Contacts of the helix formed by residues 70 - 78 (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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.8 4.5 - - - -
24A ASP 5.4 0.2 - - - +
25A LYS* 4.0 29.7 - - + -
64A ASN* 5.0 8.5 + - - +
66A ASP* 5.1 3.2 - - - +
68A LYS 3.9 0.8 - - - -
69A ILE* 1.3 76.2 - - - +
71A PHE* 1.3 66.1 + - - +
72A SER* 2.7 28.6 + - - -
73A GLU* 3.0 31.2 + - - +
74A PHE* 2.8 21.3 + - - +
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Residues in contact with PHE 71 (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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12A MET* 6.2 0.9 - - + -
13A ILE* 3.8 34.8 - - + -
16A PHE* 3.5 44.0 - + + -
24A ASP* 5.1 2.7 + - - +
70A ASP* 1.3 75.3 - - - +
72A SER* 1.3 58.0 + - - +
74A PHE* 3.2 22.3 + + - +
75A LEU* 2.9 67.8 + - + +
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Residues in contact with SER 72 (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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70A ASP* 2.7 22.9 + - - -
71A PHE* 1.3 78.4 - - - +
73A GLU* 1.4 65.3 + - - +
75A LEU* 3.4 13.7 + - - +
76A SER* 3.1 19.8 + - - -
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Residues in contact with GLU 73 (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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61A LYS* 3.2 29.0 - - - +
62A ASP* 4.0 0.4 - - - -
63A LYS* 3.1 21.4 + - + +
64A ASN* 3.1 13.5 + - - +
68A LYS 3.0 4.5 - - - +
69A ILE* 3.2 11.4 - - + +
70A ASP* 3.0 35.8 + - - +
72A SER* 1.4 80.0 - - - +
74A PHE* 1.3 67.0 + - - +
76A SER* 3.2 9.7 + - - -
77A LEU* 3.0 21.0 + - - +
102A CA 2.4 31.5 - - - -
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Residues in contact with PHE 74 (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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12A MET* 3.6 31.2 - - + -
15A MET* 3.9 15.9 - - + -
16A PHE* 3.5 34.5 - + + -
26A ILE* 4.4 8.5 - - + -
31A LEU* 5.3 0.9 - - + -
34A MET* 4.2 12.6 - - + -
69A ILE* 3.6 11.1 - - + +
70A ASP 2.8 13.0 + - - +
71A PHE* 3.4 30.3 - + - +
73A GLU* 1.3 73.6 - - - +
75A LEU* 1.3 69.0 + - + +
77A LEU* 3.1 9.3 + - + +
78A MET* 2.9 68.5 + - + +
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Residues in contact with LEU 75 (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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12A MET* 6.1 3.1 - - + -
71A PHE* 2.9 55.7 + - + +
72A SER* 3.6 12.3 - - - +
73A GLU 3.2 0.2 - - - -
74A PHE* 1.3 86.8 - - + +
76A SER* 1.3 56.0 + - - +
78A MET* 3.2 8.8 + - + +
79A GLY* 2.9 26.2 + - - -
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Residues in contact with SER 76 (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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61A LYS* 2.9 28.7 + - - -
63A LYS* 3.6 8.1 + - - -
72A SER 3.1 13.6 + - - -
73A GLU* 3.2 12.5 + - - -
75A LEU* 1.3 74.8 - - - +
77A LEU* 1.3 58.8 + - - +
79A GLY* 3.2 2.8 + - - -
80A ASP* 3.0 30.1 + - - +
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Residues in contact with LEU 77 (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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31A LEU* 3.9 37.2 - - + -
34A MET* 4.0 8.3 - - + -
35A MET* 3.9 21.1 - - + -
53A TYR* 4.6 10.1 - - + +
57A VAL* 3.8 24.9 - - + -
61A LYS* 3.6 19.0 - - + +
69A ILE* 6.0 0.7 - - + -
73A GLU 3.0 12.9 + - - +
74A PHE* 3.1 9.8 + - + +
76A SER* 1.3 77.0 - - - +
78A MET* 1.3 70.8 + - + +
80A ASP* 3.0 11.9 + - - +
81A ILE* 3.0 33.5 + - + +
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Residues in contact with MET 78 (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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12A MET* 3.8 28.5 - - + +
15A MET* 3.9 4.9 - - - -
34A MET* 4.0 7.9 - - + -
39A PHE* 3.9 26.9 - - + -
74A PHE* 2.9 52.3 + - + +
75A LEU* 3.7 11.4 - - + +
77A LEU* 1.3 87.7 - - + +
79A GLY* 1.3 56.8 + - - +
81A ILE* 3.2 24.2 + - + +
82A ALA* 2.9 30.1 + - - +
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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