Contacts of the helix formed by residues 56 - 68 (chain C) in PDB entry 1DUX
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 ASN 56 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLU* 3.5 15.3 - - - +
43C ALA* 3.2 13.5 - - - +
54C ASN 3.6 3.8 + - - +
55C MET* 1.3 78.4 - - - +
57C TYR* 1.3 61.2 + - - +
58C ASP* 3.2 12.0 + - - +
59C LYS* 3.0 38.6 + - - +
60C LEU* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A A 4.8 7.6 - - + -
4A C 2.6 29.9 + + - -
36C LEU* 3.6 27.1 - - + -
39C ALA* 3.6 26.7 - - + +
40C GLU* 3.0 27.8 + - - +
43C ALA* 3.5 5.8 - - - +
56C ASN* 1.3 73.5 - - - +
58C ASP* 1.3 59.9 + - - +
60C LEU* 4.3 5.6 - - + -
61C SER* 2.7 60.5 + - - -
81C PHE* 3.6 22.7 - + - -
83C TYR* 2.6 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A C 5.4 3.8 + - - -
5A C 4.4 7.8 + - - -
7B C 4.2 3.8 + - - -
8B C 2.9 37.8 + - - -
40C GLU* 4.8 1.0 + - - -
56C ASN* 3.2 13.2 + - - +
57C TYR* 1.3 79.5 - - - +
59C LYS* 1.3 70.9 + - - +
61C SER* 3.0 17.1 + - - -
62C ARG* 3.4 11.8 + - - +
65C ARG* 4.0 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B T 4.4 2.4 + - + -
6B T 2.6 84.7 + - + +
7B C 5.0 5.0 + - + +
54C ASN* 2.9 40.0 + - - +
55C MET* 3.6 15.7 - - + +
56C ASN* 3.0 27.9 + - - +
58C ASP* 1.3 87.2 - - - +
60C LEU* 1.3 65.1 + - - +
61C SER 3.3 0.2 - - - -
62C ARG* 3.2 4.5 + - - +
63C ALA* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B T 5.0 0.2 - - - -
7C LEU* 4.3 14.8 - - + -
11C LEU* 5.0 2.0 - - + -
36C LEU* 4.1 16.6 - - + -
39C ALA 5.3 0.4 - - - +
42C VAL* 4.1 12.8 - - + -
43C ALA* 3.7 31.4 - - + +
46C TRP* 3.9 26.9 - - + -
55C MET* 3.7 10.0 - - - -
56C ASN 3.0 17.6 + - - +
57C TYR* 4.1 5.6 - - + +
59C LYS* 1.3 72.3 - - - +
61C SER* 1.3 70.2 + - - +
63C ALA* 3.0 11.0 + - - +
64C LEU* 3.0 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 61 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A C 5.9 1.6 - - - -
57C TYR* 2.7 53.1 + - - -
58C ASP* 3.0 14.4 + - - -
60C LEU* 1.3 78.7 - - - +
62C ARG* 1.3 56.2 + - - +
64C LEU* 3.1 9.1 + - - +
65C ARG* 2.9 52.8 + - - +
83C TYR* 4.0 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A G 3.3 40.3 + - - +
7A G 2.8 48.9 + - - -
8A A 3.9 11.0 + - - +
5B T 4.3 6.5 - - + -
6B T 3.3 27.1 - - + +
7B C 4.0 2.5 - - - +
58C ASP 3.4 6.7 + - - +
59C LYS 3.2 9.8 + - - +
60C LEU 3.1 0.6 - - - -
61C SER* 1.3 78.1 + - - +
63C ALA* 1.3 66.6 + - - +
65C ARG* 3.1 22.6 + - - +
66C TYR* 2.9 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B C 4.0 16.2 - - - -
5B T 3.9 29.6 - - + +
7C LEU* 3.5 20.4 - - + -
59C LYS 3.1 10.6 + - - +
60C LEU* 3.0 11.1 + - - +
62C ARG* 1.3 77.6 - - - +
64C LEU* 1.3 61.1 + - - +
66C TYR* 3.1 24.4 + - - +
67C TYR* 3.3 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 3.5 21.8 - - + -
11C LEU* 3.8 21.3 - - + -
34C PHE* 5.4 1.3 - - + -
36C LEU* 4.5 5.4 - - + -
60C LEU* 3.0 33.1 + - + +
61C SER* 3.1 8.9 + - - +
63C ALA* 1.3 78.1 - - - +
65C ARG* 1.3 56.5 + - - +
67C TYR* 2.9 38.4 + - + +
68C TYR* 3.3 11.9 - - - -
73C ILE* 3.9 13.5 - - + +
83C TYR* 3.6 50.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A C 4.3 11.3 - - - +
5A C 3.3 59.5 + - - +
6A G 2.9 44.1 + - + +
8B C 4.8 0.6 - - - +
58C ASP* 4.0 4.9 + - - -
61C SER* 2.9 39.4 + - - +
62C ARG* 3.1 38.9 + - - +
64C LEU* 1.3 76.5 - - - +
66C TYR* 1.3 62.7 + - - +
68C TYR* 3.0 50.0 + - + +
69C ASP* 4.4 1.6 + - - +
83C TYR* 5.2 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 66 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B C 5.3 0.2 - - - +
3B A 3.4 41.8 + + + +
4B C 3.8 47.8 - + - -
5B T 5.0 4.9 - - + -
62C ARG* 2.9 22.6 + - - +
63C ALA* 3.1 18.8 + - - +
65C ARG* 1.3 76.6 - - - +
67C TYR* 1.3 76.6 + + - +
69C ASP* 3.2 12.0 - - - +
70C LYS* 3.1 51.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B C 2.6 33.4 + - - -
7C LEU* 3.3 22.1 + - + +
8C TRP* 3.1 44.5 + + + -
63C ALA 3.3 1.5 + - - -
64C LEU* 2.9 35.4 + - + +
66C TYR* 1.3 98.6 - + - +
68C TYR* 1.3 63.8 + - - +
69C ASP 3.4 0.4 - - - -
70C LYS* 3.0 13.8 + - + -
71C ASN 3.1 9.4 + - - -
72C ILE* 3.4 38.3 + - + -
73C ILE* 3.5 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A C 2.8 33.3 + - - -
6A G 3.9 19.1 - - - -
64C LEU 3.3 17.5 - - - -
65C ARG* 3.0 33.2 + - + +
67C TYR* 1.3 76.7 - - - +
69C ASP* 1.3 60.3 + - - +
71C ASN 3.2 3.8 + - - -
73C ILE* 3.3 19.1 - - + -
74C ARG* 2.8 42.3 + - + +
75C LYS* 3.5 31.5 - - + +
83C TYR* 3.5 17.1 - + - -
----------------------------------------------------------
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