Contacts of the helix formed by residues 76 - 82 (chain E) in PDB entry 3E8E
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 LYS 76 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E LEU 3.3 1.8 + - - -
75E ASP* 1.3 70.9 - - - +
77E GLN* 1.3 58.3 + - - +
79E VAL* 3.2 5.4 + - - +
80E VAL* 3.0 32.6 + - - +
111E LYS* 5.1 6.6 - - + +
112E ASP 2.7 29.8 + - - -
113E ASN* 2.9 18.0 + - - +
114E SER 2.9 21.9 + - - +
115E ASN 3.7 4.5 - - - +
116E LEU* 3.7 25.6 - - + -
341E GLU* 4.3 7.7 - - - +
342E LYS* 2.8 25.8 + - + +
343E CYS* 4.0 11.9 + - + +
344E GLY* 5.4 0.6 - - - -
347E PHE* 3.5 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E ASP* 3.1 10.7 + - - +
76E LYS* 1.3 76.1 - - - +
78E LYS* 1.3 59.0 + - + +
80E VAL* 3.4 3.6 + - - +
81E LYS* 2.9 32.2 + - - +
114E SER 4.7 0.6 + - - +
342E LYS* 3.3 51.3 + - + +
343E CYS* 4.0 13.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E SER 3.7 19.6 + - - +
54E PHE* 3.7 18.4 - - + -
55E GLY 5.3 0.2 - - - +
75E ASP* 3.1 35.9 + - + +
77E GLN* 1.3 75.4 - - + +
79E VAL* 1.3 60.7 + - - +
81E LYS* 4.0 22.4 - - + +
82E LEU* 3.0 37.5 + - + +
336E ARG* 6.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E PHE* 3.7 27.8 - - + -
74E LEU* 4.0 16.2 - - + -
75E ASP 2.9 20.1 + - - +
76E LYS* 3.2 7.8 + - - +
78E LYS* 1.3 74.0 - - - +
80E VAL* 1.3 65.7 + - - +
82E LEU 3.4 1.2 + - - -
83E LYS 3.2 3.1 + - - -
84E GLN* 2.9 60.1 + - + +
85E ILE* 3.6 3.4 - - - +
88E THR* 3.6 13.0 - - + -
116E LEU* 5.0 1.8 - - + -
347E PHE* 3.6 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E LYS 3.0 20.2 + - - +
77E GLN* 3.5 7.9 - - - +
79E VAL* 1.3 73.6 - - - +
81E LYS* 1.3 66.8 + - - +
83E LYS* 3.0 17.0 + - - +
85E ILE* 4.0 18.2 - - + +
343E CYS* 3.5 23.6 - - - -
346E GLU* 4.0 21.5 - - + +
347E PHE* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E GLN* 2.9 21.6 + - - +
78E LYS* 3.5 24.8 - - + +
80E VAL* 1.3 74.7 - - - +
82E LEU* 1.3 75.7 + - + +
83E LYS* 3.4 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E SER* 3.6 35.9 - - - +
54E PHE* 3.8 17.7 - - + -
78E LYS* 3.0 24.4 + - + +
80E VAL 3.2 0.2 - - - -
81E LYS* 1.3 91.8 - - + +
83E LYS* 1.3 64.9 - - - +
84E GLN* 3.0 30.9 - - + +
23F HIS* 6.3 3.8 - - + -
24F ASP* 4.3 5.7 - - - -
----------------------------------------------------------
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