Contacts of the helix formed by residues 75 - 81 (chain E) in PDB entry 1QGH
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 LEU 75 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E THR* 1.3 71.8 - - - +
76E LYS* 1.3 56.1 + - - +
78E PHE* 3.0 10.3 + - + +
79E LEU* 2.7 33.4 + - - +
21G ASN* 4.6 4.3 - - + +
22G VAL* 4.1 23.1 - - + -
25G VAL* 3.7 32.5 - - + -
75G LEU* 4.2 22.4 - - + +
78G PHE* 3.8 37.2 - - + -
79G LEU* 3.8 19.7 - - + -
86G GLU* 2.8 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E THR* 3.1 4.0 - - - +
75E LEU* 1.3 78.4 - - - +
77E GLU* 1.3 66.1 + - + +
79E LEU* 3.3 3.7 + - - +
80E GLU* 2.8 59.6 + - + +
79G LEU* 3.6 16.3 - - + +
86G GLU* 3.2 14.5 + - - +
88G PRO* 6.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E PHE* 3.6 36.4 - - + -
73E SER* 2.9 24.4 + - - -
74E THR* 2.7 40.7 + - - +
76E LYS* 1.3 77.4 - - + +
78E PHE* 1.3 59.3 + - - +
80E GLU* 3.2 10.9 + - - +
81E ASN* 2.7 38.0 + - - +
88G PRO* 3.8 24.2 - - + +
89G TYR 4.8 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E VAL* 3.8 6.1 - - + -
18E ALA* 3.7 27.0 - - - +
21E ASN* 3.3 43.7 - - + -
22E VAL* 4.8 1.1 - - + -
72E PHE* 3.4 38.1 - - + -
73E SER* 3.9 1.3 - - - -
74E THR 3.0 26.0 + - - -
75E LEU* 3.0 13.7 + - + +
77E GLU* 1.3 75.3 - - - +
79E LEU* 1.3 58.3 + - - +
81E ASN 3.1 0.5 + - - -
82E ALA* 2.8 35.7 + - - +
25G VAL* 3.5 30.7 - - + -
32G TRP* 4.9 4.9 - + - -
75G LEU* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E VAL* 5.0 6.3 - - + -
75E LEU 2.7 17.4 + - - +
76E LYS* 3.6 4.9 - - - +
78E PHE* 1.3 73.1 - - - +
80E GLU* 1.3 65.5 + - + +
81E ASN 3.4 0.2 + - - -
82E ALA* 4.0 9.8 + - + +
86E GLU* 3.8 24.0 - - + +
75G LEU* 3.7 17.3 - - + -
76G LYS* 3.6 34.8 - - + +
79G LEU* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E LYS* 2.8 58.3 + - + +
77E GLU* 3.7 13.4 - - - +
79E LEU* 1.3 81.5 - - + +
81E ASN* 1.3 67.3 + - - +
82E ALA 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E HIS* 2.8 33.2 + - + -
18E ALA* 3.9 6.5 - - + -
72E PHE* 3.2 46.8 - - + -
77E GLU* 2.7 29.7 + - - +
80E GLU* 1.3 89.9 + - - +
82E ALA* 1.3 60.6 + - - +
----------------------------------------------------------
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