Contacts of the helix formed by residues 243 - 247 (chain B) in PDB entry 3QNF
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 243 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B GLU 5.6 0.2 - - - -
197B PRO* 2.9 28.7 + - - -
200B LYS* 3.6 8.3 - - - +
203B PHE* 4.6 0.2 - - - -
242B MET* 1.3 86.8 - - - +
244B THR* 1.3 66.3 + - - +
245B TYR* 3.8 26.2 - - - -
246B LEU* 3.2 23.2 + - - +
247B VAL* 3.8 0.5 + - - +
362B ASN 5.7 0.2 + - - -
365B THR* 3.5 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 4.2 10.5 - - + +
182B PHE* 3.6 10.2 - - - -
187B ALA* 3.7 9.9 - - - +
191B PHE* 4.8 1.5 - - + -
193B CYS* 4.2 13.5 - - + -
194B PHE 3.8 18.0 + - - +
195B ASP* 2.8 33.0 + - - -
196B GLU 4.1 7.3 + - - +
197B PRO* 5.2 0.2 - - - +
199B PHE 4.9 6.2 + - - +
203B PHE* 3.6 28.5 - - + -
242B MET 4.0 0.8 + - - -
243B SER* 1.3 73.5 - - - +
245B TYR* 1.3 60.7 + - - +
247B VAL* 3.2 20.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B PHE* 3.6 26.8 - - - +
183B GLU* 3.5 38.5 + - + -
184B PRO 3.5 22.2 - - - +
195B ASP* 4.8 1.8 - - - +
197B PRO* 3.9 20.0 - - + -
243B SER* 3.2 25.7 - - - -
244B THR* 1.3 81.4 + - - +
246B LEU* 1.3 81.7 + - + +
247B VAL 3.4 0.4 - - - -
319B MET* 4.0 6.3 - - + +
320B GLU* 4.7 1.8 + - - -
321B ASN* 4.0 8.7 + - - -
361B GLY 3.7 15.1 + - - -
362B ASN* 4.6 0.5 + - - -
365B THR* 4.1 4.5 - - + -
366B MET* 3.2 26.1 - - + +
369B TRP* 3.8 15.5 - + + -
375B ASN* 4.3 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ASN* 3.0 18.4 + - - -
242B MET* 3.5 15.0 - - + -
243B SER* 3.2 16.3 + - - +
244B THR 3.2 1.0 - - - -
245B TYR* 1.3 108.2 - - + +
247B VAL* 1.3 62.4 + - - +
319B MET* 4.1 2.2 - - + -
320B GLU* 3.4 31.0 - - + +
321B ASN* 3.4 9.5 - - - +
322B TRP* 3.2 14.7 + - + +
361B GLY 4.1 5.2 - - - +
362B ASN* 3.3 51.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 4.9 1.1 - - + -
180B THR* 4.1 1.4 + - - -
182B PHE* 3.0 38.7 - - + -
191B PHE* 4.4 9.4 - - + -
203B PHE* 3.8 38.1 - - + -
205B ILE* 3.7 19.7 - - + -
218B ASN* 3.2 11.7 - - - +
242B MET* 3.7 16.8 - - + -
243B SER 4.0 1.6 - - - +
244B THR* 3.2 14.9 + - - +
246B LEU* 1.3 76.6 - - - +
248B ALA* 1.3 64.3 + - - +
249B PHE* 4.4 7.9 - - + -
321B ASN* 4.2 3.5 + - - -
----------------------------------------------------------
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