Contacts of the helix formed by residues 60 - 82 (chain F) in PDB entry 2QAR
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 THR 60 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F ARG* 4.4 12.1 - - - +
59F ILE* 1.3 79.2 - - - +
61F LYS* 1.3 64.7 + - - +
62F ASP* 3.3 5.3 + - - +
63F GLU* 3.3 39.3 + - - +
64F ALA* 3.4 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LEU* 4.5 23.3 - - + +
16F LEU* 5.2 15.7 - - + -
59F ILE 3.9 0.6 + - - -
60F THR* 1.3 73.7 - - - +
62F ASP* 1.3 66.3 + - - +
64F ALA* 3.7 7.5 + - - +
65F GLU* 3.5 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F THR* 3.2 4.8 + - - +
61F LYS* 1.3 82.0 - - - +
63F GLU* 1.3 64.3 + - + +
64F ALA 3.2 1.6 - - - -
65F GLU* 3.2 28.1 + - - +
66F LYS* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F ILE* 3.4 35.9 - - + +
53F ARG* 3.1 41.0 + - - +
59F ILE* 3.9 9.6 - - + +
60F THR* 3.3 28.6 + - - +
62F ASP* 1.3 77.7 - - + +
64F ALA* 1.3 57.6 + - - +
66F LYS* 3.5 9.3 + - + +
67F LEU* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LEU* 4.0 25.8 - - + -
16F LEU 5.8 0.7 - - - +
29F GLY* 4.0 10.1 - - - -
30F ILE* 5.0 4.8 + - - +
59F ILE* 3.9 19.6 - - + +
60F THR 3.4 6.7 + - - +
61F LYS* 3.8 10.5 - - - +
62F ASP 3.2 0.2 - - - -
63F GLU* 1.3 77.8 - - - +
65F GLU* 1.3 55.1 + - - +
67F LEU* 3.4 8.6 - - - +
68F PHE* 2.7 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F PHE* 3.7 34.3 - - + -
14F LEU* 6.2 0.9 - - + -
61F LYS* 3.5 14.3 + - - +
62F ASP* 3.2 32.7 + - - +
64F ALA* 1.3 76.5 - - - +
66F LYS* 1.3 60.2 + - - +
68F PHE* 3.3 8.1 + - - +
69F CYS* 2.8 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F ILE 5.1 8.4 + - - +
62F ASP 3.1 9.1 + - - +
63F GLU* 3.6 11.7 - - + +
65F GLU* 1.3 78.4 - - - +
67F LEU* 1.3 54.2 + - - +
69F CYS* 3.1 7.8 + - + +
70F GLN* 2.8 65.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ILE* 4.1 16.8 - - + +
29F GLY* 4.9 3.6 - - - -
30F ILE 5.6 0.7 - - - +
32F HIS* 3.5 57.9 - - + +
47F LEU* 5.1 4.0 - - + -
50F ALA* 5.0 12.6 - - + +
51F ILE* 4.6 12.3 - - + -
59F ILE* 4.7 10.1 - - + -
63F GLU 2.9 19.5 + - - +
64F ALA* 3.4 8.1 - - - +
66F LYS* 1.3 76.0 - - - +
68F PHE* 1.3 61.3 + - - +
70F GLN* 3.5 19.7 + - - +
71F ASP* 3.2 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ILE* 3.8 24.7 - - + -
5F PHE* 3.5 38.8 - + + -
8F LEU* 4.0 26.2 - - + -
30F ILE* 3.7 36.5 - - + +
64F ALA 2.7 21.5 + - - +
65F GLU* 3.4 5.8 - - - +
66F LYS 3.2 0.2 - - - -
67F LEU* 1.3 73.4 - - - +
69F CYS* 1.3 67.6 + - - +
71F ASP* 3.1 9.3 + - - +
72F VAL* 2.9 54.9 + - + +
105F PHE* 4.0 16.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F PHE* 5.9 1.6 - - - -
65F GLU* 2.8 23.5 + - - +
66F LYS* 3.1 7.2 + - + +
68F PHE* 1.3 85.2 - - - +
70F GLN* 1.3 60.4 + - + +
72F VAL* 3.4 7.8 + - - +
73F ASP* 3.0 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F ALA* 4.9 12.2 + - - +
66F LYS* 2.8 47.4 + - + +
67F LEU* 3.7 30.6 - - - +
68F PHE 3.3 0.2 - - - -
69F CYS* 1.3 76.1 - - + +
71F ASP* 1.3 61.8 + - - +
73F ASP* 3.5 11.6 - - - +
74F ALA* 3.0 24.4 + - - +
77F ARG* 5.0 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ILE 4.8 2.9 - - - +
