Contacts of the strand formed by residues 82 - 90 (chain T) 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 T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80T LYS 4.3 0.4 + - - -
81T LEU* 1.3 73.8 - - - +
83T TYR* 1.3 62.2 + - - -
84T ALA* 4.1 0.3 + - - +
132T PHE 3.4 2.3 - - - +
133T VAL* 3.5 0.9 - - - -
134T ASP* 2.9 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 83 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43T ASN* 5.9 5.6 - - + -
67T VAL* 4.6 9.7 - - - +
81T LEU* 3.9 23.5 - - + +
82T GLY* 1.3 73.6 - - - -
84T ALA* 1.3 60.3 + - - +
85T ASN 4.3 0.7 + - - -
131T SER* 4.9 13.9 - - - -
132T PHE 3.4 3.6 - - - +
133T VAL* 3.7 30.3 - - + -
259T ILE* 5.4 9.7 - - + +
281T GLY 4.9 4.0 - - - -
282T SER* 3.9 27.4 - - - -
335T GLY* 4.8 5.4 - - - -
336T LEU* 3.7 45.4 - - + +
410T SER* 5.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58T VAL* 4.7 20.0 - - + +
62T SER* 5.2 8.5 - - - -
67T VAL* 4.8 12.1 - - + -
82T GLY 4.1 0.9 + - - +
83T TYR* 1.3 73.2 - - - +
85T ASN* 1.3 66.1 + - - +
86T ALA* 4.9 1.0 - - - +
130T VAL 3.6 1.0 - - - +
131T SER* 3.5 2.4 - - - -
132T PHE* 2.9 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 85 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39T GLN 4.4 17.0 - - - +
62T SER* 3.4 17.7 - - - -
66T THR* 5.5 5.4 - - - -
67T VAL* 5.3 4.6 - - - +
83T TYR 4.2 1.2 + - - -
84T ALA* 1.3 72.7 - - - +
86T ALA* 1.3 60.0 + - - +
129T HIS* 5.8 2.0 - - + -
130T VAL 3.7 5.2 - - - +
131T SER* 4.4 7.2 - - - +
324T GLU* 5.8 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61T ILE* 4.9 6.3 - - + +
62T SER* 3.7 22.2 - - - +
84T ALA 4.9 1.3 - - - +
85T ASN* 1.3 77.2 - - - +
87T LYS* 1.3 59.7 + - - +
88T ILE* 3.3 8.6 + - + +
129T HIS* 3.2 7.1 - - - +
130T VAL* 2.9 44.8 + - + +
132T PHE* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T ARG 5.5 5.4 - - - +
85T ASN* 4.3 0.6 - - - +
86T ALA* 1.3 68.7 - - - +
88T ILE* 1.3 60.2 + - - +
89T TYR* 3.1 12.7 + - - +
126T LEU* 4.9 14.8 - - + -
128T ARG 4.7 0.9 - - - -
129T HIS* 4.2 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86T ALA* 3.3 10.7 + - + +
87T LYS* 1.3 69.2 - - - +
89T TYR* 1.3 62.0 + - - +
126T LEU* 4.5 1.0 - - - -
127T VAL* 4.4 9.2 + - - +
128T ARG 3.6 20.5 + - - +
130T VAL* 6.0 3.8 - - + +
236T CYS* 5.2 20.4 - - + +
240T VAL* 5.2 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87T LYS 3.1 8.7 + - - +
88T ILE* 1.3 75.3 - - - +
90T LYS* 1.3 64.8 + - - +
124T PHE* 3.8 20.9 - - + -
125T LYS 3.4 19.3 - - - +
126T LEU* 4.1 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89T TYR* 1.3 76.0 - - - +
91T LEU* 1.3 61.4 + - - +
124T PHE* 3.4 8.3 - - - +
125T LYS* 2.8 36.8 + - - +
----------------------------------------------------------
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