Contacts of the strand formed by residues 272 - 277 (chain C) in PDB entry 3F9Z
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 MET 272 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ALA* 3.6 30.3 - - - +
258C ARG* 4.3 5.4 - - + -
259C GLU* 3.5 35.9 - - + +
262C TYR* 3.7 17.9 - - - -
270C CYS* 3.8 1.6 - - - +
271C TYR* 1.3 78.6 - - - +
273C TYR* 1.3 60.3 + - - +
274C TYR* 4.0 4.3 - - + +
283C CYS* 3.7 23.6 - - - -
284C VAL 3.4 3.8 - - - -
285C ASP* 3.5 32.3 - - + +
287C THR* 4.0 2.9 - - - +
17G ARG* 3.7 13.9 - - - +
19G ARG* 4.3 2.4 - - - -
20G LYS* 3.3 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C PHE* 3.6 40.6 - + + -
272C MET* 1.3 73.6 - - - +
274C TYR* 1.3 70.9 + - - +
275C PHE* 3.7 5.9 - - - -
283C CYS* 3.2 4.0 - - - -
284C VAL* 2.9 36.1 + - + +
307C THR* 2.7 40.9 + - + -
318C LEU* 3.6 13.7 - - + -
320C LEU* 5.4 1.1 - - + -
334C TYR* 3.7 30.9 - + - -
335C ASP 4.3 6.4 + - - -
336C TYR 4.9 0.2 - - - -
20G LYS* 3.7 23.8 - - + -
21G VAL 3.9 5.2 + - - -
22G LEU* 3.7 32.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 3.6 34.5 - - + -
252C ILE* 4.6 11.0 - - + -
255C ALA* 3.5 33.3 + - + +
256C LYS* 4.0 7.2 + - + +
259C GLU* 3.1 43.5 + - - +
272C MET* 4.0 6.4 - - + +
273C TYR* 1.3 77.4 - - - +
275C PHE* 1.3 62.9 + - - +
276C GLN* 5.9 0.4 - - - +
281C THR* 4.3 12.3 - - + -
282C TYR 3.3 9.6 - - - +
283C CYS* 3.9 16.4 - - + -
19G ARG* 4.4 10.5 - - + -
20G LYS 3.0 21.4 + - - +
21G VAL* 3.5 9.9 - - + -
22G LEU 3.0 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C LEU* 3.7 12.8 - - + -
273C TYR 3.7 7.0 - - - -
274C TYR* 1.3 76.0 - - - +
276C GLN* 1.3 78.8 + - - +
277C TYR* 3.9 10.1 - - + -
281C THR* 3.5 4.4 - - - +
282C TYR* 2.8 61.8 + - + +
283C CYS 4.1 2.5 - - - -
284C VAL* 3.7 24.7 - - + -
309C LEU* 3.6 27.1 - - + -
316C PRO* 3.7 20.9 - - + -
318C LEU* 3.6 28.7 - - + -
22G LEU* 4.0 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 5.8 1.8 - - - +
225A GLY* 3.5 18.0 - - - +
226A LYS 4.3 2.0 - - - -
227A GLY* 3.2 36.0 - - - +
274C TYR* 5.9 0.2 - - - +
275C PHE* 1.3 89.1 - - - +
277C TYR* 1.3 63.8 + - - +
279C SER* 5.7 2.7 - - - +
280C LYS 3.4 2.6 - - - +
281C THR* 2.4 42.3 + - - +
309C LEU* 4.3 10.7 - - - +
21G VAL* 5.2 7.7 - - - +
22G LEU* 4.7 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C PHE* 3.9 10.7 + - + -
276C GLN* 1.3 77.2 - - - +
278C LEU* 1.3 106.0 + - + +
279C SER 3.2 0.9 - - - -
280C LYS* 2.9 19.4 + - - +
282C TYR* 3.4 32.3 - + + -
309C LEU* 3.5 23.3 - - + -
311C ASP* 2.8 42.2 + - + -
314C GLY* 3.4 34.3 - - - -
316C PRO* 3.6 22.7 - - + -
----------------------------------------------------------
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