Contacts of the helix formed by residues 80 - 92 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C LEU* 3.8 43.7 - - + -
40C LYS* 3.8 17.3 - - + -
41C THR 4.5 0.2 - - - -
42C THR* 4.0 8.7 - - + -
46C TRP* 3.8 17.0 - + - -
47C THR 3.7 9.2 - - - -
48C LEU* 3.5 33.4 - - + -
51C CYS* 3.9 18.4 - - - -
76C THR* 3.0 22.4 + - + +
79C VAL* 1.3 96.9 - - + +
81C ALA* 1.3 64.5 + - - +
82C ASP 3.2 3.4 - - - +
83C LEU* 3.0 14.4 + - + +
84C PHE* 3.1 26.8 + - + -
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C TYR 3.4 16.6 + - - +
78C GLU* 3.2 19.0 + - + +
79C VAL 3.4 1.2 + - - -
80C PHE* 1.3 77.5 - - - +
82C ASP* 1.3 59.5 + - - +
84C PHE* 4.4 2.9 - - - +
85C ASP* 2.9 51.4 + - - +
98C ARG* 3.8 7.6 - - - +
271C ARG* 4.5 4.9 - - - +
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Residues in contact with ASP 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C HIS 5.8 0.5 - - - +
33C VAL* 4.5 13.1 - - + +
36C ARG* 3.1 40.3 + - - +
37C LEU* 4.2 21.6 - - + +
79C VAL 5.2 0.6 + - - -
80C PHE 3.1 1.4 + - - -
81C ALA* 1.3 76.2 - - - +
83C LEU* 1.3 58.1 + - - +
86C PRO* 3.4 18.4 - - - +
98C ARG* 2.7 26.7 + - - +
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C MET* 4.5 7.0 - - + +
28C HIS* 4.1 33.4 - - + +
29C LEU* 4.3 18.8 - - + +
33C VAL* 4.4 6.3 - - + -
37C LEU* 4.3 11.6 - - + +
48C LEU* 3.9 23.3 - - + -
52C ILE* 3.9 12.6 - - + -
69C MET* 3.4 26.9 - - + -
80C PHE 3.0 7.2 + - - +
82C ASP* 1.3 77.5 - - - +
84C PHE* 1.3 67.7 + - + +
85C ASP 3.5 0.4 - - - -
86C PRO* 3.1 10.6 - - - +
87C VAL* 3.3 20.3 - - + +
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Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C CYS* 3.9 12.1 - - - -
69C MET* 3.3 32.5 - - + -
70C VAL 3.6 25.8 - - - -
76C THR* 3.6 28.5 - - + -
77C TYR* 3.6 39.0 - + + +
80C PHE* 3.1 33.2 + - + +
81C ALA* 4.3 5.4 - - - +
83C LEU* 1.3 77.6 - - + +
85C ASP* 1.3 56.0 + - - +
87C VAL* 3.1 4.2 + - + +
88C ILE* 2.7 42.3 + - + +
279C PRO* 3.7 26.9 - - + -
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Residues in contact with ASP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C TYR 4.9 0.2 - - - +
81C ALA* 2.9 27.9 + - - +
84C PHE* 1.3 72.5 - - - +
86C PRO* 1.3 64.7 - - + +
88C ILE* 3.1 7.1 + - - +
89C GLN* 2.8 32.1 + - - +
96C ASP* 5.5 1.1 - - - +
97C PRO* 3.4 25.6 - - + +
98C ARG* 2.8 44.5 + - - +
271C ARG* 3.3 26.4 + - - -
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Residues in contact with PRO 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C HIS* 3.7 33.7 + - + +
81C ALA 3.7 0.4 - - - +
82C ASP* 3.4 23.6 - - - +
83C LEU* 3.1 13.0 - - - +
85C ASP* 1.3 95.6 - - + +
87C VAL* 1.3 60.4 + - - +
89C GLN* 3.4 9.8 + - + +
90C GLU* 3.1 23.0 + - - +
98C ARG* 5.4 6.1 - - - +
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C CYS* 3.8 40.9 - - + +
25C MET* 4.3 0.2 - - - -
28C HIS* 4.0 10.5 - - + -
67C VAL* 3.9 22.2 - - + -
69C MET* 3.8 23.8 - - + -
83C LEU* 3.3 21.1 + - + +
84C PHE* 3.1 9.7 + - + +
86C PRO* 1.3 75.3 - - - +
88C ILE* 1.3 67.3 + - - +
90C GLU* 3.2 3.3 + - - +
91C ARG* 3.0 24.7 + - + +
279C PRO* 4.8 8.3 - - + -
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C TYR* 4.2 15.0 - - + -
84C PHE* 2.7 30.9 + - + +
85C ASP* 3.6 11.9 - - - +
87C VAL* 1.3 72.2 - - - +
89C GLN* 1.3 63.9 - - - +
91C ARG* 3.3 1.3 + - - -
92C HIS* 2.9 33.6 + - + +
95C TYR 4.6 1.8 - - - +
97C PRO* 4.2 17.0 - - + -
272C LEU* 3.8 15.9 - - + -
279C PRO* 4.4 14.1 - - + +
282C LEU* 3.5 28.9 - - + -
337C LEU* 3.9 27.1 - - + -
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ASP 2.8 17.6 + - - +
86C PRO* 3.7 9.5 - - + +
87C VAL 3.2 0.2 - - - -
88C ILE* 1.3 78.0 - - - +
90C GLU* 1.3 62.2 + - - +
93C ASN 3.4 3.8 + - - -
94C GLY* 3.0 45.0 + - - +
95C TYR 3.2 23.1 + - - +
96C ASP* 3.5 24.1 - - - +
97C PRO* 4.8 0.4 - - + -
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Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C CYS* 3.4 19.6 - - - -
27C SER* 4.2 2.3 - - - -
28C HIS* 2.8 33.5 + - + +
65C LYS* 2.8 34.2 + - - +
86C PRO 3.1 16.4 + - - +
87C VAL* 3.2 4.2 + - - +
89C GLN* 1.3 76.6 - - - +
91C ARG* 1.3 64.2 + - - +
93C ASN* 3.3 14.1 + - - +
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Residues in contact with ARG 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C CYS* 4.8 14.4 - - - -
65C LYS 4.0 18.4 + - - -
66C THR* 5.1 1.0 - - - +
67C VAL* 4.0 21.0 - - + +
87C VAL* 3.0 20.6 + - + +
88C ILE* 3.8 4.0 - - - +
90C GLU* 1.3 80.8 - - - +
92C HIS* 1.3 75.7 + - + +
93C ASN* 3.2 6.7 + - - +
279C PRO* 5.0 1.6 - - + +
280C SER* 3.6 33.7 + - - +
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Residues in contact with HIS 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ILE* 2.9 39.7 + - + +
89C GLN 3.7 1.8 - - - -
91C ARG* 1.3 87.6 + - + +
93C ASN* 1.3 74.1 + - - +
94C GLY 3.6 1.6 - - - -
95C TYR* 3.3 25.2 + - + +
279C PRO 2.8 24.5 + - - -
280C SER* 3.3 29.7 - - - -
282C LEU* 4.6 4.0 - - - +
336C ARG* 4.2 11.6 + - + +
337C LEU* 3.7 37.5 + - + +
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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