Contacts of the helix formed by residues 11 - 20 (chain L) in PDB entry 2WWA
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 ASP 11 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193H LYS* 4.5 1.6 - - - +
194H TYR* 3.6 31.9 + - - +
9L SER* 3.6 10.6 + - - -
10L SER* 1.4 85.7 + - - +
12L ARG* 1.4 77.2 + - - +
13L ARG* 3.1 32.7 + - - +
14L LYS* 3.3 16.1 + - - +
15L ALA* 3.7 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L ASP* 1.4 76.5 + - - +
13L ARG* 1.4 57.1 + - - +
14L LYS 3.3 0.2 - - - -
15L ALA* 3.3 16.8 + - - +
16L ARG* 3.1 42.1 + - + +
19L TYR* 3.4 38.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 13 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L SER* 4.2 15.0 + - - -
11L ASP* 3.2 26.2 + - + +
12L ARG* 1.4 76.0 - - - +
14L LYS* 1.4 60.7 + - - +
16L ARG* 3.3 13.2 + - + +
17L LYS* 3.2 45.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 14 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2L ALA* 5.7 8.7 - - + -
7L ASP* 3.2 44.9 + - - +
9L SER* 3.5 30.9 + - - +
10L SER 5.0 1.6 - - - +
11L ASP* 3.3 14.5 + - - +
13L ARG* 1.4 75.8 - - - +
15L ALA* 1.4 64.3 + - - +
17L LYS* 3.3 31.0 + - + +
18L ALA* 3.6 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L ASP 3.7 3.5 + - - +
12L ARG* 3.3 42.1 + - - +
13L ARG 3.3 0.2 - - - -
14L LYS* 1.4 78.3 - - - +
16L ARG* 1.4 57.0 + - - +
18L ALA* 3.3 9.8 + - - +
19L TYR* 3.2 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L ARG* 3.1 30.0 + - + +
13L ARG* 3.3 14.1 + - + +
15L ALA* 1.4 74.3 - - - +
17L LYS* 1.4 60.0 + - - +
18L ALA 3.3 0.2 - - - -
19L TYR* 3.7 13.5 - - + -
20L PHE* 3.1 54.6 + - + +
21L THR* 3.9 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 17 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L ASP* 3.1 29.9 + - - +
9L SER* 3.7 11.7 + - - -
13L ARG* 3.2 41.0 + - + +
14L LYS* 3.5 24.2 - - + +
15L ALA 3.3 0.6 - - - -
16L ARG* 1.4 75.7 - - - +
18L ALA* 1.4 57.3 + - - +
21L THR* 3.0 41.7 - - + +
22L ALA* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1L MET* 5.2 10.8 - - + -
14L LYS 3.6 5.5 + - - +
15L ALA* 3.3 13.4 + - - +
17L LYS* 1.4 79.4 - - - +
19L TYR* 1.4 60.8 + - + +
20L PHE 3.6 0.2 + - - -
21L THR 3.9 1.3 - - - +
27L ARG* 3.1 25.3 + - - -
30L LEU* 3.9 17.1 - - + +
78L PHE* 3.6 19.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 19 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L ARG* 3.4 38.4 + - - -
15L ALA* 3.2 33.4 + - + +
16L ARG* 3.5 12.5 + - + +
18L ALA* 1.4 78.9 - - + +
20L PHE* 1.4 87.1 + + + +
27L ARG* 3.2 17.6 + - - +
76L LEU* 3.7 10.6 - - - +
78L PHE* 3.8 27.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 20 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D C 4.7 1.7 + - - -
16L ARG* 3.1 45.2 + - + +
19L TYR* 1.4 98.3 - + + +
21L THR* 1.4 65.9 + - - +
22L ALA 4.0 0.9 + - - -
23L PRO* 4.7 5.2 - - - +
27L ARG* 3.6 7.5 + - - +
----------------------------------------------------------
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