Contacts of the helix formed by residues 75 - 80 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B THR* 4.2 4.0 - - + -
43B PRO* 3.8 37.1 - - + +
44B THR* 5.5 2.9 + - - +
73B ASP* 3.3 18.8 + - - +
74B GLU* 1.3 84.1 + - - +
76B THR* 1.3 66.5 + - - +
77B TYR 3.2 0.2 - - - -
78B GLU* 2.9 22.2 + - + +
79B VAL* 3.0 18.5 + - + +
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B THR* 3.9 9.8 - - - +
46B TRP* 3.3 10.2 - - - -
51B CYS* 3.8 16.4 - - - -
71B ALA* 3.9 11.9 - - + -
72B GLY 3.3 6.5 + - - +
73B ASP* 2.8 43.1 + - - -
74B GLU 3.2 0.4 - - - -
75B GLU* 1.3 74.8 - - - +
77B TYR* 1.3 63.9 + - - +
80B PHE* 3.0 28.8 + - + +
84B PHE* 3.6 31.4 - - + -
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Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA* 3.4 27.7 - - + +
73B ASP 4.4 1.6 - - - -
74B GLU 3.5 11.0 + - - +
75B GLU 3.2 1.0 - - - -
76B THR* 1.3 78.6 - - - +
78B GLU* 1.3 58.7 + - - +
81B ALA* 3.4 18.2 - - - +
84B PHE* 3.5 36.4 - + + +
85B ASP* 4.9 0.5 - - - +
88B ILE* 4.2 7.0 - - + -
269B ASN* 5.9 0.7 - - - +
271B ARG* 3.4 15.4 + - - +
272B LEU* 3.8 30.3 - - + -
275B ILE* 3.6 33.7 - - + -
276B LEU 2.9 18.9 + - - -
277B THR 3.8 0.9 + - - -
279B PRO* 3.7 16.9 - - + +
282B LEU* 3.6 29.4 - - + +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LYS* 5.1 1.0 + - - -
74B GLU 4.5 1.3 + - - +
75B GLU* 2.9 14.9 + - - +
77B TYR* 1.3 78.8 - - - +
79B VAL* 1.3 75.4 + - - +
80B PHE 3.2 1.6 - - - -
81B ALA* 3.2 18.3 + - + +
271B ARG* 4.6 6.5 - - - +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 4.1 4.5 - - - +
40B LYS* 3.0 51.8 + - + +
41B THR 4.0 15.7 - - - +
42B THR* 4.1 15.9 - - + -
43B PRO* 5.2 1.6 - - + -
75B GLU* 3.0 20.9 + - + +
78B GLU* 1.3 83.4 - - - +
80B PHE* 1.3 87.8 + - + +
81B ALA 3.7 1.0 + - - -
82B ASP 5.2 0.3 + - - -
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LEU* 3.7 45.8 - - + -
40B LYS* 3.8 15.9 - - + -
42B THR* 4.0 9.6 - - + -
46B TRP* 3.8 17.7 - + - -
47B THR 3.7 9.0 - - - -
48B LEU* 3.5 31.4 - - + -
51B CYS* 3.9 18.6 - - - -
76B THR* 3.0 22.9 + - + +
79B VAL* 1.3 97.7 - - + +
81B ALA* 1.3 65.6 + - - +
82B ASP 3.2 3.4 - - - -
83B LEU* 3.0 14.5 + - + +
84B PHE* 3.1 26.6 + - + -
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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