Contacts of the strand formed by residues 234 - 239 (chain C) in PDB entry 6A3V
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 VAL 234 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ARG* 3.3 28.7 - - - +
94C GLN* 3.6 33.4 - - + +
95C LEU 3.4 3.4 - - - +
96C VAL* 3.9 14.8 - - + -
109C TRP* 4.2 3.4 - - - -
144C PHE* 4.0 3.9 - - + +
145C PHE* 3.8 2.6 - - - -
146C GLN* 3.0 57.4 + - + +
231C GLY 3.6 10.5 - - - +
232C ALA 4.4 1.3 - - - -
233C THR* 1.3 81.3 - - - +
235C LEU* 1.3 65.4 + - - +
236C GLY 4.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ALA 4.8 0.2 - - - -
94C GLN* 3.5 1.6 - - - -
95C LEU* 3.0 33.4 + - + +
109C TRP* 3.6 26.7 - - + -
133C LEU* 3.9 32.8 - - + +
143C VAL* 3.6 24.9 - - + -
144C PHE 3.6 16.6 - - - +
145C PHE* 4.4 14.1 - - + -
165C LEU* 3.8 16.6 - - + -
212C LEU* 5.3 1.1 - - + +
214C VAL* 3.8 21.8 - - + -
234C VAL* 1.3 74.6 - - - +
236C GLY* 1.3 60.6 + - - +
237C LEU* 6.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 236 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ALA 3.5 7.2 - - - -
94C GLN* 4.1 7.0 - - - -
143C VAL* 3.5 8.7 - - - +
144C PHE* 3.3 59.9 + - - -
234C VAL* 4.1 0.2 - - - +
235C LEU* 1.3 75.2 - - - +
237C LEU* 1.3 63.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 3.7 3.4 - - - +
92C PHE* 3.3 4.0 - - - +
93C ALA* 2.7 50.2 + - + +
124C LEU* 4.3 20.9 - - + -
133C LEU* 5.1 11.2 - - + -
135C VAL* 4.3 6.3 - - + -
141C TYR* 3.5 33.0 - - + -
142C TYR 3.6 6.7 - - - -
143C VAL* 3.7 23.8 - - + -
144C PHE* 4.1 2.0 - - - -
206C LEU* 3.8 22.9 - - + -
212C LEU* 4.3 10.1 - - + -
235C LEU* 6.0 0.9 - - + -
236C GLY* 1.3 75.7 - - - +
238C PHE* 1.3 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 3.9 17.9 - + - -
203A LEU* 4.0 18.6 - - + -
238A PHE* 3.7 28.5 - + - -
240A VAL* 4.4 15.9 - - + -
91C MET 4.1 0.7 - - - +
92C PHE* 3.5 23.1 - - + +
141C TYR* 3.3 8.3 - - - -
142C TYR* 2.9 74.2 + + + -
144C PHE* 4.6 3.4 - + - -
237C LEU* 1.3 78.0 - - - +
239C ARG* 1.3 73.0 + - - +
240C VAL* 4.6 3.6 - - + -
238E PHE* 3.8 17.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C MET* 3.3 39.9 + - + +
137C LYS* 3.5 26.9 - - - +
138C ALA 2.5 27.4 + - - -
139C GLY* 4.1 6.9 - - - -
140C VAL 4.2 4.0 - - - +
141C TYR* 3.5 31.8 + - + -
238C PHE* 1.3 87.7 - - - +
240C VAL* 1.3 65.3 + - - +
241C THR* 3.1 25.9 + - - +
242C PRO 4.6 3.0 + - - -
243C GLU* 4.5 24.7 - - - +
----------------------------------------------------------
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