Contacts of the helix formed by residues 18 - 26 (chain R) in PDB entry 5L4K
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 ARG 18 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R LEU* 1.3 70.1 - - + +
19R ILE* 1.3 63.2 + - + +
20R ALA 3.1 0.7 - - - -
21R GLN* 2.8 46.2 + - - +
22R LEU* 2.4 58.3 + - + +
152R MET* 5.5 1.4 - - - -
186R LEU* 4.0 24.9 - - - +
212R GLU 4.4 3.6 - - - +
213R LEU* 3.1 30.3 - - - +
214R MET* 4.2 16.8 - - + +
222R TYR* 5.4 4.2 + - - -
287R LEU* 2.7 52.6 + - - +
288R PHE* 4.6 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R LYS* 5.2 13.5 - - - +
16R ASP* 4.6 17.5 - - - +
17R LEU 2.4 20.4 + - - +
18R ARG* 1.3 70.1 - - + +
20R ALA* 1.3 54.7 + - - +
22R LEU* 4.8 1.8 - - - -
23R ARG* 3.0 37.0 + - - +
40R GLU* 3.8 23.0 - - + +
43R ALA* 6.2 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R ASP* 3.0 36.3 + - + +
18R ARG 3.1 0.4 - - - -
19R ILE* 1.3 75.6 - - - +
21R GLN* 1.3 62.3 + - - +
23R ARG* 3.2 39.6 + - - +
24R PHE* 4.2 7.1 - - - +
150R PHE* 3.6 25.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 21 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R LEU* 3.2 20.4 - - - +
18R ARG* 2.8 60.6 + - - +
20R ALA* 1.3 79.8 - - - +
22R LEU* 1.3 57.9 + - - +
23R ARG 3.2 1.3 - - - -
24R PHE* 2.6 33.0 + - - +
25R LEU 3.1 5.9 + - - -
149R LEU* 3.3 25.2 + - - +
150R PHE* 4.0 27.3 - - + +
152R MET* 4.6 6.6 - - - +
287R LEU* 3.2 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18R ARG* 2.4 65.6 + - + +
19R ILE* 4.4 2.2 - - - +
21R GLN* 1.3 68.4 - - - +
23R ARG* 1.3 61.2 + - - +
24R PHE 2.9 1.4 + - - -
25R LEU* 3.2 2.9 + - + +
26R LEU* 3.1 45.7 + - + +
40R GLU* 4.5 5.6 - - - +
222R TYR* 5.9 0.4 - - - +
285R ASP 4.2 3.6 - - - +
286R TRP* 3.7 48.2 - - + -
287R LEU* 4.2 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R ASP* 5.5 0.2 + - - -
19R ILE* 3.0 28.7 + - - +
20R ALA* 3.2 35.9 + - - +
22R LEU* 1.3 75.5 - - - +
24R PHE* 1.3 55.8 + - - +
26R LEU* 4.0 1.4 - - - -
27R SER* 2.5 35.4 + - - -
37R VAL* 4.3 1.7 - - - +
40R GLU* 3.1 48.5 + - + +
41R LEU* 3.6 32.6 - - + +
44R ALA* 4.0 23.5 - - - +
49R ASN* 5.8 0.4 + - - -
54R TYR* 4.3 20.6 + - - -
57R LEU* 3.7 22.5 - - - +
150R PHE* 5.0 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R ALA 4.2 9.2 - - - +
21R GLN* 2.6 22.6 + - - +
22R LEU 2.9 0.2 + - - -
23R ARG* 1.3 76.6 - - + +
25R LEU* 1.3 66.4 + - - +
27R SER* 3.1 16.7 + - - -
28R LEU* 3.8 11.7 - - + +
56R ALA 5.7 1.1 - - - -
57R LEU* 4.1 30.1 - - + -
60R SER* 5.7 1.8 - - - -
61R LEU* 3.6 36.3 - - + +
152R MET* 6.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R GLN 3.1 6.7 + - - -
22R LEU* 3.2 4.0 + - + +
24R PHE* 1.3 79.4 - - - +
26R LEU* 1.3 61.3 + - + +
28R LEU* 3.1 38.7 + - + +
31R HIS* 3.4 11.2 + - + +
284R LYS 4.2 15.0 - - - +
285R ASP 4.9 2.2 - - - +
286R TRP* 4.2 9.6 - - - +
287R LEU* 3.8 38.6 - - + -
292R TYR* 3.9 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 26 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22R LEU* 3.1 35.5 + - + +
23R ARG* 4.0 3.8 - - - +
25R LEU* 1.3 77.7 - - + +
27R SER* 1.3 56.2 + - - +
28R LEU 3.2 3.4 + - - -
31R HIS* 3.6 23.4 + - + +
32R ARG* 3.9 21.1 - - + +
37R VAL* 3.4 21.0 - - + +
40R GLU* 5.3 4.5 - - - +
285R ASP* 3.3 49.1 - - + +
----------------------------------------------------------
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