Contacts of the helix formed by residues 123 - 133 (chain F) 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 VAL 123 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F GLU* 3.7 36.6 - - + +
6F ARG 5.7 1.1 - - - +
84F VAL* 4.0 6.8 - - + +
122F SER* 1.3 73.5 - - - +
124F LYS* 1.3 58.7 + - - +
126F ALA* 3.2 8.7 + - + +
127F GLU* 2.9 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F SER* 3.1 13.4 - - - +
123F VAL* 1.3 82.4 - - - +
125F SER* 1.3 63.5 + - - +
127F GLU* 3.5 5.8 + - - +
128F LYS* 3.3 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121F ASP* 2.7 32.4 + - - -
122F SER* 2.8 15.6 + - - -
124F LYS* 1.3 77.4 - - - +
126F ALA* 1.3 55.6 + - - +
128F LYS* 3.0 12.4 + - - +
129F GLU* 2.7 53.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ARG 3.5 25.1 - - - +
7F THR* 4.0 6.7 - - - -
84F VAL* 4.2 1.8 - - + -
120F SER* 3.4 23.7 - - - +
122F SER 2.9 14.2 + - - +
123F VAL* 3.3 12.6 - - - +
125F SER* 1.3 75.6 - - - +
127F GLU* 1.3 57.6 + - - +
129F GLU* 4.5 0.4 - - - -
130F ILE* 2.7 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ARG* 4.4 18.9 + - - +
123F VAL* 2.9 32.1 + - + +
124F LYS* 3.9 6.1 - - - +
125F SER 3.3 0.2 - - - -
126F ALA* 1.3 75.3 - - - +
128F LYS* 1.3 56.4 + - - +
130F ILE* 3.9 20.4 - - - +
131F SER* 2.7 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F GLN* 3.4 29.9 + - - +
51F HIS* 3.9 11.9 + - - +
53F ILE* 3.7 16.0 - - - +
54F ASP* 4.9 4.0 + - - -
124F LYS 3.3 10.9 + - - +
125F SER* 3.0 13.5 + - - +
127F GLU* 1.3 75.4 - - - +
129F GLU* 1.3 65.9 + - + +
131F SER* 3.3 7.5 + - - -
132F LEU* 2.9 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F PHE* 3.5 18.3 - - + -
51F HIS* 3.7 24.0 - - + +
118F HIS* 2.9 34.2 + - - -
120F SER* 2.6 31.6 + - - -
121F ASP 5.2 0.2 + - - -
125F SER* 2.7 31.6 + - - +
126F ALA 3.9 2.9 - - - +
128F LYS* 1.3 77.7 - - + +
130F ILE* 1.3 68.0 + - - +
132F LEU* 3.0 8.1 + - + -
133F TRP* 3.0 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ARG* 3.9 37.0 - - + +
7F THR 4.3 2.2 - - - -
8F PHE* 4.1 20.2 - - + -
77F VAL* 4.0 27.1 - - + -
126F ALA 2.7 34.6 + - - +
127F GLU* 3.9 16.2 - - - +
129F GLU* 1.3 72.0 - - - +
131F SER* 1.3 59.5 + - - +
134F PHE* 3.0 34.4 + - + +
139F LEU* 4.4 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127F GLU* 2.7 24.2 + - - -
128F LYS* 3.6 6.9 - - - -
130F ILE* 1.3 79.7 - - - +
132F LEU* 1.3 62.4 + - - +
134F PHE 3.6 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F HIS* 3.5 27.9 - - + +
50F GLN* 4.0 30.3 - - + +
51F HIS* 3.6 43.7 - - + +
128F LYS* 2.9 25.1 + - - +
129F GLU* 3.0 9.6 + - + +
131F SER* 1.3 81.1 - - - +
133F TRP* 1.3 67.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 133 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F PHE* 3.4 37.0 - + + -
10F ALA* 5.3 2.7 - - + -
39F LYS* 2.8 31.8 + - - -
41F LEU* 4.1 16.2 - - + -
43F ALA* 3.9 20.6 - - + -
47F HIS* 3.2 36.1 + + - -
48F LEU* 4.5 9.2 - - + -
51F HIS* 2.9 39.8 + + + -
68F MET* 5.4 3.8 - - + -
73F VAL* 3.9 29.6 - - + -
75F ALA* 3.9 15.7 - - + -
129F GLU 3.0 25.9 + - - +
132F LEU* 1.3 86.2 - - + +
134F PHE* 1.3 63.5 + - + +
----------------------------------------------------------
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