Contacts of the helix formed by residues 79 - 88 (chain B) in PDB entry 5WN0
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 LYS 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ILE 3.0 17.2 + - - +
77B LYS* 3.5 22.3 + - - +
78B LYS* 1.3 79.0 - - - +
80B GLY* 1.3 65.8 + - - +
81B LEU* 3.2 3.1 - - - +
82B ASP* 2.9 43.9 + - + +
83B TRP* 3.3 5.5 + - - +
107B GLU* 5.5 4.4 + - - -
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B TRP* 4.2 7.6 - - - -
75B TRP* 3.1 45.0 + - - -
76B ILE 4.3 0.6 + - - -
78B LYS 3.3 3.4 + - - -
79B LYS* 1.3 75.0 - - - +
81B LEU* 1.3 57.8 + - - +
83B TRP* 2.9 21.2 + - - +
84B VAL* 2.9 15.4 + - - +
305B LEU 5.1 2.7 - - - -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B TRP* 3.5 26.0 + - + -
76B ILE* 3.8 35.9 - - + +
79B LYS* 3.2 1.2 - - - +
80B GLY* 1.3 75.0 - - - +
82B ASP* 1.3 65.2 + - - +
84B VAL* 3.4 8.7 + - + +
85B LYS* 3.0 33.2 + - - +
92B LEU* 6.1 1.6 - - + -
94B LEU* 6.4 0.2 - - + -
107B GLU* 3.4 33.2 - - + +
108B LEU* 3.8 14.4 - - + -
111B LEU* 3.9 31.9 - - + -
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 2.9 43.4 + - + +
81B LEU* 1.3 79.2 - - - +
83B TRP* 1.3 63.6 + - - +
85B LYS* 3.2 20.1 + - - +
86B GLU* 3.1 31.0 + - - +
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Residues in contact with TRP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B CYS* 3.7 21.8 - - - -
67B TRP* 3.6 21.5 - + + -
79B LYS 3.3 5.3 + - - +
80B GLY* 2.9 11.9 + - - +
82B ASP* 1.3 77.2 - - - +
84B VAL* 1.3 64.7 - - + +
86B GLU* 3.2 17.1 + - + +
87B GLU* 2.9 68.3 + - + -
301B ARG* 3.5 33.0 - - + -
303B LYS* 6.4 0.2 - - - +
304B ALA* 3.3 28.6 - - + +
305B LEU 5.7 1.3 - - - +
311B PRO* 3.8 11.2 - - + -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TRP* 4.3 2.2 - - + -
75B TRP* 3.8 21.1 - - + -
80B GLY 2.9 16.3 + - - +
81B LEU* 3.7 13.2 - - + +
83B TRP* 1.3 91.4 - - + +
85B LYS* 1.3 53.7 + - - +
87B GLU* 4.4 2.0 - - - +
88B ALA* 2.7 31.9 + - - -
89B PRO* 3.3 6.8 - - + +
92B LEU* 3.3 37.7 - - + -
111B LEU* 4.7 8.7 - - + -
114B LEU* 3.7 23.8 - - + -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LEU* 3.0 29.4 + - - +
82B ASP* 3.2 16.4 + - - +
84B VAL* 1.3 76.5 - - - +
86B GLU* 1.3 62.8 + - + +
88B ALA* 3.7 14.3 + - - +
107B GLU* 5.8 1.6 - - - +
110B GLU* 3.3 47.4 + - - +
111B LEU* 3.7 22.0 - - + +
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS* 5.4 0.3 + - - -
82B ASP* 3.1 20.7 + - - +
83B TRP* 3.8 20.1 - - + +
84B VAL 3.2 0.2 - - - -
85B LYS* 1.3 77.7 - - + +
87B GLU* 1.3 63.8 + - - +
88B ALA* 3.2 2.8 - - - +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS* 2.9 46.8 + - + +
65B CYS* 4.7 6.3 - - + -
83B TRP* 2.9 57.9 + - + +
84B VAL 3.8 3.8 - - - +
86B GLU* 1.3 77.2 - - - +
88B ALA* 1.3 69.7 + - - +
89B PRO* 4.5 4.7 - - + -
301B ARG* 2.6 37.7 + - - -
313B THR* 3.3 14.4 - - + +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LYS* 4.0 6.8 - - - +
84B VAL 2.7 17.0 + - - -
85B LYS* 3.8 15.3 - - - +
86B GLU 3.2 3.3 - - - +
87B GLU* 1.3 76.7 - - - +
89B PRO* 1.3 69.5 - - - +
90B ASP* 3.9 1.7 + - - +
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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