Contacts of the helix formed by residues 272 - 278 (chain F) in PDB entry 3SRF
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 ASN 272 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243F PHE* 4.0 25.2 - - + +
244F ILE 4.0 3.8 + - - -
245F ARG* 3.4 46.9 + - - +
270F ILE* 3.9 0.7 - - - +
271F GLU* 1.3 78.9 - - - +
273F HIS* 1.3 66.0 + - - +
274F GLU* 3.2 4.5 - - - +
275F GLY* 3.0 41.3 + - - +
276F VAL* 3.4 16.6 + - - +
296F LEU* 4.7 2.2 - - - +
299F GLU* 3.9 22.7 - - + +
300F ILE* 4.7 3.6 - - - -
535F GOL 5.0 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 273 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ILE* 3.7 13.8 + - + +
35E ASP* 3.0 29.9 + - - -
272F ASN* 1.3 75.4 - - - +
274F GLU* 1.3 57.4 + - - +
276F VAL* 3.5 6.5 + - - +
277F ARG* 3.1 51.5 + - + +
299F GLU* 4.4 6.2 - - + +
300F ILE* 3.6 31.9 - - + +
301F PRO* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 274 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F ARG* 2.9 61.0 + - + +
246F LYS* 3.6 14.9 + - - -
272F ASN* 3.2 8.6 - - - +
273F HIS* 1.3 76.0 - - - +
275F GLY* 1.3 65.1 + - - +
277F ARG* 3.7 25.5 + - - +
278F ARG* 3.1 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 275 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F ILE 3.8 15.7 - - - -
245F ARG 4.0 1.1 + - - -
270F ILE* 3.9 15.1 - - - +
272F ASN* 3.0 23.3 + - - +
274F GLU* 1.3 77.0 - - - +
276F VAL* 1.3 55.7 + - - +
279F PHE* 3.1 25.5 + - - +
282F ILE* 3.3 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 276 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ILE* 3.8 33.0 - - + +
270F ILE* 3.8 19.5 - - + -
272F ASN 3.4 10.1 + - - +
273F HIS* 3.8 7.6 - - - +
274F GLU 3.3 0.4 - - - -
275F GLY* 1.3 74.1 - - - +
277F ARG* 1.3 68.6 + - + +
279F PHE* 3.2 20.9 + - - +
296F LEU* 4.4 9.9 - - + -
308F ALA* 4.3 22.2 - - + -
311F MET* 3.8 22.9 - - + +
312F MET* 4.5 3.1 - - + -
315F ARG* 5.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 277 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ILE* 6.2 0.2 - - + -
35E ASP* 4.3 11.7 - - - +
273F HIS* 3.1 49.0 + - + +
274F GLU* 3.7 28.3 + - - +
276F VAL* 1.3 78.4 - - + +
278F ARG* 1.3 74.7 + - + +
279F PHE 3.6 1.7 + - - -
280F ASP* 5.1 1.2 + - - +
315F ARG* 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 278 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F ARG 3.6 20.6 - - - +
246F LYS* 3.7 21.6 - - - +
274F GLU* 3.1 39.1 + - - +
275F GLY 3.5 3.4 - - - -
277F ARG* 1.3 96.2 - - + +
279F PHE* 1.3 63.2 + - - +
280F ASP* 3.3 3.4 - - - -
281F GLU* 3.2 40.3 + - + +
282F ILE* 3.2 20.2 + - + +
----------------------------------------------------------
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