Contacts of the helix formed by residues 80 - 92 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37F LEU* 3.8 42.6 - - + -
40F LYS* 3.8 13.9 - - + -
41F THR 4.5 0.2 - - - -
42F THR* 4.0 9.6 - - + -
46F TRP* 3.8 19.5 - + - -
47F THR 3.7 9.0 - - - -
48F LEU* 3.5 35.2 - - + -
51F CYS* 4.0 9.9 - - - -
76F THR* 3.0 31.9 + - + +
79F VAL* 1.3 97.0 - - + +
81F ALA* 1.3 64.5 + - - +
82F ASP 3.1 3.4 - - - +
83F LEU* 3.0 14.0 + - + +
84F PHE* 3.1 27.7 + - + -
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F TYR 3.5 17.5 + - - +
78F GLU* 3.2 18.9 + - + +
79F VAL 3.4 1.4 + - - -
80F PHE* 1.3 75.9 - - - +
82F ASP* 1.3 59.6 + - - +
84F PHE* 4.4 2.7 - - - +
85F ASP* 2.9 51.8 + - - +
98F ARG* 3.7 7.4 + - - +
271F ARG* 4.6 4.3 - - - +
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Residues in contact with ASP 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F HIS 5.7 0.5 - - - +
33F VAL* 4.5 13.2 - - + +
36F ARG* 3.1 40.4 + - - +
37F LEU* 4.2 22.5 - - + +
79F VAL 5.2 0.6 + - - -
80F PHE 3.1 1.4 + - - -
81F ALA* 1.3 76.6 - - - +
83F LEU* 1.3 56.8 + - - +
86F PRO* 3.4 18.1 - - - +
98F ARG* 2.7 34.0 + - - +
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Residues in contact with LEU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F MET* 4.5 5.6 - - + +
28F HIS* 4.1 33.2 - - + +
29F LEU* 4.3 18.8 - - + +
33F VAL* 4.4 5.8 - - + -
37F LEU* 4.3 11.6 - - + +
48F LEU* 3.9 14.1 - - + -
52F ILE* 3.9 20.6 - - + -
69F MET* 3.3 28.3 - - + -
80F PHE 3.0 7.3 + - - +
82F ASP* 1.3 77.4 - - - +
84F PHE* 1.3 68.6 + - + +
85F ASP 3.5 0.2 - - - -
86F PRO* 3.1 10.6 - - - +
87F VAL* 3.4 20.5 - - + +
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Residues in contact with PHE 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LEU* 6.1 0.2 - - + -
51F CYS* 3.9 12.1 - - - -
69F MET* 3.3 33.2 - - + -
70F VAL 3.6 25.1 - - - -
76F THR* 3.6 28.0 - - + -
77F TYR* 3.6 39.0 - + + +
80F PHE* 3.1 31.3 + - + +
81F ALA* 4.3 5.6 - - - +
83F LEU* 1.3 79.0 - - + +
85F ASP* 1.3 55.6 + - - +
87F VAL* 3.1 4.4 + - + +
88F ILE* 2.7 42.5 + - + +
279F PRO* 3.7 26.9 - - + -
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Residues in contact with ASP 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F TYR 4.8 0.3 - - - +
81F ALA* 2.9 29.3 + - - +
84F PHE* 1.3 72.3 - - - +
86F PRO* 1.3 63.2 - - + +
88F ILE* 3.2 7.1 + - - +
89F GLN* 2.8 32.3 + - - +
96F ASP* 5.5 1.3 - - - +
97F PRO* 3.4 24.6 - - + +
98F ARG* 2.8 45.4 + - - +
271F ARG* 3.3 25.8 + - - -
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Residues in contact with PRO 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F HIS* 3.6 35.4 + - + +
81F ALA 3.7 0.4 - - - +
82F ASP* 3.4 20.2 - - - +
83F LEU* 3.1 17.3 - - - +
85F ASP* 1.3 95.6 - - + +
87F VAL* 1.3 60.0 + - - +
89F GLN* 3.5 9.4 + - + +
90F GLU* 3.1 22.9 + - - +
98F ARG* 5.4 5.8 - - - +
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Residues in contact with VAL 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F CYS* 3.8 40.7 - - + +
28F HIS* 4.0 9.9 - - + -
67F VAL* 3.9 22.0 - - + -
69F MET* 3.8 23.6 - - - -
83F LEU* 3.4 20.8 + - + +
84F PHE* 3.1 9.7 + - + +
86F PRO* 1.3 75.2 - - - +
88F ILE* 1.3 67.5 + - - +
90F GLU* 3.2 3.9 + - - +
91F ARG* 3.0 24.5 + - + +
279F PRO* 4.8 9.0 - - + -
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Residues in contact with ILE 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F TYR* 4.2 15.0 - - + -
84F PHE* 2.7 31.1 + - + +
85F ASP* 3.6 11.4 - - - +
87F VAL* 1.3 72.4 - - - +
89F GLN* 1.3 63.0 + - - +
91F ARG* 4.5 1.1 - - - -
92F HIS* 3.0 42.3 + - + +
95F TYR* 4.6 1.6 - - + -
97F PRO* 4.2 16.8 - - + -
272F LEU* 3.8 15.9 - - + -
279F PRO* 4.4 13.2 - - + +
282F LEU* 3.6 28.5 - - + -
337F LEU* 3.9 18.2 - - + -
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Residues in contact with GLN 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F ASP 2.8 17.3 + - - +
86F PRO* 3.7 9.1 - - + +
87F VAL 3.2 0.2 - - - -
88F ILE* 1.3 78.6 - - - +
90F GLU* 1.3 61.7 + - - +
92F HIS 3.8 0.2 - - - -
93F ASN 3.4 3.3 + - - -
94F GLY* 3.0 45.8 + - - +
95F TYR 3.2 23.3 - - - +
96F ASP* 3.5 24.5 - - - +
97F PRO* 4.8 1.1 - - + -
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Residues in contact with GLU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F CYS* 3.4 17.8 - - - -
27F SER* 4.2 2.6 - - - -
28F HIS* 2.7 32.2 + - + +
65F LYS* 2.7 35.0 + - - +
86F PRO 3.1 17.9 + - - +
87F VAL 3.2 4.0 + - - +
89F GLN* 1.3 75.3 - - - +
91F ARG* 1.3 64.4 + - - +
93F ASN* 3.3 13.9 + - - +
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Residues in contact with ARG 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F CYS* 4.8 14.0 - - - -
65F LYS 3.9 19.2 + - - -
66F THR* 5.1 0.8 - - - +
67F VAL* 4.0 20.0 - - + +
87F VAL* 3.0 20.6 + - + +
88F ILE* 3.9 3.6 - - - +
90F GLU* 1.3 80.5 - - - +
92F HIS* 1.3 77.0 + - + +
93F ASN* 3.2 7.0 + - - +
279F PRO* 5.0 2.0 - - + +
280F SER* 3.6 33.3 + - - +
336F ARG* 6.1 0.4 - - - +
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Residues in contact with HIS 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88F ILE* 3.0 40.2 + - + +
89F GLN 3.8 1.3 - - - -
91F ARG* 1.3 85.2 + - + +
93F ASN* 1.3 76.1 + - - +
94F GLY 3.6 1.6 - - - -
95F TYR* 3.3 26.9 + - + +
279F PRO 2.9 23.4 + - - -
280F SER* 3.3 30.0 - - - -
282F LEU* 4.6 3.5 - - - +
336F ARG* 4.2 11.8 + - + +
337F LEU* 3.6 36.8 + - + +
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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