 + - - +
38A PHE* 3.5 4.1 - - + -
44A GLU* 3.1 31.2 - - + +
45A HIS 3.5 3.4 - - - -
46A ARG* 3.6 13.5 - - - -
70A TYR* 3.0 7.4 - - - +
71A GLY 2.7 46.7 + - - +
73A ARG* 3.5 27.6 - - - -
91A LEU* 4.0 8.5 - - + -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 4.0 22.2 - - + -
36A CYS* 1.3 75.6 - - - +
38A PHE* 1.3 69.5 + - - +
43A GLN 3.9 0.2 - - - +
44A GLU* 3.5 3.3 - - - +
45A HIS* 2.7 47.5 + - + +
47A TYR* 4.1 21.1 - - + +
61A LEU* 4.2 15.5 - - + -
68A LEU* 3.2 39.0 - - + -
69A ARG 3.7 3.4 - - - +
70A TYR* 4.7 2.7 - - + -
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Residues in contact with PHE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A CYS* 3.5 19.7 - - + -
37A VAL* 1.3 84.6 - - - +
39A ASP* 1.3 65.9 + - - +
42A GLY* 3.8 21.8 - - - +
43A GLN 3.5 3.1 - - - +
44A GLU* 3.8 33.4 - - + -
45A HIS* 5.1 0.4 - - - -
68A LEU* 4.6 6.2 - - - +
69A ARG* 3.3 33.5 + - + +
70A TYR* 4.3 5.6 - - - -
71A GLY 4.3 0.7 - - - -
91A LEU* 3.3 36.1 - - + -
123A ALA* 4.5 5.6 - - + -
128A LYS* 3.6 31.2 - - + -
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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