Contacts of the strand formed by residues 19 - 24 (chain E) in PDB entry 1VQ9
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 19 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E GLN* 2.8 19.2 - - - +
16E ASP* 3.0 28.7 + - - +
17E HIS* 5.4 2.8 - - - +
18E LEU* 1.3 82.5 + - - +
20E ILE* 1.3 61.2 + - - +
21E THR* 5.4 0.9 - - - +
30E THR* 4.4 13.6 - - + +
31E ARG 2.9 18.8 - - - +
32E ARG* 3.3 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E ALA* 5.1 6.1 - - + -
14E GLU 3.8 9.9 - - - +
15E GLN* 3.4 22.9 - - + +
18E LEU 4.7 2.7 - - - +
19E ASP* 1.3 74.3 - - - +
21E THR* 1.3 71.2 + - - +
22E VAL* 4.6 11.7 - - + -
29E VAL 3.8 1.0 - - - +
30E THR* 3.1 2.6 - - - -
31E ARG* 2.8 33.3 + - + +
33E LEU* 3.1 31.0 - - + -
40E VAL* 3.1 36.1 - - + -
42E VAL* 5.3 3.1 - - + -
47E VAL* 5.4 5.8 - - + -
69E ILE* 4.3 6.5 - - + -
72E MET* 4.8 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ASP 4.2 0.3 - - - +
13E ALA* 3.5 2.8 - - - +
14E GLU* 2.8 51.9 + - + +
15E GLN* 4.6 0.2 - - - +
19E ASP* 4.4 0.9 - - - +
20E ILE* 1.3 73.9 - - - +
22E VAL* 1.3 72.9 + - - +
23E GLU* 4.4 14.9 - - + +
28E SER* 4.5 6.3 - - - +
29E VAL 3.3 5.2 - - - +
30E THR* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E VAL* 3.4 25.6 - - + -
12E ASP 3.9 2.7 - - - -
13E ALA* 4.0 15.9 - - + -
20E ILE* 4.6 7.2 - - + -
21E THR* 1.3 79.5 - - - +
23E GLU* 1.3 66.6 + - - +
28E SER* 2.9 6.9 - - - -
29E VAL 2.7 37.3 + - - +
69E ILE* 5.8 0.7 - - + -
72E MET* 4.1 39.3 - - + +
73E PHE* 4.4 10.8 - - + -
76E VAL* 3.7 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ASP 4.3 0.3 - - - +
11E VAL* 3.2 20.8 - - - +
12E ASP* 3.2 24.1 + - + +
14E GLU* 4.8 10.6 - - - +
21E THR* 4.4 11.3 - - + +
22E VAL* 1.3 76.7 - - - +
24E GLY* 1.3 59.1 + - - +
27E GLY 3.4 5.2 - - - +
28E SER* 3.3 23.7 - - - -
76E VAL* 3.8 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ASP* 4.0 14.1 - - - -
23E GLU* 1.3 76.8 - - - +
25E ASP* 1.3 63.3 + - - -
26E ASN 3.0 7.1 + - - -
27E GLY* 2.8 17.6 + - - +
76E VAL* 3.4 17.2 - - - +
----------------------------------------------------------
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