Contacts of the strand formed by residues 82 - 90 (chain S) in PDB entry 6O81
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 GLY 82 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80S LYS 4.3 0.4 + - - -
81S LEU* 1.3 72.8 - - - +
83S TYR* 1.3 63.4 + - - -
84S ALA* 4.1 0.5 + - - +
132S PHE 3.4 1.9 - - - +
133S VAL* 3.5 0.9 - - - -
134S ASP* 2.9 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 83 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43S ASN* 5.9 7.0 - - + -
67S VAL* 4.6 10.0 - - - +
81S LEU* 3.9 23.7 - - + +
82S GLY* 1.3 73.9 - - - -
84S ALA* 1.3 59.5 + - - +
85S ASN 4.2 0.6 + - - -
131S SER* 4.9 13.7 - - - -
132S PHE 3.4 4.5 - - - +
133S VAL* 3.7 30.1 - - + -
259S ILE* 5.4 9.3 - - + +
281S GLY 4.9 4.0 - - - -
282S SER* 3.9 27.5 - - - -
335S GLY* 4.8 5.4 - - - -
336S LEU* 3.7 45.8 - - + +
410S SER* 5.9 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58S VAL* 4.7 20.0 - - + +
62S SER* 5.2 7.5 - - - -
67S VAL* 4.8 12.8 - - + -
82S GLY 5.4 0.7 - - - +
83S TYR* 1.3 74.1 - - - +
85S ASN* 1.3 65.2 + - - +
86S ALA* 4.9 1.4 - - - +
130S VAL 3.6 0.9 - - - +
131S SER* 3.5 2.6 - - - -
132S PHE* 2.9 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 85 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S GLN 4.4 16.6 - - - +
62S SER* 3.4 17.7 - - - -
66S THR* 5.5 5.5 - - - -
67S VAL* 5.3 4.6 - - - +
83S TYR 4.2 1.0 + - - -
84S ALA* 1.3 72.0 - - - +
86S ALA* 1.3 60.3 + - - +
87S LYS 4.3 0.4 - - - -
129S HIS* 5.8 1.8 - - + -
130S VAL 3.7 4.5 - - - -
131S SER* 4.4 7.2 - - - +
324S GLU* 5.8 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61S ILE* 4.9 6.1 - - + +
62S SER* 3.7 22.4 - - - +
84S ALA 4.9 1.3 - - - +
85S ASN* 1.3 76.1 - - - +
87S LYS* 1.3 59.7 + - - +
88S ILE* 3.3 8.0 + - + +
129S HIS* 3.2 6.5 - - - +
130S VAL* 2.9 45.4 + - + +
132S PHE* 6.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S ARG* 5.5 6.1 - - + +
86S ALA* 1.3 68.7 - - - +
88S ILE* 1.3 60.0 + - - +
89S TYR* 3.1 12.2 + - - +
126S LEU* 4.9 14.6 - - + -
128S ARG 4.7 1.1 - - - -
129S HIS* 4.2 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86S ALA* 3.3 10.5 + - + +
87S LYS* 1.3 69.6 - - - +
89S TYR* 1.3 61.9 + - - +
126S LEU* 4.5 1.0 - - - -
127S VAL* 4.4 9.0 + - - +
128S ARG 3.6 21.3 + - - +
129S HIS* 5.8 0.2 - - - -
130S VAL* 6.0 3.6 - - + +
236S CYS* 5.2 19.3 - - + +
240S VAL* 5.2 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87S LYS 3.1 9.6 + - - +
88S ILE* 1.3 76.1 - - - +
90S LYS* 1.3 64.3 + - - +
124S PHE* 3.8 21.3 - - + -
125S LYS 3.4 20.0 - - - +
126S LEU* 4.1 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89S TYR* 1.3 75.6 - - - +
91S LEU* 1.3 61.6 + - - +
124S PHE* 3.4 7.1 - - - +
125S LYS* 2.8 38.2 + - - +
----------------------------------------------------------
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