Contacts of the helix formed by residues 75 - 80 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D THR* 4.2 4.7 - - + -
43D PRO* 3.7 37.7 - - + +
44D THR* 5.5 2.4 + - - +
73D ASP* 3.3 17.3 - - - +
74D GLU* 1.3 87.1 + - + +
76D THR* 1.3 65.6 + - - +
77D TYR 3.2 0.2 - - - -
78D GLU* 2.9 22.5 + - + +
79D VAL* 3.0 17.4 + - + +
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Residues in contact with THR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D THR* 3.9 9.2 - - - +
46D TRP* 3.3 9.9 - - - -
51D CYS* 3.8 16.8 - - - -
71D ALA* 3.9 10.8 - - + -
72D GLY 3.3 6.0 + - - -
73D ASP* 2.7 42.6 + - - -
74D GLU 3.2 0.4 - - - -
75D GLU* 1.3 76.7 - - - +
77D TYR* 1.3 62.7 + - - +
80D PHE* 3.0 28.9 + - + +
84D PHE* 3.5 31.6 - - + -
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Residues in contact with TYR 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ALA* 3.4 28.0 - - + +
73D ASP 4.4 1.6 - - - -
74D GLU 3.5 10.3 + - - +
75D GLU 3.2 0.8 - - - -
76D THR* 1.3 79.2 - - - +
78D GLU* 1.3 60.1 + - - +
81D ALA* 3.4 15.8 - - - +
84D PHE* 3.6 36.9 - + + +
85D ASP* 4.8 0.9 - - - +
88D ILE* 4.2 7.0 - - + -
269D ASN* 5.9 0.7 - - - +
271D ARG* 3.4 15.2 + - - +
272D LEU* 3.8 28.7 - - + -
275D ILE* 3.6 34.8 - - + -
276D LEU 2.9 18.5 + - - -
277D THR 3.8 1.2 + - - -
279D PRO* 3.7 16.6 - - + +
282D LEU* 3.6 29.4 - - + +
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Residues in contact with GLU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LYS* 5.1 0.9 + - - -
74D GLU 4.5 1.3 + - - +
75D GLU* 2.9 15.3 + - - +
77D TYR* 1.3 77.6 - - - +
79D VAL* 1.3 74.9 + - - +
80D PHE 3.2 1.8 - - - -
81D ALA* 3.2 19.4 + - + +
271D ARG* 4.6 6.7 - - - +
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Residues in contact with VAL 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 4.1 4.3 - - - +
40D LYS* 3.0 49.8 + - + +
41D THR 4.1 15.9 - - - +
42D THR* 4.1 16.2 - - + -
43D PRO* 5.2 2.0 - - + -
75D GLU* 3.0 21.0 + - + +
78D GLU* 1.3 83.8 - - - +
80D PHE* 1.3 89.1 + - + +
81D ALA 3.6 1.4 + - - -
82D ASP 5.2 0.2 + - - -
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Residues in contact with PHE 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.8 41.7 - - + -
40D LYS* 3.8 17.7 - - + -
42D THR* 4.0 9.9 - - + -
46D TRP* 3.8 17.5 - + - -
47D THR 3.8 9.4 - - - -
48D LEU* 3.5 32.3 - - + -
51D CYS* 4.0 10.5 - - - -
76D THR* 3.0 30.7 + - + +
79D VAL* 1.3 98.1 - - + +
81D ALA* 1.3 63.4 + - - +
82D ASP 3.2 3.8 - - - -
83D LEU* 3.0 14.8 + - + +
84D PHE* 3.1 26.9 + - + -
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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