Contacts of the strand formed by residues 12 - 17 (chain D) in PDB entry 5XVO
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 SER 12 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 3.6 18.2 - - - +
10D LYS 2.5 19.3 + - - -
11D HIS* 1.3 80.4 + - - +
13D LYS* 1.3 66.6 + - - +
14D LEU* 4.2 0.6 - - - +
23D PHE* 3.7 24.4 - - - -
24D LYS 3.3 13.9 - - - -
25D ALA* 4.5 0.4 - - - +
46D ASP 3.3 7.0 + - - +
47D ILE* 3.5 8.7 - - - +
48D SER* 3.0 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LYS* 4.0 18.6 - - - +
11D HIS* 6.6 0.4 - - - -
12D SER* 1.3 74.0 - - - +
14D LEU* 1.3 64.6 + - - +
15D SER* 4.5 4.0 + - - +
22D VAL 3.4 2.8 - - - +
24D LYS* 2.8 49.0 + - + +
48D SER* 3.6 21.5 - - - +
-21R T 3.3 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 4.3 14.1 - - + -
12D SER* 5.0 0.7 - - - +
13D LYS* 1.3 73.4 - - - +
15D SER* 1.3 64.7 + - - +
21D LEU* 4.3 12.3 - - + -
22D VAL 3.2 6.3 - - - +
23D PHE* 3.9 36.1 - - + -
40D LEU* 4.4 9.4 - - + -
42D LEU* 3.7 30.1 - - + -
47D ILE* 4.0 17.3 - - + -
48D SER 2.8 12.6 + - - +
49D LEU* 3.3 29.0 - - + -
50D THR* 3.4 7.3 + - - +
53D LEU* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LYS* 4.5 4.3 + - - +
14D LEU* 1.3 76.8 - - - +
16D TYR* 1.3 62.6 + - - +
21D LEU* 3.7 4.2 - - - -
22D VAL* 2.8 48.5 + - - +
24D LYS* 5.1 5.7 - - - +
50D THR* 4.0 11.2 - - - -
53D LEU* 3.8 10.1 - - - +
-20R C 5.9 0.7 - - - -
-19R G 3.4 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D SER* 1.3 76.3 - - - +
17D LYS* 1.3 63.1 + - - +
19D ASN* 2.9 39.0 + - - -
20D HIS 3.4 13.0 - - - -
22D VAL* 4.2 1.1 - - - -
34D LEU* 3.6 20.2 - - + -
52D MET* 3.9 18.4 - - + -
53D LEU* 3.8 22.7 - - + +
56D ARG* 2.8 47.2 + - + -
-19R G 2.6 52.5 + - - +
-18R T 3.6 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D TYR* 1.3 75.3 - - - +
18D ASN* 1.3 96.3 + - + +
19D ASN 3.3 2.0 - - - -
20D HIS* 2.8 28.7 + - + +
22D VAL* 3.8 16.9 - - + +
29D GLN* 5.6 4.2 - - - +
31D LEU* 4.9 18.7 - - + +
-19R G 6.1 0.4 - - - -
-18R T 3.7 18.6 - - - +
----------------------------------------------------------
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