Contacts of the helix formed by residues 8 - 20 (chain S) in PDB entry 2DFS
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 GLN 8 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S ILE* 1.4 91.6 + - + +
10S ALA* 3.3 4.9 - - + +
11S GLU* 3.0 23.7 + - - +
12S PHE* 3.1 14.1 + - - +
39S LEU* 5.5 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ASP* 5.8 6.1 - - - +
8S GLN* 1.4 97.0 - - + +
10S ALA* 1.3 59.3 + - + +
12S PHE* 4.3 10.1 - - + -
13S LYS* 2.7 31.4 + - - +
65S PHE* 4.1 11.2 - - + -
69S LEU* 4.5 21.5 - - + -
72S MET* 6.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 10 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S GLN* 3.1 3.4 + - + +
9S ILE* 1.3 78.6 - - + +
11S GLU* 1.4 63.9 + - - +
13S LYS* 3.5 5.0 + - - +
14S GLU* 3.2 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903M LYS* 3.7 18.7 + - - +
907M LYS* 2.6 43.0 + - - +
8S GLN 3.0 13.5 + - - +
10S ALA* 1.4 76.6 - - - +
12S PHE* 1.3 58.5 + - - +
14S GLU* 3.3 5.6 + - - +
15S ALA* 3.0 30.7 + - + +
38S SER 6.0 0.7 - - - +
39S LEU* 6.0 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 12 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906M LEU* 4.2 5.4 - - + -
8S GLN 3.1 15.6 + - - +
9S ILE* 4.1 9.0 - - + +
11S GLU* 1.3 76.6 - - - +
13S LYS* 1.3 58.6 + - - +
15S ALA* 3.0 22.1 - - + +
16S PHE* 3.1 17.6 + + - +
35S VAL* 3.4 27.6 - - + -
39S LEU* 3.6 49.1 - - + -
65S PHE* 3.5 29.2 - + - -
68S PHE* 3.2 41.3 - + - -
69S LEU* 5.6 5.8 - - + -
72S MET* 5.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9S ILE 2.7 23.9 + - - +
10S ALA* 3.9 4.0 - - - +
11S GLU 3.4 0.2 - - - -
12S PHE* 1.3 72.0 - - - +
14S GLU* 1.4 92.6 + - - +
16S PHE* 3.1 3.5 + - + +
17S SER* 2.8 58.7 + - - +
65S PHE* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S ALA* 3.2 17.5 + - + +
11S GLU* 3.3 4.9 + - - +
13S LYS* 1.4 110.1 + - - +
15S ALA* 1.3 63.8 + - - +
17S SER* 3.3 6.6 + - - -
18S LEU* 3.0 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906M LEU* 3.2 50.1 - - + +
907M LYS* 5.9 3.9 - - - +
909M LEU 3.6 2.1 - - - +
11S GLU* 3.0 18.7 + - + +
12S PHE* 3.0 20.0 - - + +
14S GLU* 1.3 68.8 - - - +
16S PHE* 1.4 62.9 + - - +
18S LEU* 3.0 14.6 + - - -
19S PHE 3.1 9.2 + - - -
38S SER 5.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 16 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906M LEU* 3.6 9.3 - - + +
12S PHE* 3.1 26.2 + + + +
13S LYS* 3.1 7.0 + - + +
15S ALA* 1.4 75.4 - - - +
17S SER* 1.3 58.1 + - - +
19S PHE* 3.0 3.9 + - - +
20S ASP* 3.0 29.0 + - + +
25S GLY* 3.5 22.7 - - - -
27S ILE* 3.7 38.6 - - + -
35S VAL* 4.7 3.4 - - + -
63S ILE* 3.4 18.6 - - + -
64S ASP 3.6 4.0 - - - -
65S PHE* 3.4 55.0 - + + -
68S PHE* 4.6 8.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S LYS* 2.8 40.3 + - - -
14S GLU* 3.3 15.2 + - - -
16S PHE* 1.3 73.2 - - - +
18S LEU* 1.3 69.3 + - - +
20S ASP* 3.2 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906M LEU 5.9 0.4 - - - +
907M LYS* 5.8 2.2 - - - -
908M LYS 4.6 9.4 - - - +
909M LEU* 2.9 41.0 - - + +
14S GLU* 3.0 39.3 + - + +
15S ALA* 3.0 2.9 + - - +
17S SER* 1.3 84.8 - - - +
19S PHE* 1.4 51.2 + - - +
20S ASP 3.2 1.2 - - - +
21S LYS* 2.6 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905M GLU* 5.2 9.0 - - + -
906M LEU* 3.9 32.5 - - + -
909M LEU* 3.2 10.9 + - + -
15S ALA 3.1 5.3 + - - -
16S PHE 3.0 9.2 + - - +
18S LEU* 1.4 71.2 - - - +
20S ASP* 1.3 59.5 + - - +
21S LYS* 2.7 32.3 + - + +
27S ILE* 3.9 23.1 - - + +
28S THR 5.8 0.4 - - - -
31S GLU* 3.3 36.8 - - + -
34S THR* 3.1 36.8 - - - -
35S VAL* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 20 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16S PHE* 3.0 19.4 + - + +
17S SER* 3.2 23.5 - - - +
18S LEU* 3.2 1.9 - - - +
19S PHE* 1.3 72.1 - - - +
21S LYS* 1.3 71.9 + - - +
22S ASP* 3.7 3.3 + - - +
23S GLY* 2.7 32.9 + - - -
24S ASP 3.2 8.6 + - - -
25S GLY* 2.8 29.2 + - - -
26S THR 3.7 11.5 - - - +
27S ILE* 3.5 14.1 - - + +
----------------------------------------------------------
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