Contacts of the helix formed by residues 11 - 18 (chain F) in PDB entry 5VSU
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 VAL 11 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ILE* 5.9 2.7 - - + -
35E VAL* 3.9 23.8 - - + +
36E GLY* 3.7 33.7 - - - +
37E PHE 4.5 11.0 + - - +
44E ILE* 4.3 8.3 - - + -
70E ARG* 5.2 5.0 + - - +
10F SER* 1.3 88.8 + - - +
12F THR* 1.3 56.3 + - + +
14F GLU* 3.6 11.5 + - - +
15F PHE* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 12 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE* 4.5 4.0 - - - -
38E ASP* 3.8 44.0 + - + +
42E ASN 4.1 10.3 - - - +
44E ILE* 4.0 18.4 - - + -
72E LEU* 4.1 15.3 - - + -
10F SER 4.2 5.9 + - - -
11F VAL* 1.3 78.5 - - - +
13F THR* 1.3 66.9 + - - +
15F PHE* 3.0 9.7 + - - +
16F LEU* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 13 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F SER* 2.9 26.7 + - - +
12F THR* 1.3 83.0 + - - +
14F GLU* 1.3 66.1 + - - +
16F LEU* 3.2 18.8 + - + +
17F SER* 3.0 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 14 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E ARG* 6.3 0.2 - - - -
10F SER* 3.0 29.8 + - - +
11F VAL* 4.0 8.7 - - - +
13F THR* 1.3 78.0 - - - +
15F PHE* 1.3 55.9 + - - +
17F SER* 3.1 7.8 + - - -
18F ASP* 2.7 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 15 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ILE* 3.5 29.4 - - + -
70E ARG* 3.4 57.0 - - + +
71E MET* 4.2 0.9 - - - -
72E LEU* 3.6 31.9 - - + -
11F VAL 3.1 13.5 + - - +
12F THR 3.0 9.1 + - - +
14F GLU* 1.3 74.4 - - - +
16F LEU* 1.3 76.6 + - + +
18F ASP* 3.0 19.5 - - - +
19F ILE* 3.1 59.0 + - + +
41F ILE* 5.7 0.2 - - + -
81F ILE* 4.3 7.9 - - + -
82F SER* 5.3 0.9 - - - -
83F GLU* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 6.4 2.2 - - + -
72E LEU* 4.4 12.8 - - + -
12F THR* 2.9 20.3 + - - +
13F THR* 3.5 19.3 - - + +
15F PHE* 1.3 88.6 - - + +
17F SER* 1.3 65.0 + - - +
19F ILE* 3.4 13.1 + - - +
20F ILE* 3.4 18.6 + - - +
41F ILE* 3.4 39.8 - - + +
42F ASP* 3.7 25.1 - - - +
43F GLY* 4.4 7.6 - - - -
45F MET* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F THR 3.0 13.5 + - - -
14F GLU* 3.1 11.6 + - - -
16F LEU* 1.3 79.4 - - - +
18F ASP* 1.3 59.1 + - - +
19F ILE 3.3 3.6 + - - -
20F ILE* 3.6 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 18 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E ARG* 5.4 5.1 + - - -
14F GLU* 2.7 28.1 + - - +
15F PHE* 3.0 17.8 - - - +
17F SER* 1.3 74.7 - - - +
19F ILE* 1.3 62.6 + - - +
20F ILE 3.8 1.3 - - - -
22F LYS* 3.1 27.1 + - - +
83F GLU* 4.4 0.3 - - - +
----------------------------------------------------------
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