Contacts of the strand formed by residues 79 - 83 (chain D) in PDB entry 2WJ7
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 VAL 79 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASN* 3.7 29.8 - - + +
16D LEU 3.3 12.8 - - - +
17D ASP* 5.2 6.1 - - + +
73D SER 3.6 2.4 - - - +
74D LEU* 3.1 4.6 - - - +
75D SER* 2.9 40.6 + - - +
77D ASP* 3.2 17.7 + - - +
78D GLY* 1.3 76.9 - - - +
80D LEU* 1.3 67.8 + - - +
81D THR* 4.2 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D VAL 3.6 1.2 - - - +
15D ASN* 3.3 4.5 - - - -
16D LEU* 2.8 41.4 + - + +
18D VAL* 3.8 25.6 - - + -
26D LEU* 4.8 13.5 - - + -
28D VAL* 4.1 15.9 - - + -
37D VAL* 3.9 30.7 - - + -
72D SER* 4.8 6.1 - - - +
73D SER 4.0 14.8 - - - +
74D LEU* 4.0 14.4 - - + +
78D GLY 3.7 1.0 + - - -
79D VAL* 1.3 73.6 - - - +
81D THR* 1.3 77.1 + - - +
82D VAL* 4.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D VAL 3.4 3.4 - - - +
15D ASN* 3.3 32.6 + - - +
72D SER* 2.9 9.0 - - - -
73D SER* 2.7 49.7 + - - +
79D VAL* 4.2 4.3 - - - +
80D LEU* 1.3 75.7 - - - +
82D VAL* 1.3 70.3 + - - +
83D ASN* 3.3 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D VAL* 2.9 43.0 + - + +
16D LEU* 5.8 3.6 - - + -
28D VAL* 4.4 18.4 - - + -
35D ILE* 4.0 28.0 - - + -
37D VAL* 5.0 6.1 - - + -
59D TYR* 6.1 2.2 - - + -
70D ILE* 3.4 27.6 - - + -
71D THR 3.4 6.7 - - - +
72D SER* 3.9 10.3 - - - -
80D LEU* 4.8 9.9 - - + -
81D THR* 1.3 80.8 - - - +
83D ASN* 1.3 67.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D VAL 5.2 2.2 - - - +
69D THR 3.7 0.2 - - - +
70D ILE* 2.9 10.7 - - - +
71D THR* 2.6 74.3 + - - +
72D SER* 4.5 2.3 + - - -
73D SER* 5.7 1.8 - - - -
81D THR* 3.3 24.3 - - - +
82D VAL* 1.3 76.6 - - - +
84D GLY* 1.3 56.5 + - - +
----------------------------------------------------------
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