Contacts of the helix formed by residues 76 - 81 (chain E) in PDB entry 1UW9
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 SER 76 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E THR* 1.3 80.9 + - - +
77E LEU* 1.3 63.9 + - - +
78E ASP* 3.8 10.0 + - - +
79E ARG* 2.9 34.6 + - - +
80E TYR* 3.3 18.7 - - - -
112I ASN* 3.7 11.9 + - - +
113I GLN* 3.9 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E THR* 3.9 17.7 - - + -
24E TYR* 4.0 5.4 - - - +
63E THR* 3.8 30.7 - - + +
72E ASP* 3.5 46.7 + - + +
75E THR* 3.9 7.7 + - + +
76E SER* 1.3 72.6 - - - +
78E ASP* 1.3 57.4 - - - +
80E TYR* 3.1 2.0 + - + +
81E LYS* 2.8 44.3 + - + +
1478E EDO 3.9 16.6 - - - +
176K PRO* 4.5 8.5 - - + -
178K LEU 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E SER* 3.2 10.0 - - - +
77E LEU* 1.3 78.4 - - - +
79E ARG* 1.3 60.6 + - - +
80E TYR 3.6 0.2 + - - -
81E LYS* 3.8 19.8 + - - +
83E ARG* 3.0 33.9 + - - +
104E HYP 4.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ASP* 4.2 18.3 + - - +
370A SER* 3.1 31.5 + - - +
32E ARG* 6.0 2.2 + - - +
76E SER* 2.9 25.7 + - - +
78E ASP* 1.3 80.6 - - - +
80E TYR* 1.3 91.0 + - + +
104E HYP 3.4 24.0 + - - -
106E ASP* 3.7 11.6 + - - +
113I GLN* 3.9 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E THR* 3.7 17.2 - - + +
75E THR* 3.3 24.9 - - + -
76E SER* 3.3 23.0 + - - +
77E LEU* 3.1 4.7 + - + +
79E ARG* 1.3 117.9 + - + +
81E LYS* 1.3 67.5 + - - +
104E HYP 3.7 3.1 - - - -
106E ASP* 3.7 27.4 + - + -
107E LEU* 3.2 42.1 - - + +
115I GLN* 4.9 3.1 + - - -
178K LEU 4.6 0.2 - - - +
179K GLY* 3.7 20.4 + - - -
211K PHE* 3.5 32.3 - + + +
----------------------------------------------------------
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
----------------------------------------------------------
23E THR* 2.8 46.9 + - + +
24E TYR* 3.6 17.7 - - + -
26E THR* 4.3 5.7 - - - +
63E THR* 3.6 13.4 - - - +
77E LEU* 2.8 25.4 + - + +
78E ASP* 3.8 16.5 + - - +
79E ARG 3.8 0.4 - - - -
80E TYR* 1.3 80.4 - - - +
82E GLY* 1.3 68.5 + - - +
83E ARG* 3.6 48.9 + - + +
104E HYP 3.5 15.7 + - - -
----------------------------------------------------------
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