Contacts of the helix formed by residues 30 - 38 (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 THR 30 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15F TYR* 3.4 6.2 - - - -
28F HIS* 3.5 11.8 + - - +
29F LEU* 1.3 79.8 - - - +
31F PRO* 1.3 77.5 - - - +
32F ALA* 3.6 8.4 + - - +
33F VAL* 3.2 27.3 + - + +
34F TYR* 2.9 23.0 + - - +
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Residues in contact with PRO 31 (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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15F TYR* 3.7 15.9 - - + +
30F THR* 1.3 88.9 - - - +
32F ALA* 1.3 62.2 + - - +
34F TYR* 3.4 1.2 + - - +
35F ALA* 2.9 26.9 + - - +
260G GLN* 3.5 27.4 - - + +
263G GLY* 3.2 43.3 - - - +
264G TRP 4.3 1.6 - - - +
265G GLU* 3.9 21.1 - - + +
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Residues in contact with ALA 32 (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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30F THR* 3.1 8.0 + - - +
31F PRO* 1.3 81.5 - - - +
33F VAL* 1.3 62.4 + - + +
35F ALA* 3.5 3.5 + - - +
36F ARG* 3.1 37.2 + - - +
265G GLU* 3.9 24.7 + - - +
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Residues in contact with VAL 33 (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 4.5 9.4 - - - +
29F LEU* 4.5 5.8 - - + -
30F THR* 3.2 24.8 + - + +
32F ALA* 1.3 73.9 - - + +
34F TYR* 1.3 67.6 + - - +
36F ARG* 3.2 22.9 + - - +
37F LEU* 3.0 44.4 + - + +
48F LEU* 5.8 0.2 - - + -
82F ASP* 4.5 15.9 - - + +
83F LEU* 4.4 21.5 - - + -
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Residues in contact with TYR 34 (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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11F PRO* 3.5 31.6 - - + -
12F SER* 5.5 0.2 - - - -
14F GLU* 3.6 23.3 + - + +
15F TYR* 3.7 30.3 - + + -
16F PRO* 4.2 9.9 - - + -
29F LEU* 4.2 17.9 - - + +
30F THR 2.9 16.6 + - - +
31F PRO* 3.8 2.9 - - + +
33F VAL* 1.3 78.8 - - - +
35F ALA* 1.3 57.9 + - - +
38F CYS* 2.8 52.5 + - + +
48F LEU* 3.6 25.8 - - + -
49F ASP* 2.7 37.2 + - - -
52F ILE* 4.4 5.4 - - + -
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Residues in contact with ALA 35 (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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11F PRO* 3.9 31.7 - - + +
12F SER* 6.2 0.2 - - - +
31F PRO 2.9 19.1 + - - +
32F ALA* 4.0 4.3 - - - +
34F TYR* 1.3 78.3 - - - +
36F ARG* 1.3 62.4 + - - +
38F CYS* 3.7 12.2 - - - -
39F ASP* 4.8 5.5 + - - +
133G ARG* 6.5 0.9 - - - -
265G GLU* 5.8 2.0 - - - +
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Residues in contact with ARG 36 (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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32F ALA* 3.1 37.9 + - - +
33F VAL* 3.7 25.9 - - - +
34F TYR 3.2 0.2 - - - -
35F ALA* 1.3 79.4 - - - +
37F LEU* 1.3 68.9 + - + +
39F ASP* 4.8 4.2 + - - +
40F LYS* 4.1 12.2 - - + +
82F ASP* 3.1 31.4 + - - +
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Residues in contact with LEU 37 (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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33F VAL* 3.0 34.8 + - + +
36F ARG* 1.3 87.4 - - + +
38F CYS* 1.3 61.2 + - - +
39F ASP 2.9 8.0 + - - -
40F LYS* 3.0 41.6 + - + +
48F LEU* 3.9 17.6 - - + +
79F VAL 4.1 12.6 - - - +
80F PHE* 3.8 29.3 - - + -
82F ASP* 4.2 24.7 - - + +
83F LEU* 4.3 15.3 - - + +
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Residues in contact with CYS 38 (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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3C SER* 5.5 0.2 - - - -
5C ARG* 6.2 0.3 - - - +
6C ARG* 4.4 24.0 - - - +
11F PRO* 3.9 29.2 - - - -
34F TYR* 2.8 40.9 + - + +
35F ALA 3.7 15.3 - - - -
37F LEU* 1.3 71.9 - - - +
39F ASP* 1.3 66.1 + - - +
40F LYS 4.5 3.1 - - - +
47F THR* 5.6 4.9 - - - +
48F LEU* 4.1 11.2 - - + +
49F ASP* 6.0 1.6 - - - +
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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