Contacts of the strand formed by residues 150 - 153 (chain F) in PDB entry 3U8M
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 150 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F ILE* 3.7 11.4 - - + -
26F PRO* 4.3 0.2 - - - -
27F VAL* 3.7 6.1 - - + +
29F VAL* 3.9 17.7 - - + -
82F TRP* 3.9 24.0 - - + -
84F PRO* 4.1 10.1 - - + -
85F ASP* 3.8 5.8 - - - +
86F LEU* 5.4 0.4 - - + -
142F SER* 3.8 20.4 - - - +
145F HIS* 3.7 36.8 - - + +
146F HIS 2.8 21.4 + - - +
147F SER* 3.4 13.8 - - - -
149F GLU* 1.3 79.4 - - - +
151F SER* 1.3 69.7 + - - +
152F VAL* 4.3 9.1 + - + -
193F GLU* 4.4 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 151 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F PRO* 4.2 11.7 - - - +
27F VAL 3.2 6.7 + - - +
28F ALA* 3.8 17.0 - - - +
29F VAL* 2.9 26.5 + - - +
147F SER 4.5 7.0 - - - -
150F ILE* 1.3 75.7 - - - +
152F VAL* 1.3 61.3 + - - +
153F ASP* 4.0 10.7 + - - -
180F LYS* 4.9 0.4 - - - -
193F GLU* 3.1 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F VAL* 3.4 6.7 - - + +
31F VAL* 4.4 10.3 - - + -
86F LEU* 4.0 27.6 - - + -
140F ILE 4.9 0.9 - - - +
141F GLY* 4.4 8.5 - - - -
142F SER 4.4 2.2 - - - +
150F ILE* 4.3 10.5 - - + -
151F SER* 1.3 74.9 - - - +
153F ASP* 1.3 61.5 + - - +
180F LYS* 2.7 33.0 + - - +
193F GLU* 3.0 13.4 + - + +
194F ASP* 3.3 44.2 - - - +
195F VAL* 4.0 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 153 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F ALA* 6.0 0.5 - - - +
29F VAL 3.0 9.7 + - - +
30F SER* 3.3 8.8 - - - +
31F VAL 3.0 24.1 + - - +
151F SER* 4.0 12.6 + - - +
152F VAL* 1.3 87.4 - - - +
154F PRO* 1.3 76.7 - - + +
180F LYS* 3.1 29.6 + - - +
195F VAL* 3.9 5.4 - - - -
----------------------------------------------------------
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