Contacts of the helix formed by residues 77 - 88 (chain B) in PDB entry 2QKW
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 GLN 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B SER 2.8 10.4 + - - -
76B SER* 1.3 74.4 - - - +
78B GLY* 1.3 60.7 + - - +
79B ILE* 3.1 20.3 - - - +
80B GLU* 3.2 55.0 + - + +
81B GLU* 3.8 17.7 - - - +
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Residues in contact with GLY 78 (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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52B PHE* 5.2 11.4 - - - -
71B ARG* 4.0 13.9 + - - -
74B GLU 5.2 2.9 - - - -
75B SER* 3.9 11.0 + - - -
76B SER 3.1 5.9 - - - -
77B GLN* 1.3 75.9 - - - +
79B ILE* 1.3 64.7 + - - +
80B GLU 3.3 0.7 - - - -
81B GLU* 3.3 12.0 + - - +
82B PHE* 2.9 25.4 + - - +
110B MET* 4.6 5.3 - - - +
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Residues in contact with ILE 79 (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 SER* 3.8 32.5 - - - +
77B GLN* 3.6 16.8 - - - +
78B GLY* 1.3 76.5 - - - +
80B GLU* 1.3 63.4 + - - +
82B PHE* 3.3 5.3 + - + +
83B GLU* 3.1 44.6 + - - +
110B MET* 4.0 30.8 - - + -
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Residues in contact with GLU 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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77B GLN* 3.2 38.4 - - + +
78B GLY 3.3 0.6 - - - -
79B ILE* 1.3 78.7 - - - +
81B GLU* 1.3 56.9 + - + +
83B GLU* 3.5 11.2 + - - +
84B THR* 2.6 40.4 + - - +
202B LYS* 4.5 16.7 + - - -
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Residues in contact with GLU 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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89A TYR* 5.6 2.5 + - - -
52B PHE* 4.6 22.7 - - - +
71B ARG* 3.2 24.5 + - - +
76B SER 5.0 1.6 - - - +
77B GLN 3.8 18.4 - - - +
78B GLY* 3.3 7.3 + - - +
80B GLU* 1.3 78.4 - - + +
82B PHE* 1.3 59.8 + - - +
84B THR* 4.0 0.7 - - - -
85B GLU* 2.9 27.9 + - - +
182B ASP* 5.6 0.9 - - - +
184B GLY* 3.4 28.5 - - - +
185B ILE* 3.3 26.2 - - + +
202B LYS* 5.8 4.3 - - - +
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Residues in contact with PHE 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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71B ARG* 3.2 15.4 - - - +
78B GLY 2.9 17.8 + - - +
79B ILE* 3.3 7.2 + - + +
81B GLU* 1.3 75.9 - - - +
83B GLU* 1.3 70.2 + - + +
85B GLU* 3.6 4.0 + - - +
86B ILE* 3.3 46.4 + - + +
103B PHE* 4.3 8.1 - + - -
104B CYS 4.3 0.7 - - - -
105B ASP* 3.5 40.6 - - + -
110B MET* 3.6 51.6 - - + -
111B ILE 3.8 3.4 - - - -
112B LEU* 3.6 34.8 - - + +
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Residues in contact with GLU 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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79B ILE* 3.1 37.7 + - - +
80B GLU* 3.9 7.9 - - - +
82B PHE* 1.3 85.2 - - + +
84B THR* 1.3 64.7 + - - +
86B ILE* 3.1 20.0 + - + +
87B GLU* 3.0 29.4 + - - +
105B ASP* 5.7 1.8 - - - +
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Residues in contact with THR 84 (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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80B GLU* 2.6 30.0 + - - +
81B GLU* 3.6 9.0 - - - -
82B PHE 3.4 0.2 - - - -
83B GLU* 1.3 72.6 - - - +
85B GLU* 1.3 56.8 + - - +
86B ILE 3.0 4.3 - - - -
87B GLU* 3.6 9.9 + - + +
88B THR* 2.8 41.3 + - - +
183B PHE 3.5 17.7 - - - +
184B GLY 4.2 8.0 + - - +
186B SER 3.7 19.7 - - - +
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Residues in contact with GLU 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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69B LYS* 3.3 13.3 + - - -
71B ARG* 2.8 32.6 + - - -
81B GLU 2.9 16.5 + - - +
82B PHE 3.9 2.2 - - - +
83B GLU 3.3 0.4 - - - -
84B THR* 1.3 74.5 - - - +
86B ILE* 1.3 58.0 + - - +
89B LEU* 3.1 34.2 - - + +
100B LEU* 4.0 5.4 - - - +
112B LEU* 3.8 11.4 - - + +
114B TYR* 2.8 31.3 + - - +
182B ASP* 3.5 12.5 + - - +
183B PHE* 3.5 34.7 + - + +
184B GLY 4.0 4.0 + - - +
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Residues in contact with ILE 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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82B PHE* 3.3 48.2 - - + +
83B GLU* 3.1 13.4 + - + +
84B THR 3.0 1.0 - - - -
85B GLU* 1.3 78.4 - - - +
87B GLU* 1.3 59.0 + - + +
88B THR 3.4 0.2 - - - -
89B LEU* 3.3 2.8 + - - -
90B SER* 2.7 41.1 + - - +
100B LEU* 4.8 9.3 - - + +
103B PHE* 4.2 29.2 - - + -
112B LEU* 3.7 15.3 - - + -
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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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30B PRO* 5.6 0.7 - - - +
83B GLU* 3.0 29.8 + - - +
84B THR* 3.6 12.1 + - + +
86B ILE* 1.3 77.6 - - + +
88B THR* 1.3 70.1 + - - +
90B SER* 3.3 17.4 + - - -
91B PHE* 3.3 19.1 - - + -
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Residues in contact with THR 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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84B THR* 2.8 27.4 + - - +
85B GLU* 4.8 0.2 - - - -
87B GLU* 1.3 79.1 - - - +
89B LEU* 1.3 60.8 + - + +
91B PHE* 3.2 29.7 + - - +
97B LEU* 5.9 1.9 - - - +
155B LEU* 6.0 0.2 - - + -
160B ILE* 3.8 31.7 - - + +
183B PHE* 4.1 22.2 - - + -
186B SER* 3.4 27.1 + - - +
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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