Contacts of the helix formed by residues 46 - 66 (chain F) in PDB entry 2DYY
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 ASP 46 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F GLY* 1.3 77.5 - - - -
47F ILE* 1.3 70.1 + - + +
48F LYS* 2.9 28.6 + - - +
49F ASP* 3.0 31.1 + - - +
50F GLN* 3.4 13.3 + - - +
116F LEU* 3.9 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 47 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F ASP* 1.3 83.2 - - + +
48F LYS* 1.3 62.8 + - + +
50F GLN* 3.5 1.4 + - - -
51F THR* 2.7 40.2 + - - +
79F LEU* 3.6 31.9 - - + -
88F MET* 5.4 7.9 - - - +
116F LEU* 3.7 34.1 - - + +
117F ILE* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F ASP* 2.9 20.7 + - - +
47F ILE* 1.3 84.8 - - + +
49F ASP* 1.3 62.2 + - - +
51F THR* 3.7 2.8 + - - -
52F ARG* 3.4 28.7 + - - +
90F GLU* 5.9 2.7 - - - +
91F VAL* 3.9 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43F VAL* 4.2 20.2 - - + +
44F LYS 5.0 1.5 - - - +
45F GLY* 4.4 9.9 - - - -
46F ASP* 3.0 32.5 + - - +
47F ILE 3.3 0.6 - - - -
48F LYS* 1.3 80.7 - - - +
50F GLN* 1.3 65.4 + - - +
51F THR 3.3 0.4 - - - -
52F ARG* 3.7 10.5 + - - +
53F GLN* 3.3 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 50 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F PRO* 3.1 36.0 - - + +
42F ILE* 3.2 24.2 - - - +
43F VAL 3.4 14.9 + - - +
44F LYS* 5.2 1.6 - - - +
45F GLY 4.7 6.0 + - - +
46F ASP 3.4 16.6 + - - +
47F ILE* 4.2 3.1 - - - +
49F ASP* 1.3 75.2 - - - +
51F THR* 1.3 65.6 + - - +
53F GLN* 3.4 0.6 + - - -
54F VAL* 3.1 28.2 + - - +
115F VAL* 3.8 3.5 - - - +
116F LEU* 3.0 42.9 + - + +
117F ILE* 3.8 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 51 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F ILE* 2.7 29.3 + - - +
48F LYS* 3.8 6.2 - - - -
50F GLN* 1.3 79.3 - - - +
52F ARG* 1.3 57.1 + - - +
54F VAL* 3.4 3.6 + - - +
55F LEU* 2.9 42.0 + - + +
88F MET* 4.0 29.3 + - + -
91F VAL* 3.8 24.6 - - + +
92F TYR 4.5 0.2 - - - +
117F ILE* 3.8 23.6 - - + +
119F ILE* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LYS* 3.4 18.3 + - - +
49F ASP* 3.9 11.9 + - - +
50F GLN 3.3 0.2 - - - -
51F THR* 1.3 77.8 - - - +
53F GLN* 1.3 59.3 + - - +
55F LEU* 3.5 5.2 + - - +
56F GLU* 3.0 37.4 + - + +
91F VAL* 3.4 30.3 - - + +
94F GLU* 2.8 37.5 + - - -
95F TYR* 3.7 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F PRO* 3.8 13.9 - - + -
35F ILE 3.6 19.8 + - - +
36F ASP* 4.1 8.2 - - - +
37F PRO* 3.7 8.9 - - - +
43F VAL* 3.3 31.5 - - + +
49F ASP 3.3 14.9 + - - +
50F GLN 3.8 4.3 - - - +
51F THR 3.3 0.4 - - - -
52F ARG* 1.3 76.4 - - - +
54F VAL* 1.3 67.0 + - - +
56F GLU* 3.2 12.8 + - - +
57F ASN* 3.0 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F GLN* 3.3 32.0 - - + +
33F ILE 3.4 0.9 - - - -
34F PRO* 3.4 28.3 - - + -
50F GLN 3.1 18.1 + - - +
51F THR* 3.7 5.2 - - - +
53F GLN* 1.3 74.7 - - - +
55F LEU* 1.3 59.0 + - - +
57F ASN* 3.1 10.5 + - - +
58F ILE* 2.9 39.7 + - + +
117F ILE* 4.1 10.3 - - + +
119F ILE* 3.7 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F THR* 2.9 39.2 + - + +
52F ARG 3.7 4.7 - - - +
54F VAL* 1.3 76.8 - - - +
56F GLU* 1.3 56.3 + - - +
58F ILE* 3.4 18.6 + - + +
59F LYS* 3.0 27.0 + - - +
69F LEU* 5.2 2.0 - - + +
91F VAL* 3.9 12.8 - - + +
92F TYR* 4.0 10.8 - - + -
95F TYR* 3.4 45.1 - - + -
96F PHE* 3.8 30.1 - - + -
