Contacts of the helix formed by residues 245 - 256 (chain C) in PDB entry 3NZG
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 ASP 245 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B THR 5.6 0.3 - - - +
308B ASN* 2.9 21.8 - - - +
217C THR* 4.4 10.7 - - - +
219C TRP 5.6 0.5 + - - -
241C LEU* 3.8 14.4 - - + +
242C GLN* 3.0 26.3 + - + +
243C HIS 3.3 0.2 - - - -
244C ASP* 1.3 73.6 - - - +
246C LEU* 1.3 55.3 + - - +
247C SER* 3.5 6.2 + - - -
248C GLY* 2.9 25.3 + - - -
249C HIS* 2.7 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 6.2 0.9 - - - +
243C HIS 3.5 18.2 - - - +
244C ASP* 2.9 23.6 + - - +
245C ASP* 1.3 69.0 - - - +
247C SER* 1.3 66.7 + - - +
249C HIS* 3.1 6.6 + - - +
250C ALA 3.1 17.3 + - - -
274C GLU* 3.6 59.5 - - + +
275C TRP* 3.9 31.0 - - + +
278C LYS* 3.7 17.1 - - + +
279C GLY* 3.4 16.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ALA 3.5 1.9 + - - -
307B ASN* 5.7 0.4 - - - -
308B ASN* 2.7 23.7 + - - -
503B MG 2.4 30.8 - - - -
245C ASP* 3.5 2.4 + - - -
246C LEU* 1.3 77.7 - - - +
248C GLY* 1.3 61.4 + - - +
250C ALA* 3.3 9.9 + - - +
251C LYS* 3.2 27.2 + - - +
278C LYS* 4.1 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ASN* 3.4 14.6 - - - -
219C TRP* 3.7 3.3 - - - +
241C LEU* 3.3 17.1 - - - +
245C ASP* 2.9 28.8 + - - -
246C LEU 3.1 0.4 - - - -
247C SER* 1.3 75.5 + - - +
249C HIS* 1.3 64.5 + - - +
251C LYS* 3.2 16.1 + - - +
252C LEU 3.2 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C TYR* 5.9 0.8 - - - -
239C ALA* 5.6 1.6 - - - -
240C THR* 4.3 10.1 + - - -
241C LEU* 3.7 30.5 + - + +
242C GLN 3.3 26.0 - - - -
243C HIS* 4.9 0.2 - - - -
245C ASP 2.7 23.5 + - - -
246C LEU 3.1 7.4 + - - +
248C GLY* 1.3 76.7 - - - +
250C ALA* 1.3 63.3 + - - +
252C LEU* 3.0 9.5 + - + +
253C VAL* 2.9 24.4 + - - +
260C ILE* 3.9 12.1 - - + +
261C CYS 3.5 24.3 + - - -
262C GLY* 5.1 0.4 - - - -
275C TRP* 3.7 28.4 - + + -
279C GLY* 3.6 10.8 - - - +
281C VAL* 4.3 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C LEU 3.1 6.6 + - - +
247C SER* 3.4 12.3 - - - +
248C GLY 3.2 0.2 - - - -
249C HIS* 1.3 75.6 - - - +
251C LYS* 1.3 56.7 + - - +
253C VAL* 3.2 2.8 + - - +
254C GLU* 2.8 49.1 + - - +
278C LYS 3.4 24.7 - - - +
279C GLY 3.3 10.7 + - - +
280C LYS* 3.9 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ASN 4.4 12.7 + - - -
308B ASN* 4.5 12.1 - - - +
309B VAL* 6.5 0.4 - - - -
219C TRP* 3.4 56.5 - - + +
247C SER* 3.2 13.8 + - - +
248C GLY 3.3 9.4 - - - +
250C ALA* 1.3 79.0 - - + +
252C LEU* 1.3 56.1 + - - +
254C GLU* 3.3 14.6 + - - +
255C ASN* 2.7 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C TRP* 3.5 21.5 - - + +
222C VAL* 3.5 31.2 - - + -
223C ALA* 3.8 12.6 - - + +
226C LEU* 4.4 5.2 - - + -
240C THR* 3.2 28.3 - - - +
241C LEU* 3.9 15.3 - - + -
248C GLY 3.2 10.3 + - - +
249C HIS* 3.0 10.8 + - - +
251C LYS* 1.3 76.5 - - - +
253C VAL* 1.3 65.1 + - - +
255C ASN* 3.2 0.6 + - - -
256C THR* 2.8 34.8 + - + +
260C ILE* 4.1 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C HIS 2.9 19.0 + - - +
250C ALA 3.5 7.0 - - - +
252C LEU* 1.3 77.8 - - - +
254C GLU* 1.3 63.7 + - + +
256C THR* 3.4 14.5 - - - +
260C ILE* 3.8 27.8 - - + -
279C GLY 3.8 7.9 - - - +
280C LYS* 3.3 39.3 - - + +
281C VAL* 4.3 0.9 - - - -
282C HIS* 3.9 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ALA* 2.8 25.0 + - - +
251C LYS* 3.7 20.8 + - - +
252C LEU 3.2 0.2 - - - -
253C VAL* 1.3 79.4 - - + +
255C ASN* 1.3 68.0 + - - +
256C THR 3.8 0.7 - - - -
280C LYS* 2.5 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B VAL 5.7 1.0 - - - +
257B ARG* 6.1 0.3 - - - -
219C TRP* 3.5 33.9 - - + -
223C ALA* 4.4 5.2 - - + +
227C ASN* 3.1 21.7 + - - +
251C LYS* 2.7 35.3 + - - +
252C LEU 4.5 0.2 - - - +
254C GLU* 1.3 92.7 + - - +
256C THR* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ALA* 3.6 33.9 - - + +
226C LEU* 4.3 14.1 - - + -
227C ASN* 3.2 15.5 - - - +
252C LEU* 2.8 26.0 + - + +
253C VAL* 3.4 14.2 - - - +
254C GLU 4.8 0.3 - - - -
255C ASN* 1.3 84.1 - - - +
257C ARG* 1.3 65.6 + - - +
258C SER* 3.5 13.3 + - - +
260C ILE* 4.1 11.8 - - - +
282C HIS* 5.9 0.7 - - - -
----------------------------------------------------------
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