Contacts of the helix formed by residues 80 - 92 (chain E) in PDB entry 1QK1
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 PHE 80 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E LEU* 3.7 45.8 - - + -
40E LYS* 3.8 17.5 - - + -
42E THR* 4.0 9.6 - - + -
46E TRP* 3.8 16.4 - + - -
47E THR 3.7 9.0 - - - -
48E LEU* 3.5 31.9 - - + -
51E CYS* 4.0 10.8 - - - -
76E THR* 3.0 31.7 + - + +
79E VAL* 1.3 96.3 - - + +
81E ALA* 1.3 65.4 + - - +
82E ASP 3.2 3.1 - - - -
83E LEU* 3.1 12.7 + - + -
84E PHE* 3.1 27.0 + - + -
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Residues in contact with ALA 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E TYR 3.4 17.8 + - - +
78E GLU* 3.2 18.5 + - + +
79E VAL 3.4 1.2 + - - -
80E PHE* 1.3 77.6 - - - +
82E ASP* 1.3 60.4 + - - +
84E PHE* 4.4 3.1 - - - +
85E ASP* 2.9 50.1 + - - +
98E ARG* 3.8 7.4 - - - +
271E ARG* 4.5 4.9 - - - +
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Residues in contact with ASP 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E HIS 5.7 0.5 - - - +
33E VAL* 4.5 13.0 - - + +
36E ARG* 3.1 39.6 + - - +
37E LEU* 4.3 21.3 - - + +
79E VAL 5.2 0.4 + - - -
80E PHE 3.1 1.8 + - - -
81E ALA* 1.3 77.1 - - - +
83E LEU* 1.3 57.0 + - - +
86E PRO* 3.4 18.3 - - - +
98E ARG* 2.7 33.0 + - - +
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Residues in contact with LEU 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E MET* 4.5 6.3 - - + +
28E HIS* 4.1 33.7 - - + +
29E LEU* 4.3 19.3 - - + +
33E VAL* 4.4 6.3 - - + -
37E LEU* 4.3 12.0 - - + +
48E LEU* 3.9 15.0 - - + -
52E ILE* 3.9 20.9 - - + -
69E MET* 3.3 28.7 - - + -
80E PHE 3.1 7.6 + - - +
82E ASP* 1.3 78.1 - - - +
84E PHE* 1.3 68.2 + - + +
85E ASP 3.4 0.7 - - - -
86E PRO* 3.1 10.5 - - - +
87E VAL* 3.4 19.5 + - + +
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Residues in contact with PHE 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LEU* 6.1 0.2 - - + -
51E CYS* 3.8 12.3 - - + -
69E MET* 3.3 31.6 - - + -
70E VAL 3.6 25.8 - - - -
71E ALA* 4.3 0.2 - - - -
76E THR* 3.5 28.5 - - + -
77E TYR* 3.5 38.6 - + + +
80E PHE* 3.1 33.5 + - + +
81E ALA* 4.3 5.4 - - - +
83E LEU* 1.3 80.4 - - + +
85E ASP* 1.3 58.3 + - - +
87E VAL* 3.2 4.1 + - + +
88E ILE* 2.7 38.1 + - + +
279E PRO* 3.7 26.5 - - + -
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Residues in contact with ASP 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E TYR 4.9 0.2 - - - +
81E ALA* 2.9 29.2 + - - +
84E PHE* 1.3 72.7 - - - +
86E PRO* 1.3 63.7 - - + +
88E ILE* 3.2 7.9 + - - +
89E GLN* 2.8 32.1 + - - +
96E ASP* 5.5 1.3 - - - +
97E PRO* 3.4 23.9 - - + +
98E ARG* 2.7 45.9 + - + +
271E ARG* 3.3 26.2 + - - -
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Residues in contact with PRO 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E HIS* 3.7 34.1 + - + +
81E ALA 3.8 0.7 - - - +
82E ASP 3.4 22.2 - - - +
