Contacts of the helix formed by residues 5 - 14 (chain A) in PDB entry 5NS3
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 5 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA* 1.3 69.2 + - - +
7A LEU 3.2 3.8 - - - +
8A LYS* 3.1 15.7 + - + +
9A ARG* 3.0 51.3 + - + +
97A ASP* 5.3 11.2 - - - +
100A TRP* 4.5 13.7 - - - +
101A ILE* 4.4 28.0 - - + +
104A GLU* 3.6 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 1.3 77.9 - - - +
7A LEU* 1.3 55.0 + - - +
9A ARG* 3.3 15.3 + - - +
10A LYS* 3.0 27.9 + - - +
104A GLU* 2.9 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL 3.2 0.8 - - - -
6A ALA* 1.3 72.1 - - - +
8A LYS* 1.3 65.9 + - - +
10A LYS* 3.3 13.7 + - + +
11A TYR 3.1 17.3 + - - -
100A TRP* 3.9 24.7 - - + +
103A LEU* 3.6 33.0 - - + -
104A GLU* 3.1 32.3 + - + +
107A LEU* 4.0 16.8 - - + -
176A LEU* 3.4 41.0 - - + +
178A PHE* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 3.1 17.9 + - + +
7A LEU* 1.3 76.9 - - - +
9A ARG* 1.3 66.8 + - + +
11A TYR* 3.1 12.0 + - - +
12A TYR* 3.2 46.1 + - + -
96A ARG 6.3 0.2 - - - -
97A ASP* 3.0 27.6 + - - +
100A TRP* 3.6 50.4 - - + +
33D G 5.8 4.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 3.0 39.6 + - + +
6A ALA* 3.3 14.3 + - - +
8A LYS* 1.3 74.8 - - + +
10A LYS* 1.3 58.6 + - - +
12A TYR* 3.1 8.0 + - - +
13A GLU* 2.8 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA 3.0 14.1 + - - +
7A LEU* 3.4 17.5 - - + +
8A LYS 3.2 0.2 - - - -
9A ARG* 1.3 75.8 - - - +
11A TYR* 1.3 57.4 + - - +
13A GLU* 4.9 1.3 - - - -
14A GLU* 2.8 62.5 + - + +
15A VAL* 3.0 13.8 + - + -
175A LEU 3.5 22.5 + - - -
176A LEU* 3.7 23.2 + - + +
177A GLY* 4.1 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU 3.1 6.2 + - - +
8A LYS 3.1 10.6 + - - +
10A LYS* 1.3 76.0 - - - +
12A TYR* 1.3 92.7 - + - +
15A VAL* 3.9 17.7 - - + -
16A ARG* 2.8 60.2 + - + +
19A LEU* 4.8 0.7 - - + -
28A VAL 5.4 0.2 + - - -
31A VAL* 3.8 7.3 + - - +
32A PRO 2.6 29.9 + - - -
33A ARG* 3.4 21.9 - - + +
34A LEU 5.8 0.2 - - - -
100A TRP* 3.7 28.9 - + + -
172A LEU* 3.6 24.2 - - + -
176A LEU* 3.9 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 3.2 51.7 + - + -
9A ARG* 3.1 8.7 + - - +
11A TYR* 1.3 99.3 - + - +
13A GLU* 1.3 61.6 + - - +
16A ARG* 3.5 45.3 + - - +
17A PRO* 3.5 15.9 - - - +
33A ARG* 6.1 0.5 - - - -
100A TRP* 5.4 3.1 - + - -
33D G 5.4 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 2.8 24.0 + - + +
10A LYS* 4.9 0.9 - - - -
12A TYR* 1.3 73.8 - - - +
14A GLU* 1.3 75.7 + - + +
17A PRO* 3.4 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 2.8 52.5 + - + +
13A GLU* 1.3 94.8 - - + +
15A VAL* 1.3 63.9 + - + +
16A ARG 3.6 0.7 - - - -
17A PRO* 3.8 3.0 - - - +
18A GLU* 3.4 23.2 + - - +
21A ARG* 5.1 1.2 + - - -
----------------------------------------------------------
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