Contacts of the helix formed by residues 267 - 278 (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 THR 267 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ARG* 3.4 29.5 - - - +
101C GLY* 3.4 14.3 + - - +
104C MSE 3.8 9.9 - - - -
105C PHE* 3.8 22.0 - - + -
265C MSE 4.4 4.3 - - - +
266C SER* 1.3 82.8 - - - +
268C THR* 1.3 77.1 + - - +
271C GLU* 3.1 20.2 + - - +
290C ARG* 3.5 21.8 - - - +
291C CYS* 3.7 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TYR* 4.6 4.7 - - + -
99C MSE 3.1 28.0 - - - +
100C ARG* 3.7 9.2 + - - +
104C MSE 4.0 18.2 - - + -
266C SER* 5.0 1.6 + - - -
267C THR* 1.3 87.2 + - - +
269C ARG* 1.3 62.6 + - - +
270C PHE* 3.1 28.1 + - + +
271C GLU* 3.4 5.5 + - - +
272C ALA* 3.3 17.2 + - - +
286C SER* 5.3 0.2 + - - -
291C CYS* 2.9 23.3 + - - +
296C GLU* 3.5 8.3 - - - +
300C ILE* 4.0 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C TRP* 3.7 14.1 - - - -
88C ASP* 5.2 4.6 + - - -
268C THR* 1.3 71.1 - - - +
270C PHE* 1.3 97.9 + - + +
271C GLU 3.4 0.2 - - - -
272C ALA* 3.7 2.0 - - - +
273C GLU* 2.9 30.4 + - - +
296C GLU* 2.8 45.4 + - - +
299C ARG* 3.7 37.5 - - + +
300C ILE* 3.7 28.7 - - + +
303C MSE 3.8 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ASP* 3.3 55.9 - - + +
274A GLU* 5.0 4.4 - - - +
91C TYR* 3.6 14.6 - + - -
100C ARG* 3.4 21.8 - - - +
268C THR* 3.1 19.5 - - - +
269C ARG* 1.3 121.2 - - + +
271C GLU* 1.3 65.3 + - - +
273C GLU* 3.5 16.6 + - - +
274C GLU* 3.4 19.6 + - - +
296C GLU* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 3.7 29.9 + - - +
271A GLU* 4.6 0.9 - - - +
100C ARG* 3.3 26.6 - - - +
101C GLY 5.4 0.2 + - - -
243C HIS* 5.0 2.6 - - - -
266C SER* 3.2 19.3 - - - -
267C THR* 3.1 40.2 + - - +
268C THR* 3.4 3.2 + - - +
270C PHE* 1.3 76.5 - - - +
272C ALA* 1.3 66.5 + - - +
274C GLU* 3.2 13.9 + - - +
275C TRP* 3.1 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C ALA* 5.1 1.1 - - - -
266C SER* 5.0 0.8 + - - -
268C THR 3.3 12.2 + - - +
269C ARG 3.7 7.6 - - - +
270C PHE 3.3 0.4 - - - -
271C GLU* 1.3 81.1 - - - +
273C GLU* 1.3 60.7 + - - +
275C TRP* 3.1 12.5 + - - +
276C ILE* 3.0 24.9 + - - +
284C LEU* 4.0 9.6 - - + +
286C SER* 4.3 7.6 - - - +
300C ILE* 3.9 34.1 - - + -
303C MSE 4.0 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LYS* 5.3 13.5 - - - +
269C ARG 2.9 17.1 + - - +
270C PHE* 3.6 17.1 - - - +
271C GLU 3.2 0.2 - - - -
272C ALA* 1.3 77.4 - - - +
274C GLU* 1.3 57.1 + - - +
276C ILE* 3.2 5.6 + - + +
277C THR* 2.9 44.9 + - + +
303C MSE 3.6 27.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE* 4.9 6.1 - - - +
274A GLU* 2.5 51.3 - - + +
278A LYS* 4.4 7.6 - - - +
246C LEU* 3.6 22.1 - - + +
270C PHE 3.4 9.6 + - - +
271C GLU* 3.2 16.9 + - - +
273C GLU* 1.3 75.7 - - - +
275C TRP* 1.3 61.0 + - - +
277C THR* 3.9 6.1 - - - +
278C LYS* 2.7 51.6 + - + +
279C GLY 3.1 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C TYR* 6.4 0.2 - + - -
243C HIS* 3.0 52.2 - + - -
246C LEU* 3.9 26.4 - - + +
249C HIS* 3.7 39.0 - + - -
262C GLY* 3.6 20.6 - - - -
263C ALA* 3.3 38.7 - - + +
266C SER* 4.1 5.3 - - - -
271C GLU* 3.1 33.5 + - + +
272C ALA* 3.4 7.6 - - - +
274C GLU* 1.3 75.6 - - - +
276C ILE* 1.3 58.5 + - - +
279C GLY* 3.0 6.9 + - - -
280C LYS 2.9 24.6 + - - -
281C VAL* 3.5 20.0 + - + +
284C LEU* 3.7 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ALA 3.0 12.5 + - - +
273C GLU* 3.2 6.3 + - - +
275C TRP* 1.3 77.0 - - - +
277C THR* 1.3 66.2 + - + +
280C LYS* 3.2 24.5 + - - +
281C VAL* 4.7 5.3 - - - +
284C LEU* 3.9 24.7 - - + -
303C MSE 3.6 43.7 - - + +
304C ALA* 4.0 14.1 - - - -
307C ASN* 3.8 29.2 - - + +
309C VAL* 4.2 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LYS* 5.1 9.9 + - - -
273C GLU* 2.9 34.8 + - + +
274C GLU* 3.8 6.6 + - - +
276C ILE* 1.3 84.2 - - + +
278C LYS* 1.3 63.4 + - - +
280C LYS* 4.0 13.7 - - - +
307C ASN* 5.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLU* 4.2 27.7 + - - +
274A GLU* 6.1 1.6 - - + -
278A LYS* 6.1 1.1 - - - +
246C LEU* 3.7 14.9 - - + +
247C SER* 4.1 29.5 - - - +
250C ALA* 3.4 18.7 - - - +
274C GLU* 2.7 43.9 + - + +
277C THR* 1.3 76.0 + - - +
279C GLY* 1.3 62.2 + - - +
280C LYS* 3.3 4.0 + - - +
----------------------------------------------------------
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