Contacts of the helix formed by residues 80 - 90 (chain A) in PDB entry 2WND
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 ASP 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A PHE* 5.4 0.2 - - - -
53A TYR* 3.7 21.3 + - - +
61A LYS* 2.7 38.6 + - - +
76A SER* 3.0 16.4 + - - +
77A LEU* 3.0 10.5 + - + +
79A GLY* 1.4 75.7 - - - +
81A ILE* 1.3 64.2 + - - +
83A THR* 3.4 8.1 + - - -
84A ASP* 3.1 21.3 + - - +
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Residues in contact with ILE 81 (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 MET* 3.7 27.8 - - + -
39A PHE* 3.9 28.0 - - + -
42A PHE* 4.3 27.8 - - + -
53A TYR* 4.7 1.8 - - - +
77A LEU* 3.0 20.9 + - + +
78A MET* 3.2 30.5 + - + +
80A ASP* 1.3 72.5 - - - +
82A ALA* 1.3 66.6 + - - +
84A ASP* 3.1 6.2 + - - +
85A TYR* 3.1 44.8 + - + -
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Residues in contact with ALA 82 (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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78A MET 2.9 16.9 + - - +
79A GLY* 3.7 7.2 - - - +
81A ILE* 1.3 78.4 - - - +
83A THR* 1.3 50.3 + - - +
85A TYR* 3.1 11.1 + - - +
86A HIS* 2.8 34.2 + - - +
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Residues in contact with THR 83 (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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79A GLY 2.8 24.9 + - - -
80A ASP* 3.6 8.2 - - - -
81A ILE 3.3 0.2 - - - -
82A ALA* 1.3 67.2 - - - +
84A ASP* 1.3 67.5 + - - +
86A HIS* 3.3 9.0 + - + +
87A LYS* 3.0 54.8 + - + +
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Residues in contact with ASP 84 (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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42A PHE* 3.4 30.6 - - + -
53A TYR* 6.3 0.4 - - + -
80A ASP 3.1 9.7 + - - +
81A ILE 3.1 10.7 + - - +
83A THR* 1.3 78.3 - - - +
85A TYR* 1.3 63.7 + - - +
87A LYS* 3.3 6.3 + - - +
88A LYS* 3.1 27.5 + - - +
93A ALA 4.5 1.3 - - - +
94A PRO* 4.1 3.7 - - - +
95A CYS* 3.1 20.5 + - - -
96A SER* 2.9 37.2 + - - +
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Residues in contact with TYR 85 (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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39A PHE* 5.1 7.7 - + - -
41A ASN* 4.7 5.0 - - - +
42A PHE* 3.6 37.2 + + + +
81A ILE* 3.1 45.4 + - + -
82A ALA* 3.1 11.5 + - - +
84A ASP* 1.3 72.4 - - - +
86A HIS* 1.3 66.8 + - - +
88A LYS* 3.4 36.9 + - + +
89A SER* 3.0 23.9 + - - -
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Residues in contact with HIS 86 (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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82A ALA 2.8 15.1 + - - +
83A THR* 3.3 9.6 + - - +
85A TYR* 1.3 76.0 - - - +
87A LYS* 1.3 70.2 + - + +
89A SER* 2.7 26.0 + - - -
90A HIS* 3.3 22.2 - + - -
103A ZN 2.5 36.0 - - - -
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Residues in contact with LYS 87 (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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83A THR* 3.0 40.1 + - + +
84A ASP* 3.8 5.2 - - - +
86A HIS* 1.3 83.1 - - - +
88A LYS* 1.3 56.4 + - - +
90A HIS* 3.2 20.0 + - - +
92A ALA* 3.0 34.1 + - + +
93A ALA 5.7 0.2 - - - +
96A SER* 4.0 19.2 - - - +
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Residues in contact with LYS 88 (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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84A ASP* 3.1 25.4 + - - +
85A TYR* 3.4 40.6 + - + +
87A LYS* 1.3 72.5 - - - +
89A SER* 1.3 65.9 + - - +
90A HIS 3.0 5.2 - - - -
91A GLY* 3.0 14.2 + - - -
92A ALA* 3.4 20.8 - - - +
93A ALA 4.6 1.1 + - - -
94A PRO* 4.4 25.8 - - + -
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Residues in contact with SER 89 (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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85A TYR 3.0 16.4 + - - -
86A HIS* 2.7 23.5 + - - -
88A LYS* 1.3 81.3 - - - +
90A HIS* 1.3 71.1 + - - +
91A GLY 3.3 2.2 + - - -
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Residues in contact with HIS 90 (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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86A HIS* 3.3 31.6 + + - +
87A LYS* 3.2 10.2 + - - +
88A LYS 3.0 1.2 - - - -
89A SER* 1.3 84.3 + - - +
91A GLY* 1.3 60.2 + - - +
92A ALA* 3.3 3.8 + - - +
103A ZN 2.1 36.2 - - - -
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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