Contacts of the helix formed by residues 80 - 92 (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 PHE 80 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR 3.4 18.6 + - - +
78B GLU* 3.2 19.5 + - - +
79B VAL 3.4 1.4 + - - -
80B PHE* 1.3 76.7 - - - +
82B ASP* 1.3 62.9 + - - +
84B PHE* 4.4 3.4 - - - +
85B ASP* 2.9 47.1 + - - +
98B ARG* 3.7 7.1 + - - +
271B ARG* 4.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 4.6 14.4 - - + +
36B ARG* 3.1 39.1 + - - +
37B LEU* 4.2 21.3 - - + +
79B VAL 5.2 0.4 + - - -
80B PHE 3.1 2.0 + - - -
81B ALA* 1.3 76.5 - - - +
83B LEU* 1.3 56.5 + - - +
86B PRO* 3.4 18.5 - - - +
98B ARG* 2.7 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 4.5 6.7 - - + +
28B HIS* 4.1 33.0 - - + +
29B LEU* 4.3 19.3 - - + +
33B VAL* 4.4 5.8 - - + -
37B LEU* 4.3 11.8 - - + +
48B LEU* 3.9 22.4 - - + -
52B ILE* 3.9 13.0 - - + -
69B MET* 3.3 26.9 - - + -
80B PHE* 3.0 8.0 + - + +
82B ASP* 1.3 77.8 - - - +
84B PHE* 1.3 66.8 + - + +
85B ASP 3.4 0.2 - - - -
86B PRO* 3.1 10.5 - - - +
87B VAL* 3.4 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 6.1 0.2 - - + -
51B CYS* 3.9 11.4 - - + -
69B MET* 3.3 33.0 - - + -
70B VAL 3.6 26.2 - - - -
76B THR* 3.6 28.7 - - + -
77B TYR* 3.5 39.5 - + + +
80B PHE* 3.1 31.4 + - + +
81B ALA* 4.3 6.1 - - - +
83B LEU* 1.3 80.0 - - + +
85B ASP* 1.3 53.3 + - - +
87B VAL* 3.1 5.5 + - + +
88B ILE* 2.7 42.2 + - + +
279B PRO* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR 4.9 0.3 - - - +
81B ALA* 2.9 30.1 + - - +
84B PHE* 1.3 71.8 - - - +
86B PRO* 1.3 62.4 - - + +
88B ILE* 3.2 7.7 + - - +
89B GLN* 2.8 32.8 + - - +
96B ASP* 5.5 1.3 - - - +
97B PRO* 3.4 25.2 - - + +
98B ARG* 2.7 44.6 + - - +
271B ARG* 3.3 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 3.6 33.7 + - + +
81B ALA 3.8 0.2 - - - +
82B ASP* 3.4 23.6 - - - +
83B LEU* 3.1 13.7 - - - +
85B ASP* 1.3 95.2 - - + +
87B VAL* 1.3 59.9 + - - +
89B GLN* 3.5 9.1 + - + +
90B GLU* 3.1 23.6 + - - +
98B ARG* 5.4 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B CYS* 3.8 41.2 - - + +
28B HIS* 4.0 10.3 - - + -
67B VAL* 4.0 21.3 - - + -
69B MET* 3.8 24.2 - - - -
83B LEU* 3.4 20.8 + - + +
84B PHE* 3.1 8.6 + - + +
86B PRO* 1.3 75.6 - - - +
88B ILE* 1.3 65.3 + - - +
90B GLU* 3.2 2.8 + - - +
91B ARG* 3.0 25.3 + - + +
279B PRO* 4.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TYR* 4.2 15.0 - - + -
84B PHE* 2.7 30.4 + - + +
85B ASP* 3.6 12.1 - - - +
87B VAL* 1.3 72.9 - - - +
89B GLN* 1.3 59.1 + - - +
91B ARG* 4.6 1.3 - - - -
92B HIS* 3.0 47.1 + - + +
95B TYR* 4.6 1.6 - - + -
97B PRO* 4.2 17.3 - - + -
272B LEU* 3.8 16.2 - - + -
279B PRO* 4.3 13.9 - - + +
282B LEU* 3.6 28.7 - - + -
337B LEU* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASP 2.8 17.4 + - - +
86B PRO* 3.7 8.8 - - + +
88B ILE* 1.3 78.3 - - - +
90B GLU* 1.3 62.1 + - - +
92B HIS 3.7 0.2 - - - -
93B ASN 3.4 3.3 + - - -
94B GLY* 3.0 46.8 + - - +
95B TYR 3.2 24.0 - - - +
96B ASP* 3.5 24.4 - - - +
97B PRO* 4.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B CYS* 3.5 14.4 - - - -
27B SER* 4.2 3.3 - - - -
28B HIS* 2.7 33.9 + - + +
65B LYS* 2.9 39.4 + - - +
86B PRO 3.1 17.1 + - - +
87B VAL 3.2 3.8 + - - +
89B GLN* 1.3 75.9 - - - +
91B ARG* 1.3 63.1 + - - +
93B ASN* 3.3 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B CYS* 4.7 14.6 - - - -
65B LYS 3.8 20.2 + - - -
66B THR* 4.9 1.2 - - - +
67B VAL* 4.1 20.8 - - + +
87B VAL* 3.0 20.7 + - + +
88B ILE* 3.9 3.8 - - - +
90B GLU* 1.3 79.9 - - - +
92B HIS* 1.3 76.6 + - + +
93B ASN* 3.2 6.7 + - - +
279B PRO* 5.2 1.6 - - + -
280B SER* 3.7 32.7 + - - +
336B ARG* 6.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 3.0 41.2 + - + +
89B GLN 3.7 1.3 - - - -
91B ARG* 1.3 87.0 + - + +
93B ASN* 1.3 75.5 + - - +
94B GLY 3.5 1.3 - - - -
95B TYR* 3.3 25.7 + - + +
279B PRO 2.9 24.4 + - - -
280B SER* 3.3 29.4 - - - -
282B LEU* 4.5 3.5 - - - +
336B ARG* 4.2 11.2 + - + +
337B LEU* 3.6 37.7 + - + +
376B HIS* 5.5 2.8 - - - -
----------------------------------------------------------
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