Contacts of the helix formed by residues 23 - 29 (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 ASN 23 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F HIS* 4.0 6.7 - - - -
22F ASN* 1.3 70.2 - - - +
24F CYS* 1.3 65.6 + - - +
25F MET* 3.4 8.3 + - - +
26F ALA* 2.8 43.0 + - - +
27F SER* 3.2 13.0 + - - -
55F GLY* 3.1 28.3 + - - -
58F ASN 3.3 15.4 + - - -
59F PRO 4.0 6.5 + - - -
65F LYS* 3.8 11.0 - - - +
66F THR* 3.0 35.6 + - - +
67F VAL 4.0 2.9 - - - +
68F GLY* 4.1 7.8 - - - -
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Residues in contact with CYS 24 (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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23F ASN* 1.3 70.5 - - - +
25F MET* 1.3 62.7 + - - +
27F SER* 3.1 10.7 + - - -
28F HIS* 3.1 22.2 - - + -
65F LYS* 4.1 15.8 - - - +
66F THR 2.9 17.2 + - - -
67F VAL* 3.5 13.9 - - - +
87F VAL* 3.8 22.8 - - + +
90F GLU* 3.4 33.2 - - - +
91F ARG* 4.8 20.0 - - - -
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Residues in contact with MET 25 (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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18F LEU* 4.2 12.1 - - + -
23F ASN* 3.2 10.0 - - - +
24F CYS* 1.3 75.4 - - - +
26F ALA* 1.3 66.5 + - - +
28F HIS* 3.1 3.1 + - - +
29F LEU* 3.1 40.6 + - - +
52F ILE* 3.6 34.8 - - + +
55F GLY* 3.5 36.3 - - - +
56F VAL* 3.8 12.1 - - + +
67F VAL 2.9 10.4 + - - +
68F GLY 3.5 17.9 - - - +
69F MET* 3.9 11.0 - - - -
83F LEU* 4.5 4.4 - - + +
87F VAL* 4.3 10.0 - - - +
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Residues in contact with ALA 26 (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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18F LEU* 3.9 30.1 - - + +
21F HIS* 3.8 29.4 - - + +
22F ASN* 5.4 0.2 - - - -
23F ASN* 2.8 27.3 + - - +
25F MET* 1.3 74.2 - - + +
27F SER* 1.3 62.4 + - - +
28F HIS 3.3 0.9 + - - -
29F LEU* 3.9 11.3 + - - +
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Residues in contact with SER 27 (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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22F ASN* 5.9 0.2 - - - -
23F ASN 3.2 4.3 + - - -
24F CYS 3.1 10.1 + - - -
26F ALA* 1.3 76.7 - - - +
28F HIS* 1.3 75.2 + - - +
29F LEU 5.0 0.4 - - - -
30F THR* 6.0 0.3 - - - +
65F LYS* 2.9 34.5 + - - -
90F GLU* 4.2 1.3 - - - -
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Residues in contact with HIS 28 (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* 3.1 24.9 + - - +
25F MET 3.1 2.4 + - - -
27F SER* 1.3 86.7 + - - +
29F LEU* 1.3 64.4 + - - +
30F THR* 3.5 11.8 + - - +
33F VAL* 4.5 8.8 - - - +
82F ASP 5.7 0.3 - - - +
83F LEU* 4.1 20.6 - - + +
86F PRO* 3.6 41.4 + - + +
87F VAL* 4.0 12.8 - - + -
90F GLU* 2.7 31.0 + - + +
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Residues in contact with LEU 29 (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* 3.3 23.4 + - + +
16F PRO* 3.9 20.4 - - + -
18F LEU* 3.8 26.1 - - + +
25F MET* 3.1 27.7 + - - +
26F ALA 3.9 8.1 + - - +
27F SER 5.0 0.5 - - - -
28F HIS* 1.3 78.6 - - - +
30F THR* 1.3 65.2 + - - +
33F VAL* 4.5 4.9 - - + -
34F TYR* 4.2 26.9 - - + +
48F LEU* 4.9 5.6 - - + -
52F ILE* 4.3 8.7 - - + -
83F LEU* 4.3 24.9 - - + +
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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