Contacts of the helix formed by residues 47 - 67 (chain E) in PDB entry 2QXU
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 47 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ASP* 2.8 20.0 + - - +
45E THR* 3.6 19.1 - - - +
46E GLY* 1.3 75.8 - - - +
48E ASN* 1.3 59.7 + - - +
49E TYR* 3.9 10.9 - - - +
50E ASN* 3.2 20.4 + - - +
51E ASN* 3.0 24.6 + - - +
78E MET* 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E GLY 3.5 1.5 + - - +
47E THR* 1.3 69.9 - - - +
49E TYR* 1.3 62.9 - - - +
52E GLY* 2.7 32.0 + - - +
53E PRO* 3.7 1.0 - - - +
78E MET* 5.4 1.1 - - - +
81E ALA* 3.3 8.7 - - - +
82E ASN* 2.8 39.7 + - - +
85E TYR* 3.5 38.3 - - + -
108E LEU* 4.1 12.7 + - - +
109E THR* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E THR* 3.1 10.0 - - - +
48E ASN* 1.3 80.6 - - - +
50E ASN* 1.3 86.6 + - - +
53E PRO* 3.2 19.9 - - - +
85E TYR* 4.8 12.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TRP* 3.5 38.0 + - + -
43E ASP* 2.9 28.3 + - + +
47E THR* 3.2 14.4 + - - +
48E ASN 3.2 0.2 - - - -
49E TYR* 1.3 104.1 - - - +
51E ASN* 1.3 64.5 + - - +
52E GLY 3.4 0.2 - - - -
53E PRO* 3.4 9.8 - - - +
54E VAL* 3.4 19.7 + - - +
57E ARG* 5.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E HIS* 5.3 0.8 - - - -
11E GLY 6.3 0.4 - - - -
41E PHE* 3.3 46.7 - - + +
42E TRP* 5.7 0.9 + - - -
43E ASP* 3.6 18.3 + - - +
46E GLY* 3.4 21.3 - - - -
47E THR 3.0 14.4 + - - +
50E ASN* 1.3 76.8 - - - +
52E GLY* 1.3 66.8 + - - +
54E VAL* 4.3 1.9 - - - +
55E LEU* 2.9 26.4 + - - +
82E ASN* 3.1 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E ASN* 2.7 22.1 + - - +
51E ASN* 1.3 72.0 - - - +
53E PRO* 1.3 59.6 - - - +
55E LEU* 3.4 5.4 + - - +
56E SER* 3.0 22.3 + - - -
82E ASN* 4.7 10.2 - - - +
85E TYR* 3.9 11.4 - - - -
86E TYR* 4.4 2.4 - - - -
90E LEU* 3.2 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E ASN 3.7 1.3 - - - +
49E TYR 3.2 25.1 - - - +
50E ASN 3.4 7.4 - - - +
52E GLY* 1.3 86.7 - - - +
54E VAL* 1.3 65.9 + - - +
56E SER* 3.2 5.9 + - - -
57E ARG* 3.0 50.1 + - - +
85E TYR* 5.0 3.1 - - + -
90E LEU* 4.0 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E VAL* 4.0 13.2 - - + -
40E ASP 4.7 6.5 - - - +
41E PHE* 3.7 23.8 - - + -
42E TRP* 4.1 25.1 - - + +
50E ASN 3.4 17.2 + - - +
51E ASN* 3.3 9.1 + - - +
53E PRO* 1.3 77.5 - - - +
55E LEU* 1.3 58.9 - - - +
57E ARG* 3.3 23.9 + - - +
58E PHE* 2.9 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E VAL* 4.1 11.0 - - + -
9E VAL* 4.0 27.8 - - + -
39E VAL* 4.9 3.4 - - + -
41E PHE* 4.0 11.6 - - + -
51E ASN 2.9 17.5 + - - +
52E GLY 3.6 4.0 - - - +
54E VAL* 1.3 77.8 - - - +
56E SER* 1.3 57.7 + - - +
58E PHE* 3.2 6.9 + - + +
59E VAL* 2.9 52.0 + - + +
73E ILE* 5.0 2.5 - - + -
82E ASN* 4.0 6.1 - - + +
83E THR* 3.9 37.5 - - + +
86E TYR* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E GLY 3.0 14.0 + - - -
53E PRO* 3.2 12.8 + - - -
55E LEU* 1.3 76.5 - - - +
57E ARG* 1.3 65.8 + - - +
59E VAL* 3.8 2.3 - - - +
60E GLN* 3.1 24.0 + - - +
