Contacts of the helix formed by residues 30 - 38 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G TYR* 3.4 5.8 - - - -
27G SER 6.0 0.2 - - - +
28G HIS* 3.5 12.4 + - - +
29G LEU* 1.3 79.8 - - - +
31G PRO* 1.3 77.0 - - - +
32G ALA* 3.5 8.3 + - - +
33G VAL* 3.2 27.8 + - + +
34G TYR* 3.0 22.9 + - - +
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Residues in contact with PRO 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E GLN 5.6 1.8 - - - +
263E GLY* 4.0 27.6 - - - +
265E GLU* 4.3 25.8 - - + +
12G SER* 5.1 3.6 - - - +
15G TYR* 3.7 28.9 - - + +
30G THR* 1.3 88.2 - - - +
32G ALA* 1.3 57.3 + - - +
34G TYR* 3.7 1.2 - - - +
35G ALA* 2.9 32.2 + - - +
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Residues in contact with ALA 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E GLU* 4.8 10.6 + - - +
30G THR* 3.1 8.0 + - - +
31G PRO* 1.3 80.9 - - - +
33G VAL* 1.3 63.6 + - + +
35G ALA* 3.5 4.4 + - - +
36G ARG* 3.1 36.3 + - - +
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Residues in contact with VAL 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G HIS 4.6 9.6 - - - +
29G LEU* 4.5 5.8 - - + -
30G THR* 3.2 24.9 + - + +
32G ALA* 1.3 75.1 - - + +
34G TYR* 1.3 66.4 + - - +
36G ARG* 3.3 23.4 + - - +
37G LEU* 3.0 45.1 + - + +
82G ASP* 4.5 15.3 - - + +
83G LEU* 4.4 20.9 - - + -
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Residues in contact with TYR 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ARG* 3.5 7.3 + - - -
11G PRO* 3.5 31.0 - - + -
14G GLU* 3.6 17.0 - - + +
15G TYR* 3.7 29.2 - + + -
16G PRO* 4.2 10.1 - - + -
29G LEU* 4.2 17.0 - - + +
30G THR 3.0 17.0 + - - +
31G PRO* 3.7 3.1 - - + +
33G VAL* 1.3 77.5 - - - +
35G ALA* 1.3 57.2 + - - +
38G CYS* 2.9 53.9 + - + +
48G LEU* 3.7 24.9 - - + -
49G ASP* 2.7 37.1 + - - -
52G ILE* 4.4 5.6 - - + -
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Residues in contact with ALA 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G PRO* 3.8 32.5 - - + +
31G PRO 2.9 17.8 + - - +
32G ALA* 4.0 5.2 - - - +
34G TYR* 1.3 78.1 - - - +
36G ARG* 1.3 63.4 + - - +
38G CYS* 3.7 12.0 - - - -
39G ASP* 4.8 5.5 + - - +
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Residues in contact with ARG 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G ALA* 3.1 37.8 + - - +
33G VAL* 3.7 26.2 - - - +
34G TYR 3.2 0.2 - - - -
35G ALA* 1.3 79.6 - - - +
37G LEU* 1.3 65.5 + - + +
39G ASP* 4.8 4.2 + - - +
40G LYS* 4.1 14.5 - - + +
82G ASP* 3.1 32.4 + - - +
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Residues in contact with LEU 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G VAL* 3.0 34.9 + - + +
36G ARG* 1.3 87.6 - - + +
38G CYS* 1.3 61.4 + - - +
39G ASP 2.9 8.0 + - - -
40G LYS* 3.0 41.4 + - + +
48G LEU* 3.8 17.1 - - + +
79G VAL 4.0 13.0 - - - +
80G PHE* 3.8 30.4 - - + -
82G ASP* 4.2 23.6 - - + +
83G LEU* 4.3 15.7 - - + +
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Residues in contact with CYS 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER* 4.7 2.4 + - - -
6A ARG* 4.2 32.2 - - + +
11G PRO* 3.9 27.8 - - - -
34G TYR* 2.9 45.0 + - + +
35G ALA 3.7 11.4 - - - -
36G ARG 3.7 0.2 - - - -
37G LEU* 1.3 70.9 - - - +
39G ASP* 1.3 61.7 + - - +
40G LYS 3.5 2.8 - - - +
47G THR* 5.7 4.9 - - - +
48G LEU* 4.1 12.0 - - - +
49G ASP* 6.0 1.1 - - - +
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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