Contacts of the strand formed by residues 88 - 91 (chain C) in PDB entry 6E90
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 ILE 88 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LYS* 4.2 11.7 - - + -
5C LYS 3.0 7.0 + - - +
6C VAL* 3.4 9.5 - - + +
7C CYS 2.9 27.5 + - - +
32C PHE* 4.1 20.2 - - + -
86C ALA* 3.4 1.8 - - - +
87C ASP* 1.3 87.1 - - + +
89C LEU* 1.3 65.7 + - - +
90C ILE* 4.3 17.5 - - + -
114C THR* 3.4 15.3 - - - +
116C ILE* 4.9 1.3 - - + +
173C GLN* 4.8 1.6 - - - +
176C LEU* 3.8 29.8 - - + -
177C LEU* 4.1 23.6 - - + -
180C LEU* 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C CYS* 3.5 11.2 - - + +
9C VAL* 4.6 5.4 - - + -
83C ALA* 3.6 31.2 - - + +
86C ALA* 3.8 20.6 - - + +
88C ILE* 1.3 73.2 - - - +
90C ILE* 1.3 58.4 + - - +
91C PHE* 3.6 23.0 - - + -
105C LEU* 5.7 0.4 - - + -
109C LEU* 4.0 25.1 - - + -
113C ALA* 3.9 21.8 - - + -
114C THR 2.8 19.2 + - - +
115C GLY* 3.1 1.7 - - - -
116C ILE* 2.8 32.7 + - - +
142C ILE* 4.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 3.6 29.2 - - + -
7C CYS 2.9 11.6 + - - +
8C ILE* 3.7 12.7 - - + -
9C VAL* 2.8 29.3 + - - +
18C ILE* 4.3 11.0 - - + -
22C VAL* 4.0 24.2 - - + -
88C ILE* 4.3 5.6 - - + -
89C LEU* 1.3 71.9 - - - +
91C PHE* 1.3 60.6 + - - +
92C VAL* 3.7 8.4 + - + +
116C ILE* 3.5 17.5 - - + -
118C LEU* 3.8 32.8 - - + -
180C LEU* 4.3 8.7 - - + -
181C MET* 4.7 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.9 19.1 - - + -
89C LEU* 3.6 36.6 - - + -
90C ILE* 1.3 69.0 - - - +
92C VAL* 1.3 61.4 + - - +
93C VAL* 3.9 0.9 - - + -
98C ILE* 3.9 22.2 - - + -
101C ILE* 5.0 0.4 - - + -
102C CYS* 4.8 1.6 - - - -
105C LEU* 4.1 22.7 - - + -
115C GLY* 4.2 2.2 - - - -
116C ILE 2.8 16.4 + - - +
117C SER* 4.3 5.4 - - - +
118C LEU* 2.9 29.5 + - - +
119C ILE* 3.6 18.9 - - + +
136C ILE* 3.8 16.4 - - + -
140C LEU* 3.7 26.2 - - + -
142C ILE* 4.1 12.1 - - + -
144C MET* 4.1 11.7 - - + -
----------------------------------------------------------
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