Contacts of the helix formed by residues 21 - 31 (chain E) in PDB entry 1F9N
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 21 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ILE* 3.4 5.0 - - - +
20E GLU* 1.3 92.4 - - + +
22E GLN* 1.3 65.2 + - - +
23E ASP* 3.8 13.7 + - - +
24E GLU* 2.9 41.6 + - - +
25E LEU 3.2 7.6 + - - -
62E TYR* 4.0 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E THR* 1.3 74.3 - - - +
23E ASP* 1.3 59.4 + - - +
25E LEU* 3.1 10.6 + - - +
26E VAL* 2.9 34.8 + - + +
38E GLN 4.5 2.6 - - - +
41E VAL* 4.4 3.7 - - + +
42E SER* 3.3 29.1 + - - -
45E ILE* 3.3 31.0 - - + +
62E TYR* 3.3 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E THR* 3.1 11.6 + - - +
22E GLN* 1.3 76.7 - - - +
24E GLU* 1.3 65.3 + - + +
26E VAL* 2.9 17.6 + - - +
27E ASP* 3.0 26.8 + - - +
38E GLN* 3.5 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E GLU 3.9 4.0 - - - +
19E ILE* 3.4 19.5 - - + +
20E GLU* 2.7 36.7 + - - +
21E THR* 2.9 23.7 + - - +
23E ASP* 1.3 78.7 - - + +
25E LEU* 1.3 60.9 + - - +
27E ASP* 3.7 5.4 + - - +
28E MET* 3.2 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ILE* 4.4 27.8 - - + -
13E ILE* 4.2 29.6 - - + -
14E ILE* 4.3 15.3 - - + -
19E ILE* 3.8 16.3 - - + +
21E THR 3.2 3.0 + - - +
22E GLN* 3.1 10.7 + - - +
24E GLU* 1.3 79.0 - - - +
26E VAL* 1.3 60.0 + - - +
28E MET* 4.2 1.7 - - - -
29E LEU* 3.0 32.1 + - + +
41E VAL* 4.0 22.7 - - + -
45E ILE* 4.1 18.4 - - + -
50E LEU* 4.7 7.0 - - + -
62E TYR* 5.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLN* 2.9 22.3 + - + +
23E ASP* 2.9 11.4 + - - +
25E LEU* 1.3 75.6 - - - +
27E ASP* 1.3 65.4 + - - +
29E LEU* 3.2 7.0 + - - +
30E LYS* 2.9 48.3 + - + +
36E VAL* 4.2 11.6 - - + +
37E THR* 5.2 0.4 - - - -
38E GLN* 4.3 27.1 - - + +
41E VAL* 3.5 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ASP* 3.0 26.0 + - - +
24E GLU* 4.2 4.7 + - - +
26E VAL* 1.3 78.1 - - - +
28E MET* 1.3 59.1 + - - +
30E LYS* 2.9 33.0 + - - +
31E GLN* 3.1 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E ILE* 3.9 27.0 - - + +
17E ASN* 3.8 30.5 - - + +
19E ILE* 4.1 14.4 - - + -
24E GLU 3.2 17.4 + - - +
25E LEU 4.5 2.0 - - - +
27E ASP* 1.3 79.5 - - - +
29E LEU* 1.3 56.1 + - - +
31E GLN* 3.1 32.5 - - - +
32E ASP* 2.7 31.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ARG* 3.8 31.6 - - + -
9E LYS* 4.7 10.5 - - + -
10E ILE* 4.1 25.1 - - + -
13E ILE* 3.6 24.4 - - + +
25E LEU* 3.0 23.4 + - + +
26E VAL* 3.2 5.8 + - - +
27E ASP 3.1 0.6 - - - -
28E MET* 1.3 77.8 - - - +
30E LYS* 1.3 63.6 + - - +
32E ASP* 3.5 5.5 + - + -
34E TYR* 3.3 41.0 + - + +
36E VAL* 4.2 14.4 - - + -
41E VAL* 4.3 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E VAL* 2.9 27.8 + - - +
27E ASP* 2.9 22.7 + - - +
29E LEU* 1.3 73.6 - - - +
31E GLN* 1.3 57.8 + - - +
32E ASP 2.9 10.3 + - - -
33E GLY* 3.0 14.4 + - - -
34E TYR 3.7 17.5 + - - +
36E VAL* 3.7 24.9 - - + +
37E THR* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E ASP* 3.1 8.7 + - - +
28E MET* 3.1 51.1 - - - +
30E LYS* 1.3 78.7 - - - +
32E ASP* 1.3 63.4 + - - +
33E GLY 3.3 2.5 + - - -
----------------------------------------------------------
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