Contacts of the helix formed by residues 75 - 80 (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 GLU 75 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42G THR* 4.3 4.5 - - + -
43G PRO* 3.7 38.5 - - + +
44G THR* 5.6 2.8 + - - +
73G ASP* 3.3 17.5 - - - +
74G GLU* 1.3 87.0 + - - +
76G THR* 1.3 65.6 + - - +
77G TYR 3.2 0.2 - - - -
78G GLU* 2.9 22.3 + - + +
79G VAL* 3.0 18.0 + - + +
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Residues in contact with THR 76 (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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42G THR* 3.9 10.2 - - - +
46G TRP* 3.3 10.2 - - - -
51G CYS* 3.7 16.4 - - - -
71G ALA* 3.9 11.0 - - + -
72G GLY 3.3 6.7 + - - -
73G ASP* 2.7 42.6 + - - -
74G GLU 3.2 0.2 - - - -
75G GLU* 1.3 75.2 - - - +
77G TYR* 1.3 63.4 + - - +
80G PHE* 3.0 29.3 + - + +
84G PHE* 3.6 31.9 - - + -
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Residues in contact with TYR 77 (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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71G ALA* 3.4 27.7 - - + +
73G ASP 4.4 1.8 - - - -
74G GLU 4.1 10.5 - - - +
75G GLU 3.2 1.0 - - - -
76G THR* 1.3 76.2 - - - +
78G GLU* 1.3 60.0 + - - +
81G ALA* 3.5 16.4 - - - +
84G PHE* 3.6 35.9 - + + +
85G ASP* 4.8 0.5 - - - +
88G ILE* 4.2 6.5 - - + -
269G ASN* 5.9 0.7 - - - +
271G ARG* 3.4 16.4 + - - +
272G LEU* 3.8 29.4 - - + -
275G ILE* 3.6 34.5 - - + -
276G LEU 2.9 18.8 + - - -
277G THR 3.7 1.0 + - - -
279G PRO* 3.7 16.6 - - + +
282G LEU* 3.6 29.2 - - + +
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Residues in contact with GLU 78 (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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40G LYS* 5.1 1.2 + - - -
74G GLU 4.5 1.5 + - - +
75G GLU* 2.9 15.7 + - - +
77G TYR* 1.3 78.4 - - - +
79G VAL* 1.3 73.2 + - - +
80G PHE 3.2 1.6 - - - -
81G ALA* 3.2 18.7 + - + +
271G ARG* 4.6 6.5 - - - +
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Residues in contact with VAL 79 (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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37G LEU* 4.0 4.9 - - - +
40G LYS* 3.0 49.1 + - + +
41G THR 4.0 16.2 - - - +
42G THR* 4.2 15.0 - - + -
43G PRO* 5.2 2.2 - - + -
75G GLU* 3.0 20.0 + - + +
78G GLU* 1.3 84.9 - - - +
80G PHE* 1.3 88.8 + - + +
81G ALA 3.7 1.2 + - - -
82G ASP 5.2 0.3 + - - -
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Residues in contact with PHE 80 (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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37G LEU* 3.8 41.5 - - + -
40G LYS* 3.8 17.0 - - + -
42G THR* 4.0 9.4 - - + -
46G TRP* 3.8 17.7 - + - -
47G THR 3.7 9.9 - - - -
48G LEU* 3.5 33.2 - - + -
51G CYS* 4.0 10.3 - - - -
76G THR* 3.0 30.8 + - + +
79G VAL* 1.3 98.2 - - + +
81G ALA* 1.3 65.2 + - - +
82G ASP 3.2 3.4 - - - -
83G LEU* 3.0 14.0 + - + +
84G PHE* 3.1 26.4 + - + -
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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