119F ILE* 4.6 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F ARG* 3.0 30.9 + - + +
53F GLN* 3.5 17.0 - - - +
55F LEU* 1.3 73.2 - - - +
57F ASN* 1.3 61.6 + - - +
59F LYS* 3.2 13.4 + - - +
60F ALA* 2.8 29.9 + - - +
95F TYR* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ASN 4.1 1.6 - - - +
10F ALA* 3.8 5.8 - - + +
11F PRO* 3.2 24.6 - - + +
32F GLN* 3.7 18.1 + - + +
33F ILE 3.4 18.4 + - - -
35F ILE 3.0 21.4 + - - -
37F PRO* 3.5 10.2 - - - +
53F GLN* 3.0 36.3 + - - +
54F VAL* 3.6 6.7 - - - +
56F GLU* 1.3 76.7 - - - +
58F ILE* 1.3 61.5 + - - +
60F ALA* 3.3 4.1 + - - +
61F ILE* 3.1 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F ILE* 4.0 20.6 - - + +
32F GLN* 3.9 18.6 - - + -
54F VAL* 2.9 35.4 + - + +
55F LEU* 3.5 22.0 - - + +
57F ASN* 1.3 76.5 - - - +
59F LYS* 1.3 62.6 + - - +
61F ILE* 3.2 7.2 + - - +
62F LEU* 3.0 34.4 + - + +
69F LEU* 5.4 2.2 - - + -
72F VAL* 5.4 0.7 - - + -
96F PHE* 5.3 11.7 - - + -
119F ILE* 3.8 25.8 - - + +
120F GLU 5.7 0.2 - - - -
121F ALA* 4.6 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F LEU 3.0 15.4 + - - +
56F GLU* 3.2 22.9 + - - +
58F ILE* 1.3 76.3 - - - +
60F ALA* 1.3 61.3 + - - +
62F LEU* 3.4 11.6 + - + +
63F GLU* 3.0 54.8 + - + +
69F LEU* 3.4 39.2 - - + +
95F TYR* 4.4 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F THR* 4.1 4.7 + - - +
9F ASN* 3.4 45.0 + - + +
10F ALA* 4.2 1.1 - - + -
56F GLU 2.8 16.4 + - - +
57F ASN 3.6 6.3 - - - +
58F ILE 3.3 0.2 - - - -
59F LYS* 1.3 77.2 - - - +
61F ILE* 1.3 56.4 + - - +
63F GLU* 3.5 11.8 + - - +
64F ALA* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 4.2 8.0 - - + +
7F THR* 4.4 3.6 - - + -
10F ALA* 3.7 15.9 - - + -
19F GLN* 3.9 23.6 - - + +
20F ALA* 3.5 29.8 - - + -
27F LEU* 5.0 1.6 - - + -
29F ILE* 4.0 17.7 - - + -
32F GLN* 3.5 36.8 - - + +
57F ASN 3.1 15.8 + - - +
58F ILE* 3.2 5.8 + - - +
60F ALA* 1.3 73.3 - - - +
62F LEU* 1.3 66.5 + - - +
64F ALA* 3.1 8.3 + - - +
65F ALA* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F LEU* 3.8 19.3 - - + -
29F ILE* 3.9 8.7 - - + -
58F ILE* 3.0 31.8 + - + +
59F LYS* 3.7 5.4 - - + +
61F ILE* 1.3 75.7 - - - +
63F GLU* 1.3 58.8 + - + +
65F ALA* 3.0 4.7 + - - +
66F GLY 3.0 5.0 + - - -
67F TYR* 2.7 57.7 + - + +
68F SER* 3.7 17.0 - - - +
69F LEU* 4.1 13.5 - - + +
72F VAL* 3.6 24.2 - - + -
123F ALA* 3.9 17.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
59F LYS* 3.0 58.8 + - + +
60F ALA* 3.6 10.0 - - - +
62F LEU* 1.3 77.6 - - + +
64F ALA* 1.3 62.9 + - - +
66F GLY* 2.9 14.7 + - - -
67F TYR 3.7 11.0 - - - +
68F SER* 5.9 1.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
5F ILE* 3.7 17.9 - - + +
6F PHE 4.2 3.4 - - - +
7F THR* 3.5 29.4 - - + +
60F ALA 3.0 14.5 + - - +
61F ILE 3.4 8.5 - - - +
63F GLU* 1.3 76.7 - - - +
65F ALA* 1.3 57.8 + - - +
66F GLY 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F ILE* 3.7 27.1 - - + -
22F LYS* 4.8 4.2 + - + +
27F LEU* 3.9 16.4 - - + -
61F ILE 3.0 12.2 + - - +
62F LEU 3.0 7.8 + - - +
64F ALA* 1.3 77.2 - - - +
66F GLY* 1.3 57.1 + - - +
67F TYR* 3.3 27.0 - - + -
125F LYS* 4.0 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F GLU 2.9 13.8 + - - -
64F ALA 3.3 1.2 + - - -
65F ALA* 1.3 79.2 - - - +
67F TYR* 1.3 63.7 + - - +
71F ASP* 4.7 0.3 - - - +
125F LYS* 3.7 18.6 + - - +
----------------------------------------------------------
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