Contacts of the helix formed by residues 104 - 108 (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 ILE 104 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ILE* 4.2 20.6 - - + -
27E ARG* 3.8 34.1 - - + +
28E PHE* 4.0 27.8 - - + -
90E MET* 2.9 22.4 + - + +
91E LEU* 4.0 20.6 - - + +
103E THR* 1.3 70.8 - - - +
105E ARG* 1.3 62.2 + - - +
108E PHE* 3.1 35.1 + - + +
116E ILE* 3.6 23.1 - - + +
117E ILE* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LYS* 3.6 0.7 + - - -
88E ARG* 5.3 1.8 - - - +
91E LEU* 2.9 34.2 + - - +
92E GLY 4.1 7.7 + - - -
93E GLU 3.1 32.8 + - - -
94E THR* 3.6 7.3 - - - +
96E PRO* 3.9 6.5 - - + +
99E SER* 3.7 12.3 - - - +
104E ILE* 1.3 77.7 - - - +
106E GLY* 1.3 61.2 + - - +
109E CYS* 3.3 41.4 + - - +
115E ASN* 3.2 49.7 + - - +
116E ILE* 4.7 0.9 - - + -
117E ILE* 2.7 40.5 + - + +
118E HIS* 4.4 1.2 - - - +
119E GLY 5.2 0.2 - - - +
160E GDP 3.6 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LYS* 2.8 26.9 + - - +
90D MET* 5.3 4.3 - - - +
99E SER* 3.6 15.4 - - - -
100E LYS 3.6 11.0 - - - -
101E PRO* 4.5 7.2 - - - +
103E THR* 3.0 20.0 + - - -
105E ARG* 1.3 79.1 - - - +
107E ASP* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ARG 4.6 2.1 - - - +
30D GLN* 3.8 8.9 + - - +
31D LYS* 3.4 24.7 + - - +
90D MET* 5.9 0.7 - - - +
102D GLY 5.0 2.4 - - - +
27E ARG* 2.8 39.3 + - - +
101E PRO* 3.7 7.3 - - - +
102E GLY* 2.9 28.1 + - - -
103E THR 2.9 14.7 + - - +
106E GLY* 1.3 79.6 - - - +
108E PHE* 1.3 73.3 + - + +
109E CYS 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D GLN* 3.5 43.3 - - + -
31D LYS 3.7 6.7 - - - -
18E ARG* 2.6 38.8 + - - -
20E LEU* 3.8 35.2 - - + -
23E GLU* 3.4 28.7 - - + -
24E ILE* 5.1 4.9 - - + -
27E ARG* 3.4 38.4 - - - -
104E ILE* 3.1 36.5 + - + +
107E ASP* 1.3 84.1 - - + +
109E CYS* 1.3 53.1 + - - +
116E ILE* 3.9 8.5 - - + -
----------------------------------------------------------
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