Contacts of the helix formed by residues 270 - 277 (chain A) in PDB entry 1NOZ
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 TYR 270 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A THR* 3.4 21.7 - - + +
212A GLY 3.1 22.2 + - - +
213A TRP* 3.7 21.8 - + + -
268A LEU 3.4 3.2 + - - -
269A ASP* 1.3 71.1 + - - +
271A LEU* 1.3 60.4 + - - +
272A ASP 3.2 0.2 - - - -
273A LEU* 3.8 14.4 - - + -
274A TYR* 2.9 33.4 + - + +
328A VAL* 4.4 12.3 - - + -
331A ILE* 3.9 21.1 - - + -
332A ASP* 2.5 48.7 + - + -
335A ARG* 4.2 1.4 - - - +
337A PHE* 3.0 41.6 + + + +
338A ILE* 3.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A TRP* 3.9 29.1 - - + +
214A ASN* 4.2 28.7 - - + +
269A ASP* 2.9 17.1 + - - +
270A TYR* 1.3 78.8 - - - +
272A ASP* 1.3 60.9 + - - +
274A TYR* 3.8 1.1 - - + +
275A LYS* 3.0 58.4 + - + +
285A PHE* 3.6 40.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
216A GLU* 3.9 18.4 - - - +
269A ASP* 3.1 31.7 + - - +
271A LEU* 1.3 82.4 - - - +
273A LEU* 1.3 54.8 + - - +
275A LYS* 3.2 9.3 + - - +
276A LYS* 2.7 44.5 + - - +
356A MET* 3.9 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 3.9 14.8 - - + +
269A ASP 2.9 32.6 + - - +
270A TYR* 3.9 23.3 - - + +
272A ASP* 1.3 79.0 - - - +
274A TYR* 1.3 55.1 + - - +
276A LYS* 4.0 9.2 - - - +
277A PHE* 2.7 42.5 + - + +
337A PHE* 3.7 31.9 - - + -
338A ILE* 4.0 11.9 - - + -
341A VAL* 4.0 20.6 - - + -
356A MET* 3.4 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A TRP* 3.7 12.1 - + + -
270A TYR* 2.9 21.0 + - + +
271A LEU 3.8 2.7 - - - +
273A LEU* 1.3 77.4 - - - +
275A LYS* 1.3 57.8 + - - +
278A ALA* 2.9 50.3 + - + +
280A THR* 3.0 36.8 - - + +
282A LEU* 4.2 3.5 - - + +
285A PHE* 3.8 26.7 - + - -
290A VAL* 3.6 22.9 - - + +
293A HIS* 3.7 6.2 + - - -
294A GLU* 2.6 38.2 + - - -
331A ILE* 4.1 15.3 - - + -
335A ARG* 4.1 4.4 + - + -
337A PHE* 3.8 14.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.0 54.6 + - + +
272A ASP* 3.6 7.9 - - - +
274A TYR* 1.3 79.7 - - - +
276A LYS* 1.3 59.2 + - - +
278A ALA 4.4 6.7 - - - +
279A PHE* 6.1 0.5 - - - -
280A THR* 5.4 0.4 - - - -
285A PHE* 4.2 35.9 - - + -
53B LYS* 3.2 31.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ASP* 2.7 23.3 + - - +
273A LEU* 3.9 3.6 - - - +
275A LYS* 1.3 74.9 - - + +
277A PHE* 1.3 97.0 + - + +
278A ALA 5.6 0.2 - - - -
279A PHE* 5.4 0.3 - - - -
356A MET* 2.8 74.6 - - - +
357A SER* 5.3 0.2 - - - -
52B GLY* 3.1 23.6 - - - +
53B LYS* 3.5 9.8 - - - +
54B ASN 3.0 27.4 + - - +
362B TRP* 4.6 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 2.7 38.6 + - + +
276A LYS* 1.3 108.4 - - + +
278A ALA* 1.3 55.5 + - - +
335A ARG* 4.5 1.4 + - - -
337A PHE* 3.6 30.0 - + + -
340A LEU* 3.9 21.5 - - + -
341A VAL* 5.2 3.6 - - + -
344A MET* 4.4 4.3 - - - -
355A VAL* 3.8 33.2 - - + -
356A MET* 4.7 1.3 - - - -
40B HIS* 5.7 0.2 - - - -
54B ASN 3.2 9.5 - - - +
55B CYS* 3.1 32.8 - - - +
56B ALA 3.8 2.7 + - - +
362B TRP* 3.7 22.4 - + - -
366B ILE* 3.8 18.4 - - + -
----------------------------------------------------------
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