Contacts of the strand formed by residues 45 - 49 (chain Q) in PDB entry 2WUB
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 LYS 45 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Q TYR* 3.4 5.4 - - - -
37Q GLN* 2.7 56.1 + - + +
39Q LYS* 5.2 14.7 - - - +
42Q LYS* 6.2 3.4 - - - -
43Q ALA 4.1 9.4 - - - +
44Q PRO* 1.3 78.0 - - - +
46Q LEU* 1.3 65.2 + - - +
47Q LEU* 3.4 6.3 + - + +
101R ASP 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q TRP 3.5 6.5 - - - +
36Q TYR* 3.9 20.5 - - + -
44Q PRO 4.2 0.8 + - - -
45Q LYS* 1.3 71.3 - - - +
47Q LEU* 1.3 61.7 + - - +
48Q ILE 3.4 26.7 - - - +
49Q TYR* 5.0 5.8 - - + -
55Q TYR* 3.4 47.3 - - + +
58Q VAL* 3.8 6.8 - - - +
98R TRP* 5.0 4.7 - - + -
100R PHE* 3.7 36.1 + - + +
101R ASP* 3.7 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q TRP* 3.0 11.3 + - + +
36Q TYR* 4.1 6.7 - - - +
37Q GLN* 3.7 29.4 - - + +
45Q LYS* 4.0 7.0 - - + +
46Q LEU* 1.3 75.7 - - - +
48Q ILE* 1.3 77.7 + - + +
55Q TYR* 2.8 28.4 + - - +
58Q VAL* 3.4 30.1 - - + +
59Q PRO* 6.0 0.7 - - + -
62Q PHE* 4.1 17.5 - - + -
73Q LEU* 4.2 9.4 - - + -
86Q TYR* 3.6 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Q ALA* 3.1 7.2 - - - +
35Q TRP* 2.8 36.6 + - + -
46Q LEU* 3.4 7.1 - - - +
47Q LEU* 1.3 95.3 - - + +
49Q TYR* 1.3 66.9 + - - +
51Q ALA* 3.7 20.6 - - - +
52Q SER* 3.7 2.7 - - - +
53Q PHE 3.3 23.6 - - - +
54Q LEU* 3.4 37.9 - - + -
58Q VAL* 4.9 0.2 - - + -
62Q PHE* 4.5 10.5 - - + +
64Q GLY* 4.6 8.1 - - - +
73Q LEU* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C PHE 5.8 2.9 - - - -
33Q VAL 3.9 4.3 - - - -
34Q ALA* 4.1 2.5 - - + -
46Q LEU* 4.9 4.3 - - + -
48Q ILE* 1.3 75.6 - - - +
50Q SER* 1.3 86.2 + - - +
51Q ALA 3.2 2.7 - - - -
53Q PHE* 2.9 74.4 + + + +
54Q LEU 3.8 14.9 + - - -
55Q TYR* 4.3 19.5 - + + -
98R TRP* 4.0 35.3 - + + -
99R PRO* 4.0 18.6 - - + +
100R ALA* 4.5 19.1 - - + -
----------------------------------------------------------
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