Contacts of the helix formed by residues 80 - 92 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H LEU* 3.8 46.2 - - + -
40H LYS* 3.8 16.8 - - + -
41H THR 4.4 0.2 - - - -
42H THR* 4.0 9.4 - - + -
46H TRP* 3.8 17.5 - + - -
47H THR 3.7 9.4 - - - -
48H LEU* 3.5 30.5 - - + -
51H CYS* 3.9 19.3 - - - -
76H THR* 3.0 21.0 + - + +
79H VAL* 1.3 97.4 - - + +
81H ALA* 1.3 64.4 + - - +
82H ASP 3.2 3.4 - - - -
83H LEU* 3.0 14.7 + - + +
84H PHE* 3.1 26.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H TYR 3.5 17.3 + - - +
78H GLU* 3.2 19.3 + - - +
79H VAL 3.4 1.0 + - - -
80H PHE* 1.3 76.7 - - - +
82H ASP* 1.3 60.5 + - - +
84H PHE* 4.4 2.9 - - - -
85H ASP* 2.9 51.0 + - - +
98H ARG* 3.8 6.7 - - - +
271H ARG* 4.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H VAL* 4.5 14.2 - - + +
36H ARG* 3.1 39.5 + - - +
37H LEU* 4.2 22.0 - - + +
79H VAL 5.2 0.8 + - - -
80H PHE 3.1 1.4 + - - -
81H ALA* 1.3 76.6 - - - +
83H LEU* 1.3 56.7 + - - +
86H PRO* 3.4 18.6 - - - +
98H ARG* 2.7 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H MET* 4.4 6.7 - - + +
28H HIS* 4.1 33.4 - - + +
29H LEU* 4.3 18.6 - - + +
33H VAL* 4.4 6.3 - - + -
37H LEU* 4.3 11.8 - - + +
48H LEU* 3.9 22.7 - - + -
52H ILE* 3.9 13.0 - - + -
69H MET* 3.3 28.3 - - + -
80H PHE 3.0 7.8 + - - +
82H ASP* 1.3 77.4 - - - +
84H PHE* 1.3 66.8 + - + +
85H ASP 3.4 0.2 - - - -
86H PRO* 3.1 11.2 - - - +
87H VAL* 3.4 19.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H LEU* 6.1 0.2 - - + -
51H CYS* 3.8 11.9 - - - -
69H MET* 3.3 32.1 - - + -
70H VAL 3.6 25.6 - - - -
76H THR* 3.6 30.1 - - + -
77H TYR* 3.6 39.9 - + + +
80H PHE* 3.1 31.3 + - + +
81H ALA* 4.3 5.4 - - - +
83H LEU* 1.3 81.5 - - + +
85H ASP* 1.3 52.9 + - - +
87H VAL* 3.1 4.2 + - + +
88H ILE* 2.7 42.6 + - + +
279H PRO* 3.7 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H TYR 4.8 0.3 - - - +
81H ALA* 2.9 28.3 + - - +
84H PHE* 1.3 72.4 - - - +
86H PRO* 1.3 63.4 - - + +
88H ILE* 3.2 8.1 + - - +
89H GLN* 2.8 32.1 + - - +
96H ASP* 5.5 0.9 - - - +
97H PRO* 3.4 24.9 - - + +
98H ARG* 2.7 44.2 + - - +
271H ARG* 3.3 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H HIS* 3.7 35.5 + - + +
81H ALA 3.7 0.4 - - - +
82H ASP* 3.4 23.8 - - - +
83H LEU* 3.1 12.8 - - - +
85H ASP* 1.3 95.7 - - + +
87H VAL* 1.3 54.8 + - - +
89H GLN* 3.4 9.2 + - + +
90H GLU* 3.1 28.1 + - - +
98H ARG* 5.4 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H CYS* 3.8 40.8 - - + +
28H HIS* 4.1 9.4 - - + -
67H VAL* 3.9 22.2 - - + -
69H MET* 3.8 24.7 - - + -
83H LEU* 3.4 20.8 + - + +
84H PHE* 3.1 9.5 + - - +
86H PRO* 1.3 74.7 - - - +
88H ILE* 1.3 66.3 + - - +
90H GLU* 3.2 3.2 + - - +
91H ARG* 2.9 24.3 + - + +
279H PRO* 4.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H TYR* 4.2 15.0 - - + -
84H PHE* 2.7 31.5 + - + +
85H ASP* 3.5 11.9 - - - +
87H VAL* 1.3 74.4 - - - +
89H GLN* 1.3 63.0 + - - +
91H ARG* 4.5 1.1 - - - -
92H HIS* 3.0 42.4 + - + +
95H TYR 4.6 1.6 - - - +
97H PRO* 4.2 17.0 - - + -
272H LEU* 3.8 16.2 - - + -
279H PRO* 4.3 13.5 - - + +
282H LEU* 3.5 29.4 - - + -
337H LEU* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H ASP 2.8 17.1 + - - +
86H PRO* 3.6 9.0 - - + +
87H VAL 3.2 0.2 - - - -
88H ILE* 1.3 77.7 - - - +
90H GLU* 1.3 61.7 + - - +
92H HIS 3.8 0.3 - - - -
93H ASN 3.4 3.6 + - - -
94H GLY* 3.0 45.4 + - - +
95H TYR 3.2 23.3 - - - +
96H ASP* 3.6 24.5 - - - +
97H PRO* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H CYS* 3.4 15.3 - - - -
27H SER* 4.3 2.9 - - - -
28H HIS* 2.8 32.9 + - + +
65H LYS* 3.0 37.9 + - - +
86H PRO 3.1 16.2 + - - +
87H VAL 3.2 4.0 + - - +
89H GLN* 1.3 75.5 - - - +
91H ARG* 1.3 64.6 + - - +
93H ASN* 3.3 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H CYS* 4.7 14.0 - - - -
65H LYS 3.8 19.8 + - - -
66H THR* 5.0 1.2 - - - +
67H VAL* 4.0 21.6 - - + +
87H VAL* 2.9 21.2 + - + +
88H ILE* 3.9 3.6 - - - +
90H GLU* 1.3 80.1 - - - +
92H HIS* 1.3 76.9 + - + +
93H ASN* 3.2 7.0 + - - +
279H PRO* 5.5 1.3 - - + +
280H SER* 3.7 33.7 + - - +
336H ARG* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H ILE* 3.0 32.4 + - + +
89H GLN 3.8 1.6 - - - -
91H ARG* 1.3 86.2 + - + +
93H ASN* 1.3 76.6 + - - +
94H GLY 3.5 1.8 - - - -
95H TYR* 3.3 25.0 + - + +
279H PRO 2.8 23.8 + - - -
280H SER* 3.3 30.3 - - - -
282H LEU* 4.5 3.9 - - - +
336H ARG* 4.2 11.3 + - + +
337H LEU* 3.7 46.4 + - + +
----------------------------------------------------------
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