86E TYR* 3.5 20.7 + - - -
90E LEU* 4.2 5.4 - - - -
91E ASP* 2.6 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TRP* 5.9 0.2 - - - +
53E PRO* 3.0 38.6 + - - +
54E VAL* 3.7 32.3 - - - +
56E SER* 1.3 77.3 - - - +
58E PHE* 1.3 63.4 + - - +
60E GLN* 3.4 6.8 + - - +
61E LYS* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E VAL* 3.7 25.4 - - + -
37E TYR* 3.7 33.9 - + + -
38E ALA 3.6 21.1 - - - -
39E VAL* 3.7 39.0 - - + -
40E ASP 5.2 0.4 - - - -
54E VAL* 2.9 17.7 + - + +
55E LEU* 3.5 6.7 - - + +
57E ARG* 1.3 78.5 - - - +
59E VAL* 1.3 62.0 + - - +
61E LYS* 3.2 18.2 + - + +
62E VAL* 3.0 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E VAL* 4.4 10.5 - - + -
55E LEU* 2.9 36.9 + - + +
56E SER 3.8 0.9 - - - +
58E PHE* 1.3 73.5 - - - +
60E GLN* 1.3 60.6 + - - +
62E VAL* 3.0 9.0 + - - +
63E LEU* 2.9 39.2 + - + +
71E VAL* 3.7 35.2 - - + -
73E ILE* 4.7 2.9 - - + -
86E TYR* 3.3 36.1 - - + +
95E LYS* 4.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E SER* 3.1 17.9 + - - +
57E ARG* 3.8 7.2 - - - +
59E VAL* 1.3 77.0 - - - +
61E LYS* 1.3 57.5 + - - +
63E LEU* 3.4 13.7 + - - +
64E ASP* 2.9 64.9 + - - +
91E ASP* 4.4 5.3 + - - +
95E LYS* 3.4 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E ARG 3.0 14.5 + - - +
58E PHE* 3.3 22.9 - - + +
59E VAL 3.1 0.2 - - - -
60E GLN* 1.3 78.6 - - - +
62E VAL* 1.3 57.1 + - + +
64E ASP* 3.3 7.6 + - - +
65E GLU* 2.8 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E PRO* 3.6 31.2 - - + -
7E VAL* 4.0 16.4 - - + -
37E TYR* 3.6 44.9 - - + -
58E PHE* 3.0 21.6 + - + +
59E VAL* 3.0 8.4 + - - +
61E LYS* 1.3 77.7 - - + +
63E LEU* 1.3 55.6 + - - +
65E GLU* 3.4 4.4 + - - -
66E THR* 2.7 36.1 + - + +
71E VAL* 3.8 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E VAL* 2.9 23.0 + - + +
60E GLN* 3.7 18.4 - - - +
62E VAL* 1.3 76.8 - - - +
64E ASP* 1.3 57.7 + - - +
66E THR* 3.8 3.1 - - - -
67E GLY* 2.8 32.1 + - - -
68E ALA* 3.5 25.2 + - + +
69E LYS 3.7 8.7 - - - +
70E LYS 3.7 17.9 - - - +
71E VAL* 3.5 24.7 - - + -
95E LYS* 3.8 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E GLN* 2.9 50.8 + - - +
61E LYS* 3.6 7.8 - - + +
63E LEU* 1.3 79.5 - - - +
65E GLU* 1.3 61.8 + - + +
66E THR 3.4 0.3 + - - -
67E GLY* 3.8 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E TYR* 3.7 29.2 + - - +
61E LYS* 2.8 53.9 + - + +
62E VAL* 3.9 3.4 - - - +
64E ASP* 1.3 75.7 - - + +
66E THR* 1.3 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E PRO* 3.5 22.8 - - + +
34E ASP 5.5 0.2 - - - +
35E LYS* 4.5 23.5 + - + +
37E TYR* 3.3 28.9 - - + +
62E VAL 2.7 22.4 + - - +
63E LEU 3.5 0.7 + - - -
65E GLU* 1.3 77.4 - - - +
67E GLY* 1.3 63.4 + - - +
68E ALA* 3.1 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LEU 2.8 11.4 + - - -
64E ASP 3.8 5.1 + - - -
65E GLU 3.7 1.0 - - - -
66E THR* 1.3 78.3 - - - +
68E ALA* 1.3 64.5 + - - +
69E LYS 3.9 0.5 + - - -
----------------------------------------------------------
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