Contacts of the helix formed by residues 83 - 90 (chain B) in PDB entry 4UTX
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 THR 83 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLN 3.1 27.6 - - - +
80B ASP 3.9 7.3 + - - +
81B LEU 3.0 4.5 + - - +
82B ALA* 1.3 80.8 - - - +
84B PRO* 1.3 72.4 - - - +
85B GLU* 3.2 17.6 + - - +
86B ALA* 3.0 24.3 + - - +
87B PHE* 3.5 13.0 + - - +
218B TRP* 3.6 13.1 - - - -
219B PHE* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B THR* 1.3 86.9 - - - +
85B GLU* 1.3 77.6 + - - +
87B PHE* 3.4 2.1 + - - +
88B SER* 3.0 30.1 + - - -
213B ARG* 5.2 1.6 - - - +
218B TRP* 3.7 18.2 - - + -
219B PHE 3.4 16.6 - - - +
220B GLY 5.7 1.8 - - - +
221B GLU* 3.8 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B THR* 3.3 16.0 + - - +
84B PRO* 1.3 96.2 - - - +
86B ALA* 1.3 66.0 + - - +
88B SER* 3.3 6.0 + - - -
89B ARG* 2.9 43.2 + - - +
219B PHE 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP 3.6 14.6 - - - +
81B LEU* 3.6 29.6 - - + +
83B THR* 3.0 13.9 + - - +
85B GLU* 1.3 79.0 - - - +
87B PHE* 1.3 56.3 + - - +
89B ARG* 3.4 10.6 + - - +
90B ASP* 2.8 31.2 + - - +
94B VAL* 3.6 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B THR 3.5 3.1 + - - +
84B PRO 3.4 8.0 + - - +
85B GLU 3.2 0.6 - - - -
86B ALA* 1.3 75.1 - - - +
88B SER* 1.3 70.0 + - - +
91B PRO* 3.1 37.0 - - + +
94B VAL* 3.7 23.5 - - + +
95B TRP* 3.6 29.2 - + - -
163B MET* 3.4 34.8 - - + -
211B LEU* 3.8 19.1 - - + -
212B LEU 3.5 22.0 - - - -
213B ARG* 3.7 14.4 - - + -
214B PRO* 4.5 2.5 - - + -
218B TRP* 3.7 32.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PRO 3.0 18.2 + - - -
85B GLU* 3.5 8.7 - - - -
87B PHE* 1.3 83.4 - - - +
89B ARG* 1.3 63.6 + - - +
91B PRO* 4.0 5.7 - - - +
163B MET* 6.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLU* 2.9 33.9 + - - +
86B ALA* 3.9 9.7 - - - +
88B SER* 1.3 79.9 - - - +
90B ASP* 1.3 64.0 + - + +
91B PRO* 3.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA 2.8 16.1 + - - +
89B ARG* 1.3 80.9 - - + +
91B PRO* 1.3 66.2 - - - +
92B SER* 3.8 7.4 + - - -
93B LEU* 3.1 41.1 + - + +
94B VAL* 3.1 15.0 + - + +
192B GLU* 3.4 15.9 - - - +
194B ARG* 5.5 4.6 + - - -
----------------------------------------------------------
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