Contacts of the helix formed by residues 12 - 20 (chain R) 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 PHE 12 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R ALA* 3.4 21.9 + - + -
11R GLU* 1.3 82.0 - - - +
13R LYS* 1.3 63.7 + - - +
14R GLU* 4.5 5.2 - - + +
15R ALA* 3.6 21.7 - - + +
16R PHE* 3.2 16.3 + - - +
38R SER 5.6 0.4 - - - -
39R LEU* 3.7 35.2 - - + +
65R PHE* 3.5 10.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11R GLU* 3.5 4.9 + - - +
12R PHE* 1.3 71.0 - - - +
14R GLU* 1.3 63.5 + - + +
16R PHE* 3.2 5.3 + - + +
17R SER* 2.9 28.9 + - - -
65R PHE* 3.3 41.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R PHE* 3.3 5.1 - - + -
13R LYS* 1.3 82.9 - - + +
15R ALA* 1.3 61.4 + - - +
17R SER* 3.2 19.0 + - - -
18R LEU* 3.2 27.7 + - + +
115S LYS* 4.9 13.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R PHE* 3.3 26.3 + - + +
14R GLU* 1.3 77.4 - - - +
16R PHE* 1.3 61.7 + - - +
18R LEU* 3.2 24.2 + - - +
19R PHE* 3.3 18.5 + - - -
35R VAL* 5.2 2.7 - - + -
38R SER* 4.8 19.0 + - - +
39R LEU* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 16 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R PHE 3.2 7.0 + - - +
13R LYS* 3.2 11.0 + - + +
15R ALA* 1.3 75.7 - - - +
17R SER* 1.4 57.0 + - - +
19R PHE* 3.0 7.9 + - - +
20R ASP* 2.8 32.5 + - + -
25R GLY* 3.3 25.1 - - - -
27R ILE* 3.5 41.3 - - + -
35R VAL* 4.5 3.3 - - + +
39R LEU* 5.7 0.4 - - - +
63R ILE* 3.6 17.9 - - + -
64R ASP 4.2 2.5 - - - -
65R PHE* 3.5 55.4 - + + -
68R PHE* 3.7 25.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R LYS* 2.9 14.5 + - - -
14R GLU* 3.2 21.5 + - - -
16R PHE* 1.4 74.3 - - - +
18R LEU* 1.3 59.5 + - - +
19R PHE 3.5 0.2 - - - -
20R ASP* 2.9 24.1 - - - +
111S ASN* 3.7 12.3 + - - -
112S LEU* 4.0 4.9 - - - +
115S LYS* 3.0 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887M LEU* 3.7 44.6 - - + -
14R GLU* 3.2 22.2 - - + +
15R ALA* 3.2 15.7 + - - +
16R PHE 3.1 0.4 - - - -
17R SER* 1.3 81.3 - - - +
19R PHE* 1.3 63.2 + - + +
20R ASP 4.0 1.8 - - - -
21R LYS* 3.1 20.1 + - - +
111S ASN 4.3 2.9 - - - +
112S LEU* 3.6 39.0 - - + +
113S GLY 4.5 1.6 - - - +
115S LYS* 5.3 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 19 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882M HIS* 3.5 38.1 - + - -
15R ALA 3.3 11.8 + - - +
16R PHE* 3.0 9.5 + - - +
18R LEU* 1.3 79.6 - - + +
20R ASP* 1.3 61.2 + - - +
21R LYS* 2.7 30.8 + - - +
22R ASP* 5.0 0.5 - - - +
27R ILE* 3.8 24.4 - - + +
31R GLU* 3.6 30.1 - - + -
34R THR* 3.4 29.4 - - - -
35R VAL* 3.8 28.5 - - + -
38R SER* 4.0 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 20 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R PHE* 2.8 21.8 + - + +
17R SER* 2.9 31.4 - - - +
18R LEU 4.0 1.6 - - - -
19R PHE* 1.3 71.1 - - - +
21R LYS* 1.3 57.9 + - - +
22R ASP* 3.2 6.5 + - - +
23R GLY* 2.6 36.1 + - - -
24R ASP* 3.4 3.8 + - - +
25R GLY* 3.1 30.5 + - - -
26R THR 4.2 7.6 - - - +
27R ILE* 3.4 16.1 - - + +
107S HIS* 4.5 0.5 - - - -
111S ASN* 3.3 7.9 + - - -
----------------------------------------------------------
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