Contacts of the strand formed by residues 13 - 17 (chain F) in PDB entry 3JUT
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 HIS 13 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU 3.6 0.2 - - - +
7F TYR* 3.6 1.6 - - - -
8F CYS* 2.7 31.5 + - + +
10F ASN 4.1 5.9 + - - -
11F GLY 3.9 1.8 - - - -
12F GLY* 1.3 83.4 + - - +
14F PHE* 1.3 63.0 + - - +
25F GLY* 3.7 7.0 - - - -
26F THR* 3.7 22.7 - - - +
27F ARG* 3.4 54.1 + - + +
103F LEU* 3.7 21.3 - - + -
104F LYS 4.2 2.4 + - - -
105F LYS 3.4 15.5 - - - -
106F ASN 3.9 4.0 + - - -
107F GLY* 3.5 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 14 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LEU* 3.7 32.8 - - + -
6F LEU 3.1 6.1 - - - +
7F TYR* 3.9 32.1 - + + -
12F GLY 5.0 2.5 - - - -
13F HIS* 1.3 73.5 - - - +
15F LEU* 1.3 65.3 + - - +
16F ARG 3.4 0.5 + - - -
25F GLY* 3.2 4.4 - - - -
26F THR 2.9 47.5 + - - +
27F ARG* 3.8 17.3 - - - -
28F ASP 4.1 10.5 - - - -
29F ARG* 3.8 31.2 - - + -
34F ILE* 3.8 27.0 - - + +
103F LEU* 4.5 0.2 - - - -
127F LEU* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 2.7 44.0 + - + +
13F HIS 4.0 0.4 + - - -
14F PHE* 1.3 71.4 - - - +
16F ARG* 1.3 59.4 + - - +
17F ILE* 4.4 4.6 + - + -
23F VAL* 3.8 26.2 - - + -
24F ASP 3.8 9.2 - - - +
33F HIS 4.2 0.2 - - - +
34F ILE* 3.5 17.5 - - - +
36F LEU* 3.9 19.8 - - + +
48F ILE* 4.7 2.7 - - + -
57F LEU* 3.9 29.2 - - + -
65F LEU* 4.9 2.0 - - + -
101F VAL* 4.3 17.7 - - + -
103F LEU* 3.8 22.4 - - + +
124F PHE* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LYS* 3.8 10.3 - - - +
14F PHE 4.3 2.9 - - - +
15F LEU* 1.3 73.9 - - - +
17F ILE* 1.3 64.6 + - - +
18F LEU* 3.6 31.1 - - + +
22F THR 3.9 0.5 - - - +
23F VAL* 3.3 23.0 - - - +
24F ASP* 2.9 58.3 + - - +
25F GLY* 4.2 4.4 + - - -
26F THR* 3.8 20.5 + - + +
31F ASP* 3.2 36.9 + - - -
33F HIS* 3.5 23.6 - - + +
34F ILE* 3.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 17 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F LEU* 4.4 4.2 + - + -
16F ARG* 1.3 75.5 - - - +
18F LEU* 1.3 73.6 + - - +
19F PRO 3.8 0.5 - - - -
22F THR 3.9 1.6 - - - +
23F VAL* 3.8 17.5 - - + -
33F HIS* 2.9 31.4 + - - +
36F LEU* 4.1 22.7 - - + -
48F ILE* 4.2 8.5 - - + +
50F SER* 4.3 19.6 + - - +
55F GLN* 4.0 18.6 + - + +
57F LEU* 3.9 36.1 - - + +
67F GLY* 3.8 27.8 - - - -
----------------------------------------------------------
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