Contacts of the strand formed by residues 80 - 86 (chain E) in PDB entry 3T0E
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 ASP 80 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ASN* 3.9 13.0 + - - +
31E SER* 2.9 44.2 + - - -
32E ASN* 4.7 0.7 - - - +
77E GLU 5.2 0.7 - - - +
78E ASP 3.2 5.5 + - - +
79E SER* 1.3 76.9 - - - +
81E THR* 1.3 66.1 + - - +
82E TYR* 3.6 20.8 + - + -
94E GLN* 3.2 11.0 - - - +
95E LEU* 2.8 32.6 + - - +
96E LEU* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ASN 3.8 0.5 - - - -
31E SER* 3.1 36.1 + - - +
80E ASP* 1.3 77.8 + - - +
82E TYR* 1.3 63.3 + - - +
83E ILE* 3.9 8.1 - - + +
92E GLU* 3.7 28.9 - - + +
93E VAL 3.6 12.1 - - - +
94E GLN* 3.3 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E LEU* 4.5 15.7 - - + -
28E TRP* 4.3 9.0 - - + -
29E LYS 3.5 2.9 - - - +
30E ASN* 4.0 23.8 - - + -
36E ILE* 4.7 5.4 - - + -
51E LEU* 3.9 22.1 - - + +
69E LEU* 4.4 19.3 - - + -
71E ILE* 3.9 23.7 - - + +
78E ASP* 3.1 24.8 + - - -
80E ASP* 3.6 22.7 + - + +
81E THR* 1.3 81.0 - - - +
83E ILE* 1.3 63.1 + - - +
92E GLU* 3.7 4.9 - - - +
93E VAL* 3.0 46.7 + - + +
95E LEU* 4.6 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TRP* 2.7 28.0 - - - -
29E LYS* 2.8 41.2 + - + +
30E ASN 4.4 2.0 - - - +
31E SER* 4.4 15.3 - - - +
33E GLN* 5.0 5.6 - - - +
81E THR* 3.9 17.7 - - + +
82E TYR* 1.3 79.5 - - - +
84E CYS* 1.3 69.7 + - - +
85E GLU* 3.6 33.4 - - + +
90E LYS* 4.4 14.1 - - + +
91E GLU 3.8 4.5 - - - -
92E GLU* 4.8 8.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E CYS* 2.0 49.9 - - + -
26E PHE* 5.5 4.3 - - - -
27E HIS 3.8 7.6 - - - -
28E TRP* 3.8 30.1 - - + -
67E PHE* 4.8 0.9 - - - -
83E ILE* 1.3 78.0 - - - +
85E GLU* 1.3 69.9 + - - +
86E VAL* 3.9 2.5 + - - -
89E GLN* 2.9 14.4 - - - +
90E LYS 3.6 1.2 - - - -
91E GLU* 3.0 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E PHE* 3.3 24.0 - - - -
27E HIS* 2.7 49.0 + - + +
29E LYS* 3.6 23.9 + - - +
33E GLN* 5.2 1.4 + - - -
83E ILE* 3.6 17.6 - - + +
84E CYS* 1.3 77.0 - - - +
86E VAL* 1.3 59.6 + - - +
88E ASP* 5.3 0.9 - - - -
89E GLN 3.2 11.2 - - - +
90E LYS* 5.1 12.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E CYS* 3.9 25.1 - - - -
17E THR* 4.5 0.4 - - - -
18E ALA* 3.8 22.9 - - + +
24E ILE* 3.5 22.7 - - + -
25E GLN 3.3 20.2 - - - +
26E PHE* 4.0 10.8 - - + -
67E PHE* 4.2 9.2 - - + -
84E CYS 5.2 0.2 - - - +
85E GLU* 1.3 74.1 - - - +
87E GLU* 1.3 75.3 + - - +
88E ASP 3.0 3.1 + - - -
89E GLN* 3.1 30.5 + - + +
----------------------------------------------------------
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