31F GLY 5.0 1.0 - - - +
32F HIS* 2.9 45.6 + - - +
67F LEU* 3.2 16.3 + - - +
68F PHE* 3.1 10.7 + - - +
70F GLN* 1.3 79.7 - - - +
72F VAL* 1.3 60.1 + - - +
73F ASP 3.3 0.2 - - - -
74F ALA* 3.2 10.0 + - + +
75F ALA* 2.8 28.8 + - - +
105F PHE* 3.7 19.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F ILE* 4.6 14.8 - - + -
68F PHE* 2.9 52.8 + - + +
69F CYS* 3.7 10.1 - - - +
71F ASP* 1.3 73.7 - - - +
73F ASP* 1.3 61.8 + - - +
75F ALA* 3.2 3.2 + - - +
76F VAL* 2.9 37.6 + - + +
101F ILE* 4.4 24.2 - - + -
105F PHE* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F CYS* 3.0 18.4 + - - +
70F GLN* 3.5 13.3 - - - +
71F ASP 3.3 0.2 - - - -
72F VAL* 1.3 80.6 - - - +
74F ALA* 1.3 56.5 + - - +
76F VAL* 3.3 7.7 + - - +
77F ARG* 3.0 57.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F GLN 3.0 15.6 + - - +
71F ASP* 3.2 14.8 + - + +
73F ASP* 1.3 72.5 - - - +
75F ALA* 1.3 59.6 + - - +
77F ARG* 3.6 10.8 + - - +
78F GLY* 3.0 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F ASP 2.8 17.0 + - - +
72F VAL 3.4 9.2 - - - +
74F ALA* 1.3 72.3 - - - +
76F VAL* 1.3 57.0 + - - +
78F GLY* 3.3 2.0 + - - -
79F ILE* 2.9 36.0 + - - +
101F ILE* 3.9 25.1 - - + -
104F VAL* 4.1 26.8 - - + +
105F PHE* 4.2 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F VAL* 2.9 26.8 + - + +
73F ASP* 3.3 8.0 + - - +
75F ALA* 1.3 76.2 - - - +
77F ARG* 1.3 58.2 + - + +
79F ILE* 3.2 8.5 + - - +
80F LEU* 2.9 48.6 + - + +
89F TYR* 3.7 28.0 - - + +
101F ILE* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F GLN 5.0 1.2 + - - -
73F ASP* 3.0 48.6 + - - +
74F ALA* 3.9 9.6 - - - +
76F VAL* 1.3 77.6 - - + +
78F GLY* 1.3 58.1 + - - +
80F LEU* 3.8 6.9 - - + +
81F ARG* 2.9 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ALA 3.0 15.2 + - - -
75F ALA* 3.7 3.6 - - - -
77F ARG* 1.3 76.2 - - - +
79F ILE* 1.3 61.1 + - - +
81F ARG* 3.5 6.8 + - - +
82F ASN* 3.1 17.7 + - - +
109F GLU* 3.2 34.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ALA 2.9 23.4 + - - +
76F VAL* 3.2 6.5 + - - +
78F GLY* 1.3 76.6 - - - +
80F LEU* 1.3 61.9 + - - +
82F ASN* 3.2 12.1 + - - +
85F LEU* 3.6 23.1 - - + +
86F LYS 3.2 15.8 + - - -
89F TYR* 3.5 48.5 - - + -
100F LEU* 4.2 8.1 - - + -
101F ILE* 3.9 29.8 - - + -
104F VAL* 4.0 28.7 - - + -
109F GLU* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F VAL* 2.9 35.8 + - + +
77F ARG* 4.0 6.5 - - + +
79F ILE* 1.3 74.2 - - - +
81F ARG* 1.3 62.5 + - - +
82F ASN 3.3 0.4 - - - +
86F LYS* 3.4 39.8 - - + +
89F TYR* 3.8 22.2 - - + -
90F ASP* 3.5 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F ARG* 2.9 50.9 + - - +
78F GLY* 3.8 7.9 - - - +
80F LEU* 1.3 76.9 - - - +
82F ASN* 1.3 61.3 + - - +
83F ALA* 3.5 3.5 + - - +
109F GLU* 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F GLY 3.1 11.3 + - - +
79F ILE 3.2 7.8 + - - +
80F LEU 4.5 0.2 - - - -
81F ARG* 1.3 75.4 - - - +
83F ALA* 1.3 58.6 + - - +
84F LYS* 2.8 38.3 + - - +
85F LEU* 3.3 20.7 + - + +
86F LYS* 3.0 34.5 + - - +
109F GLU* 2.7 39.9 + - - +
110F THR* 5.1 3.0 + - - +
113F ALA* 4.3 9.1 - - - +
----------------------------------------------------------
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