Contacts of the helix formed by residues 269 - 279 (chain A) in PDB entry 1EZF
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 HIS 269 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASP* 4.7 2.2 + - - -
206A SER* 3.9 32.5 - - - +
209A LEU* 3.3 35.8 - - + +
210A PHE* 4.0 14.5 + - + -
213A LYS* 2.9 41.6 + - + +
265A ASN 4.3 7.2 - - - -
266A ALA* 3.2 20.9 + - - +
267A LEU 2.9 1.8 + - - -
268A HIS* 1.3 81.3 - - + +
270A ILE* 1.3 65.4 + - - +
271A PRO 3.4 1.8 - - - -
272A ASP* 3.2 8.7 + - - +
273A VAL* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PHE* 3.5 26.7 - - + -
267A LEU* 3.0 25.7 + - - +
269A HIS* 1.3 75.8 - - - +
271A PRO* 1.3 67.6 - - + +
273A VAL* 2.9 10.3 + - + +
274A ILE* 2.8 36.6 + - + +
297A ILE* 3.4 32.3 - - + -
338A ILE* 4.0 10.5 - - + -
342A MET* 4.4 14.1 - - + -
366A ILE* 3.7 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU 4.0 0.7 - - - +
268A HIS 3.7 11.9 - - - +
269A HIS 3.6 3.6 - - - -
270A ILE* 1.3 95.9 - - + +
272A ASP* 1.3 60.3 + - - +
274A ILE* 3.3 9.5 + - + +
275A THR* 2.9 32.7 + - - -
362A ILE* 5.3 1.8 - - + -
365A THR* 5.0 1.8 - - + -
366A ILE* 3.4 25.1 - - + -
369A GLN* 3.2 31.6 - - - +
370A ASN* 5.4 2.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 3.9 11.4 - - - +
203A ARG* 3.4 39.7 + - + +
206A SER* 2.8 38.3 + - - -
268A HIS 5.3 1.3 + - - +
269A HIS* 3.2 7.5 + - - +
271A PRO* 1.3 83.2 - - - +
273A VAL* 1.3 57.2 + - - +
275A THR* 3.5 3.4 + - - -
276A TYR* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER 4.3 1.1 - - - +
207A MET* 3.8 28.7 - - - +
210A PHE* 4.1 15.9 - - + -
269A HIS 3.0 17.4 + - - +
270A ILE* 2.9 13.9 + - + +
272A ASP* 1.3 77.0 - - - +
274A ILE* 1.3 56.8 + - - +
276A TYR* 3.8 1.0 - - - +
277A LEU* 3.0 45.8 + - + +
293A GLN* 3.3 45.5 - - + +
297A ILE* 5.8 0.4 - - + -
338A ILE* 4.8 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 2.8 32.2 + - + +
271A PRO* 3.7 9.4 - - + +
273A VAL* 1.3 75.1 - - - +
275A THR* 1.3 58.3 + - - +
277A LEU* 3.5 2.4 + - - -
278A SER* 2.9 28.8 + - - -
331A MET* 3.3 9.9 - - + +
334A VAL* 6.3 0.2 - - + -
335A LYS* 3.8 32.8 - - + -
338A ILE* 4.1 24.5 - - + -
339A TYR* 4.0 29.4 - - + +
366A ILE* 4.7 2.9 - - + +
370A ASN* 4.0 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ARG* 3.9 18.2 + - - +
271A PRO 2.9 18.8 + - - -
272A ASP* 3.5 5.9 + - - -
274A ILE* 1.3 77.2 - - - +
276A TYR* 1.3 62.6 + - - +
278A SER* 2.9 22.4 + - - +
279A ARG* 3.4 43.9 - - - +
370A ASN* 4.1 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLY* 4.8 1.6 + - - -
183A LEU* 5.4 0.3 - - - +
184A SER* 2.8 30.5 + - - -
187A PHE* 3.6 25.3 - - - -
197A VAL* 3.7 18.4 - - + +
200A ASP* 5.3 0.4 - - + -
203A ARG* 3.9 14.6 - - + +
204A ALA* 3.8 28.0 - - + -
207A MET* 3.5 37.5 - - + -
272A ASP 2.8 20.6 + - - +
273A VAL 3.8 3.6 - - - +
275A THR* 1.3 74.2 - - - +
277A LEU* 1.3 68.1 + - + +
279A ARG* 3.4 17.0 + - - +
280A LEU* 3.7 23.7 - - + +
289A CYS* 4.0 10.8 - - - -
991A IN0 5.9 3.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A MET* 4.1 9.6 - - + -
273A VAL* 3.0 42.4 + - + +
274A ILE* 3.9 3.4 - - - +
276A TYR* 1.3 77.5 - - + +
278A SER* 1.3 61.8 + - - +
279A ARG 3.1 1.8 + - - -
280A LEU* 3.2 27.5 + - + +
286A PHE* 3.6 13.1 - - + -
289A CYS* 3.8 30.5 - - + -
290A ALA* 3.8 23.6 - - + +
293A GLN* 4.5 5.8 - - + -
331A MET* 3.6 16.2 - - + +
334A VAL* 4.0 25.8 - - + -
338A ILE* 5.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 2.9 18.0 + - - -
275A THR* 2.9 23.6 + - - +
277A LEU* 1.3 76.2 - - - +
279A ARG* 1.3 60.0 + - - +
280A LEU 3.5 1.4 - - - +
281A ARG* 3.2 16.5 + - - -
331A MET* 3.5 26.9 - - - +
335A LYS* 5.3 4.0 - - - -
370A ASN* 4.8 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLU* 4.2 2.9 - - - +
194A ASP* 5.7 2.9 - - - +
196A LEU* 3.7 39.9 + - + +
197A VAL* 4.6 15.2 - - + +
200A ASP* 2.7 42.0 + - - +
203A ARG* 3.7 15.7 - - - +
275A THR* 3.4 38.7 - - - +
276A TYR* 3.4 11.1 + - - +
277A LEU 3.1 1.2 - - - -
278A SER* 1.3 79.2 - - - +
280A LEU* 1.3 65.0 + - - +
281A ARG* 3.5 19.1 + - - +
----------------------------------------------------------
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