Contacts of the strand formed by residues 78 - 83 (chain S) in PDB entry 2A3W
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 HIS 78 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74S TYR* 3.1 5.4 - - - -
75S ILE 2.9 35.4 + - - +
76S GLY 3.1 13.9 + - - -
77S ARG* 1.3 82.4 - - + +
79S LYS* 1.3 59.7 + - - +
119S LEU* 3.3 12.1 - - + +
120S ARG* 3.8 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348M CPJ 5.9 1.4 + - - -
66S GLU* 3.9 24.8 + - - +
72S SER* 4.3 0.7 - - - +
73S LEU 3.5 3.6 - - - -
74S TYR* 3.3 43.4 + - + +
77S ARG 4.0 0.9 + - - +
78S HIS* 1.3 76.0 - - - +
80S VAL* 1.3 74.0 + - - +
81S THR* 3.4 23.8 - - - +
119S LEU* 4.0 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12R PRO 5.1 1.1 - - - +
71S TYR 4.0 0.2 - - - +
72S SER* 3.2 5.5 - - - -
73S LEU* 2.9 49.6 + - + +
79S LYS* 1.3 78.4 - - - +
81S THR* 1.3 63.4 + - - +
105S ALA* 4.0 25.6 - - + -
107S PHE* 4.8 4.9 - - + -
117S LYS* 3.7 24.9 - - + -
118S GLY 3.7 24.7 - - - +
119S LEU* 3.8 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R ASP* 4.6 0.2 - - - +
66S GLU* 4.3 3.5 + - + -
70S GLU* 4.2 27.1 - - + +
71S TYR 3.3 9.6 - - - +
72S SER* 2.6 24.3 + - - +
79S LYS* 3.4 20.3 - - - +
80S VAL* 1.3 75.2 - - - +
82S SER* 1.3 68.2 + - - +
83S LYS* 5.5 2.0 - - + -
107S PHE* 5.7 0.2 - - - -
117S LYS* 3.0 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R ASP* 3.4 6.8 + - - -
70S GLU* 3.5 2.8 - - - -
71S TYR* 2.9 33.3 + - - +
81S THR* 1.3 71.7 + - - +
83S LYS* 1.3 64.6 + - - +
107S PHE* 4.3 12.8 - - - -
114S LEU* 3.8 25.3 - - - +
115S VAL 2.7 27.1 + - - -
117S LYS* 3.4 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 83 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40R TYR* 5.0 2.9 + - - -
42R ASP* 2.8 38.4 + - + +
43R LEU* 4.9 0.4 - - - +
44R SER* 3.0 28.7 + - - +
88R PHE* 4.0 14.3 - - + -
89R PRO* 3.6 25.1 - - + +
69S GLY 3.3 6.3 - - - +
70S GLU* 3.7 35.0 - - + +
81S THR* 5.5 2.7 - - + -
82S SER* 1.3 75.2 - - - +
84S VAL* 1.3 62.8 + - - +
114S LEU* 3.8 14.7 - - - +
115S VAL* 5.2 1.0 + - - +
----------------------------------------------------------
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