Contacts of the helix formed by residues 162 - 165 (chain w) in PDB entry 5XTD
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 162 (chain w).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61w THR* 4.5 18.9 + - - -
63w ASP* 4.3 3.5 + - - -
139w ARG* 4.9 3.1 - - - -
143w TYR* 3.2 23.3 - - - -
159w LEU* 5.2 3.6 - - - -
160w GLU 3.6 2.1 + - - -
161w ARG* 1.3 75.4 - - - +
163w ILE* 1.3 60.6 + - - +
164w PHE* 2.9 26.3 - - - +
165w SER* 2.8 28.4 + - - -
166w ASP* 3.5 10.4 + - - +
201w PRO* 5.0 3.7 - - - +
245w PHE* 4.7 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 163 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136w TYR* 3.0 55.3 - - + +
139w ARG* 3.5 18.7 + - + +
140w LEU* 3.8 11.2 - - + +
143w TYR* 3.1 38.8 + - + +
162w SER* 1.3 74.5 - - - +
164w PHE* 1.3 66.3 + - + +
165w SER 3.1 0.2 - - - -
166w ASP* 3.1 39.7 + - - +
167w PHE* 4.2 3.8 + - - -
187w TYR* 4.8 0.2 + - - -
195w ILE* 3.5 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 164 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143w TYR* 3.3 22.9 - + - -
162w SER* 3.2 11.0 - - - +
163w ILE* 1.3 92.2 - - + +
165w SER* 1.3 54.2 + - - +
166w ASP 3.2 1.1 - - - -
167w PHE* 2.8 38.5 - + + -
168w VAL* 5.3 0.3 - - - +
195w ILE* 3.5 36.1 - - + -
198w TYR* 5.4 4.9 - - + -
199w LEU 5.0 3.1 - - - -
200w PRO* 3.6 25.1 - - + -
201w PRO* 3.5 29.4 - - + -
245w PHE* 3.6 24.6 - + + -
248w GLU* 5.0 9.0 - - - -
252w LYS* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain w).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63w ASP* 4.2 9.1 + - - +
161w ARG* 3.4 34.9 + - - +
162w SER* 2.8 32.3 + - - -
164w PHE* 1.3 78.0 - - - +
166w ASP* 1.3 59.0 + - - +
167w PHE 3.6 0.4 - - - -
168w VAL* 3.1 24.9 - - - +
169w PHE* 4.4 2.3 + - - +
241w TYR* 4.3 18.6 - - - -
245w PHE* 5.1 2.0 - - - -
----------------------------------------------------------
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