Contacts of the strand formed by residues 242 - 246 (chain B) in PDB entry 6Q0R
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 242 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TRP* 3.0 16.3 + - - -
236B GLN 3.3 10.8 - - - +
237B LEU* 3.7 0.9 - - - -
239B LYS* 3.2 44.5 + - + +
240B ASP 4.1 2.2 - - - +
241B GLN* 1.4 82.0 - - + +
243B VAL* 1.3 74.4 + - - +
244B LEU* 4.5 11.7 - - + -
253B ALA* 4.1 15.3 - - + -
254B CYS 3.3 12.6 - - - +
255B ALA* 4.1 15.9 - - + -
523C LEU* 5.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TRP* 3.6 28.9 - - + -
153B ILE* 4.4 10.8 - - + -
155B PHE* 3.7 22.7 - - + -
182B VAL* 5.2 2.5 - - + -
184B THR* 5.0 5.2 - - - +
236B GLN* 3.3 4.5 - - - +
237B LEU* 3.6 16.6 - - + -
242B VAL* 1.3 72.7 - - - +
244B LEU* 1.3 64.5 + - - +
245B LEU* 3.9 24.0 + - + +
252B VAL 3.2 3.8 - - - +
253B ALA* 3.6 0.7 - - - -
254B CYS* 2.8 42.7 + - + +
256B VAL* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B PHE 3.7 22.7 - - - +
236B GLN* 2.8 48.3 + - - +
238B LYS 5.8 0.2 - - - +
239B LYS* 6.1 1.8 - - + +
242B VAL* 4.5 8.7 - - + -
243B VAL* 1.3 74.0 - - - +
245B LEU* 1.3 59.1 + - - +
246B ASN 4.2 0.6 + - - -
251B LEU* 3.9 28.9 - - + -
252B VAL 3.4 2.0 - - - -
253B ALA* 4.4 14.4 - - + -
478C ILE* 4.2 9.6 - - + -
481C VAL* 3.7 23.1 - - + -
488C VAL* 3.8 24.0 - - + -
521C TRP* 4.3 9.9 - - + -
523C LEU* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PHE* 3.8 28.9 - - + -
182B VAL* 3.8 23.6 - - + -
220B THR* 4.7 4.7 - - + -
222B TYR* 3.4 29.8 - - + +
236B GLN* 4.2 2.2 - - - +
243B VAL* 3.9 17.7 - - + +
244B LEU* 1.3 75.5 - - - +
246B ASN* 1.3 62.4 + - - +
247B THR* 3.4 2.5 + - + -
250B SER 3.5 0.7 - - - +
251B LEU* 3.4 5.7 - - - +
252B VAL* 2.9 42.2 + - + +
254B CYS* 4.4 19.3 - - + -
415C LEU* 4.2 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B TYR* 3.3 18.6 + - - -
224B VAL* 3.7 6.6 - - - +
229B PRO* 3.3 30.9 - - + +
230B THR 5.0 5.0 + - - +
232B GLN* 5.7 0.6 + - - -
236B GLN* 5.0 4.1 - - - +
244B LEU 4.2 0.8 + - - -
245B LEU* 1.3 69.6 - - - +
247B THR* 1.3 57.3 + - - +
248B SER* 3.0 23.5 + - - +
250B SER 3.7 3.4 - - - -
251B LEU* 4.1 12.6 - - + +
450C PHE* 3.2 22.7 - - - -
475C ASP* 5.4 0.2 + - - -
476C ILE* 3.1 35.0 + - - +
478C ILE* 6.2 1.3 - - + -
----------------------------------------------------------
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