Contacts of the helix formed by residues 61 - 69 (chain E) in PDB entry 1NUE
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 61 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LYS* 4.0 32.8 - - + -
52E TYR* 3.0 39.0 - - + -
53E ILE* 5.8 0.4 - - + -
55E LEU* 3.0 27.6 - - + +
56E LYS* 3.8 26.0 - - + +
58E ARG 3.1 18.1 + - - +
59E PRO 3.2 0.2 - - - -
60E PHE* 1.3 84.5 - - - +
62E PRO* 1.3 73.0 - - + +
64E LEU* 3.1 7.6 + - + +
65E VAL* 3.0 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E LYS 5.8 0.2 - - - +
58E ARG 4.1 2.7 - - - +
59E PRO 3.5 15.3 - - - +
61E PHE* 1.3 101.0 - - + +
63E GLY* 1.3 55.8 + - - +
65E VAL* 3.5 5.6 + - + +
66E LYS* 2.9 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E PRO 5.2 0.2 + - - -
60E PHE* 3.0 7.8 + - - +
62E PRO* 1.3 80.0 - - - +
64E LEU* 1.3 63.0 + - - +
66E LYS* 3.4 7.0 + - - +
67E TYR* 3.0 25.1 + - - +
160E GDP 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E TYR* 3.7 48.2 - - + +
55E LEU* 3.8 13.2 - - + -
60E PHE* 2.8 23.4 + - + +
61E PHE* 3.1 13.0 + - + +
63E GLY* 1.3 71.3 - - - +
65E VAL* 1.3 60.7 + - + +
67E TYR* 3.1 16.5 + - + -
68E MET* 2.8 41.0 + - + +
160E GDP 3.6 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E GLU* 3.9 37.9 - - + +
48E LEU* 3.9 12.0 - - + +
49E LYS* 4.0 22.7 - - + +
52E TYR* 5.4 1.8 - - + -
61E PHE* 3.0 55.1 + - + +
62E PRO* 3.9 5.4 - - + +
64E LEU* 1.3 76.4 - - + +
66E LYS* 1.3 66.0 + - + +
68E MET* 3.2 8.4 + - - +
69E ASN* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E GLU* 3.8 32.0 + - - +
62E PRO* 2.9 33.1 + - + +
63E GLY* 3.6 6.3 - - - +
65E VAL* 1.3 78.9 - - + +
67E TYR* 1.3 57.2 + - - +
69E ASN* 3.3 9.0 + - - +
70E SER* 3.0 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D TRP* 4.6 4.9 - + - -
12E LYS* 3.1 25.1 - - + +
13E PRO* 3.5 14.7 - - + +
14E ASP* 2.9 36.1 + - + -
63E GLY 3.0 14.0 + - - +
64E LEU* 3.7 27.8 - - + -
66E LYS* 1.3 75.9 - - - +
68E MET* 1.3 69.6 + - + +
70E SER* 2.5 36.2 + - - +
113E GLY 3.3 21.5 - - - -
114E ARG* 3.5 39.0 - - - +
115E ASN* 3.8 9.9 + - - -
160E GDP 4.6 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ALA* 5.6 6.5 - - + -
12E LYS* 3.8 37.9 - - + -
13E PRO* 3.7 15.6 - - - +
43E ALA* 4.8 3.8 + - - +
48E LEU* 3.6 30.3 - - + +
51E HIS* 5.6 2.0 - - + -
52E TYR* 3.9 35.0 - - + +
64E LEU* 2.8 25.4 + - + +
65E VAL* 3.7 5.2 - - - +
67E TYR* 1.3 82.7 - - + +
69E ASN* 1.3 58.5 + - - +
71E GLY 3.6 12.5 - - - +
73E VAL* 4.2 25.3 - - + +
118E HIS* 5.6 1.1 - - + -
133E TRP* 5.5 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ARG* 3.2 28.8 + - - +
43E ALA 2.8 24.7 + - - -
44E SER* 4.0 9.1 - - - +
45E GLU* 4.1 23.8 - - + +
48E LEU* 3.5 11.4 - - + -
65E VAL 3.0 15.6 + - - +
66E LYS* 3.6 8.0 - - - +
67E TYR 3.1 0.4 - - - -
68E MET* 1.3 78.2 - - - +
70E SER* 1.3 60.4 + - - +
71E GLY 3.1 7.5 + - - -
----------------------------------------------------------
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