Contacts of the strand formed by residues 42 - 47 (chain C) in PDB entry 4WNP
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 GLU 42 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LYS* 2.7 35.1 + - - -
33C GLY 3.6 8.7 - - - +
34C ARG* 4.6 1.3 - - + +
39C HIS 5.5 1.6 - - - +
40C ASP* 3.4 12.8 + - - +
41C LEU* 1.3 79.2 - - - +
43C VAL* 1.3 67.5 + - - +
79C TYR* 4.5 4.3 + - - -
94C TYR* 3.6 39.6 + - + +
96C ASN* 5.1 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 3.4 35.2 - - + -
32C LYS* 3.6 7.1 - - - +
33C GLY* 2.7 49.8 + - - +
34C ARG 3.7 3.6 - - - +
41C LEU* 4.1 7.0 - - + +
42C GLU* 1.3 82.3 - - - +
44C ALA* 1.3 57.4 + - - +
45C VAL* 4.2 10.3 - - + -
79C TYR* 3.8 17.0 - - + -
91C VAL* 3.9 17.9 - - + -
92C MET 3.3 10.3 - - - +
94C TYR* 3.9 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.8 20.2 - - + -
30C VAL* 4.0 2.9 - - + -
31C PHE 3.4 4.0 - - - -
43C VAL* 1.3 73.9 - - - +
45C VAL* 1.3 61.0 + - - +
46C LYS 3.8 0.9 + - - -
90C LEU 3.5 1.6 - - - +
92C MET* 2.9 34.8 + - - +
93C GLU 4.3 0.7 - - - +
94C TYR* 4.2 1.9 - - + +
401C 3RJ 3.5 46.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C VAL* 4.6 4.5 - - + -
14C PHE* 5.5 2.7 - - + -
15C GLU 5.1 1.8 - - - +
16C PHE* 3.9 43.5 - - + -
29C VAL 3.7 0.9 - - - +
30C VAL* 3.3 4.5 - - - -
31C PHE 2.8 39.7 + - - +
33C GLY* 4.8 0.9 - - - -
43C VAL* 4.2 18.6 - - + -
44C ALA* 1.3 73.4 - - - +
46C LYS* 1.3 61.9 + - - +
47C CYS* 3.8 21.2 + - - -
89C TYR* 4.1 14.4 - - + -
90C LEU 3.3 10.8 - - - +
91C VAL* 4.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA* 3.7 22.2 - - + -
29C VAL 3.5 2.7 - - - -
30C VAL* 3.9 14.8 - - + -
44C ALA 3.8 1.0 + - - -
45C VAL* 1.3 70.6 - - - +
47C CYS* 1.3 61.5 + - - +
60C LEU* 3.4 21.1 - - + +
63C GLU* 2.4 41.4 + - - +
88C VAL 3.8 0.9 - - - +
89C TYR* 3.3 6.6 - - - -
90C LEU* 2.9 47.8 + - + +
92C MET* 4.7 8.3 - - - -
165C ASP* 3.6 24.4 + - - +
167C GLY* 5.5 0.6 - - - -
401C 3RJ 4.3 25.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PHE* 4.1 4.5 - - - -
18C ARG* 4.6 7.4 - - - +
28C ALA* 3.2 9.4 - - - +
29C VAL* 2.7 34.7 + - + +
31C PHE* 3.6 35.4 - - + -
45C VAL* 3.9 10.8 - - - -
46C LYS* 1.3 75.4 - - - +
48C ILE* 1.3 66.7 + - - +
60C LEU* 3.5 7.1 - - - +
88C VAL 3.6 5.6 - - - -
89C TYR* 3.5 34.1 - - + -
----------------------------------------------------------
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