Contacts of the helix formed by residues 75 - 80 (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 GLU 75 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F THR* 4.2 4.7 - - + -
43F PRO* 3.7 37.8 - - + +
44F THR* 5.9 2.8 - - - +
73F ASP* 3.3 17.4 - - - +
74F GLU* 1.3 85.6 + - - +
76F THR* 1.3 67.0 + - - +
77F TYR 3.2 0.2 - - - -
78F GLU* 2.9 22.8 + - + +
79F VAL* 3.0 18.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F THR* 3.9 9.6 - - - +
46F TRP* 3.3 14.2 - - - -
51F CYS* 3.7 18.2 - - - -
71F ALA* 3.9 10.8 - - + -
72F GLY 4.0 2.2 - - - -
73F ASP* 2.7 42.3 + - - -
74F GLU 3.2 0.8 - - - -
75F GLU* 1.3 75.4 - - - +
77F TYR* 1.3 63.1 + - - +
80F PHE* 3.0 28.8 + - + +
84F PHE* 3.6 30.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 77 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F ALA* 3.4 29.0 - - + +
73F ASP 4.4 1.6 - - - -
74F GLU 4.0 10.5 - - - +
75F GLU 3.2 1.0 - - - -
76F THR* 1.3 78.6 - - - +
78F GLU* 1.3 58.4 + - - +
81F ALA* 3.5 16.5 - - - +
84F PHE* 3.6 36.8 - + + +
85F ASP* 4.8 0.5 - - - +
88F ILE* 4.2 6.7 - - + -
269F ASN* 5.9 0.7 - - - +
271F ARG* 3.4 15.6 + - - +
272F LEU* 3.8 29.8 - - + -
275F ILE* 3.6 34.3 - - + -
276F LEU 2.9 18.2 + - - -
277F THR 3.7 1.2 + - - -
279F PRO* 3.7 16.0 - - + +
282F LEU* 3.6 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F LYS* 5.1 1.2 + - - -
74F GLU 4.5 0.9 + - - +
75F GLU* 2.9 15.2 + - - +
77F TYR* 1.3 77.3 - - - +
79F VAL* 1.3 74.5 + - - +
80F PHE 3.2 1.3 - - - -
81F ALA* 3.2 18.3 + - - +
271F ARG* 4.6 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 4.1 5.0 - - - +
40F LYS* 3.0 50.7 + - + +
41F THR 4.0 16.2 - - - +
42F THR* 4.2 15.5 - - + -
43F PRO* 5.2 2.5 - - + -
75F GLU* 3.0 20.2 + - + +
78F GLU* 1.3 83.2 - - - +
80F PHE* 1.3 87.9 + - + +
81F ALA 3.7 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 3.8 42.6 - - + -
40F LYS* 3.8 13.9 - - + -
41F THR 4.5 0.2 - - - -
42F THR* 4.0 9.6 - - + -
46F TRP* 3.8 19.5 - + - -
47F THR 3.7 9.0 - - - -
48F LEU* 3.5 35.2 - - + -
51F CYS* 4.0 9.9 - - - -
76F THR* 3.0 31.9 + - + +
79F VAL* 1.3 97.0 - - + +
81F ALA* 1.3 64.5 + - - +
82F ASP 3.1 3.4 - - - +
83F LEU* 3.0 14.0 + - + +
84F PHE* 3.1 27.7 + - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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