Contacts of the strand formed by residues 48 - 53 (chain A) in PDB entry 4WPN
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 48 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO* 3.8 20.6 - - + +
40A VAL 3.6 7.9 - - - +
41A PHE* 3.6 18.5 - - + -
46A GLU 3.9 0.2 + - - -
47A GLU* 1.3 77.1 + - - +
49A LEU* 1.3 62.5 + - - +
50A CYS 3.7 15.3 - - - +
51A GLN* 3.3 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.7 20.3 - - + +
40A VAL* 2.7 14.7 + - + +
41A PHE 4.1 10.1 - - - +
42A ASN* 3.9 19.7 - - + +
47A GLU* 3.5 2.0 + - + +
48A GLU* 1.3 74.5 - - - +
50A CYS* 1.3 64.2 + - - +
109A MET* 3.5 53.6 - - + +
110A ASN* 4.0 20.2 - - + +
200A LEU* 4.4 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 3.8 28.3 - - + -
21A THR* 4.4 4.0 - - + -
39A PRO* 3.7 3.1 - - - +
40A VAL* 3.0 27.8 + - - +
48A GLU* 3.7 8.9 - - - +
49A LEU* 1.3 80.7 - - - +
51A GLN* 1.3 67.0 + - - +
52A VAL* 4.1 11.2 - - - -
200A LEU* 3.7 33.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.5 22.2 + - - +
37A LYS* 3.8 37.7 - - + +
38A PHE* 3.4 25.3 + - - +
39A PRO* 3.7 7.6 - - + +
48A GLU* 3.3 23.0 - - - +
50A CYS* 1.3 75.4 - - - +
52A VAL* 1.3 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.5 18.8 - - - +
37A LYS* 3.2 6.1 - - - -
38A PHE* 2.8 45.8 + - + +
40A VAL* 3.7 21.3 - - + -
50A CYS* 4.1 2.7 - - - -
51A GLN* 1.3 78.1 - - - +
53A GLU* 1.3 75.3 + - - +
199A PRO* 4.2 4.0 - - + -
200A LEU* 3.9 22.4 - - + -
203A LEU* 4.1 7.0 - - + -
223A PRO* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.0 20.2 + - - +
22A LYS* 3.6 24.7 + - + +
23A ILE* 4.0 22.5 - - + +
30A HIS 3.9 6.5 - - - +
31A ASP* 3.6 21.4 - - - +
32A SER* 3.4 22.2 + - - +
35A GLY 4.6 2.9 - - - +
36A LYS 3.9 5.2 - - - +
37A LYS* 3.4 31.8 + - - +
38A PHE* 3.6 5.0 - - - -
52A VAL* 1.3 81.0 - - - +
54A GLU* 1.3 60.0 + - - +
55A GLY 3.6 2.9 + - - -
223A PRO* 3.7 10.0 - - - +
----------------------------------------------------------
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