83E LEU* 3.1 13.9 - - - +
85E ASP* 1.3 95.6 - - + +
87E VAL* 1.3 58.4 + - - +
89E GLN* 3.4 9.3 + - + +
90E GLU* 3.1 22.5 + - - +
98E ARG* 5.4 6.3 - - - +
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Residues in contact with VAL 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E CYS* 3.8 40.7 - - + +
25E MET* 4.3 0.2 - - - -
28E HIS* 4.0 10.5 - - + -
67E VAL* 3.9 21.8 - - + -
69E MET* 3.8 24.7 - - + -
83E LEU* 3.4 21.7 + - + +
84E PHE* 3.2 9.6 + - - +
85E ASP 3.2 0.4 - - - -
86E PRO* 1.3 73.1 - - - +
88E ILE* 1.3 68.0 + - - +
90E GLU* 3.2 2.4 + - - +
91E ARG* 3.0 24.3 + - + +
279E PRO* 4.8 8.5 - - + -
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Residues in contact with ILE 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E TYR* 4.2 14.8 - - + -
84E PHE* 2.7 31.1 + - + +
85E ASP* 3.5 12.1 - - - +
87E VAL* 1.3 73.3 - - + +
89E GLN* 1.3 63.3 + - - +
91E ARG* 4.6 1.3 - - - -
92E HIS* 3.0 42.0 + - + +
95E TYR 4.6 1.8 - - - +
97E PRO* 4.1 18.2 - - + -
272E LEU* 3.8 15.9 - - + -
279E PRO* 4.4 12.8 - - + +
282E LEU* 3.6 28.5 - - + -
337E LEU* 3.9 17.5 - - + -
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Residues in contact with GLN 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ASP 2.8 16.8 + - - +
86E PRO* 3.6 8.9 - - + +
87E VAL 3.2 0.2 - - - -
88E ILE* 1.3 79.2 - - - +
90E GLU* 1.3 60.7 + - - +
92E HIS 3.7 0.3 - - - -
93E ASN 3.4 3.3 + - - -
94E GLY* 3.0 45.8 + - - +
95E TYR 3.2 23.1 - - - +
96E ASP* 3.6 23.9 - - - +
97E PRO* 4.8 0.9 - - + -
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Residues in contact with GLU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E CYS* 3.5 19.9 - - - -
27E SER* 4.2 2.3 - - - -
28E HIS* 2.8 33.2 + - + +
65E LYS* 2.7 35.9 + - - +
86E PRO 3.1 15.8 + - - +
87E VAL 3.2 3.8 + - - +
89E GLN* 1.3 76.9 - - - +
91E ARG* 1.3 62.7 + - - +
93E ASN* 3.3 14.8 + - - +
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Residues in contact with ARG 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E CYS* 4.7 14.3 - - - -
64E ILE* 6.1 0.8 - - - +
65E LYS 3.7 20.4 + - - -
66E THR* 4.8 1.6 - - - +
67E VAL* 4.1 21.5 - - + +
87E VAL* 3.0 20.5 + - + +
88E ILE* 3.9 3.8 - - - +
90E GLU* 1.3 79.6 - - - +
92E HIS* 1.3 77.8 + - + +
93E ASN* 3.2 6.5 + - - +
279E PRO* 5.1 1.6 - - + +
280E SER* 3.6 32.0 + - - +
336E ARG* 6.2 0.2 - - - +
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Residues in contact with HIS 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E ILE* 3.0 39.2 + - + +
89E GLN 3.7 1.6 - - - -
91E ARG* 1.3 86.4 + - + +
93E ASN* 1.3 75.4 + - - +
94E GLY 3.6 1.6 - - - -
95E TYR* 3.2 26.2 + - + +
279E PRO 2.9 23.0 + - - -
280E SER* 3.3 29.8 - - - -
282E LEU* 4.5 4.2 - - - +
336E ARG* 4.2 11.8 + - + +
337E LEU* 3.6 37.8 + - + +
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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