Contacts of the helix formed by residues 271 - 284 (chain A) in PDB entry 3N6J
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 SER 271 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLY* 3.8 2.2 - - - -
269A GLY 4.1 0.8 + - - -
270A TYR* 1.3 75.7 - - - +
272A GLY* 1.3 60.4 + - - +
273A ARG* 3.8 31.0 + - - +
274A GLU* 3.0 35.7 + - - +
275A ILE* 2.8 27.7 + - - +
305A LEU* 4.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ILE* 4.0 8.0 - - - +
266A GLY* 3.5 23.2 - - - +
271A SER* 1.3 73.2 - - - +
273A ARG* 1.3 53.2 + - - +
275A ILE* 3.7 0.7 - - - +
276A MSE 2.7 40.0 + - - +
292A ILE* 3.6 22.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A SER* 3.1 26.4 + - - +
272A GLY* 1.3 73.9 - - - +
274A GLU* 1.3 64.9 + - - +
277A ALA* 3.0 13.3 + - - +
292A ILE* 2.8 60.1 + - + +
298A GLU* 3.3 53.6 + - - +
301A HIS* 3.8 17.6 - - - +
302A ALA* 3.8 13.9 - - - +
305A LEU* 4.0 12.0 - - + +
307A SER* 2.4 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLY 4.1 3.8 - - - +
270A TYR* 3.4 25.3 - - + -
271A SER* 3.0 37.5 + - - +
273A ARG* 1.3 80.5 - - - +
275A ILE* 1.3 62.3 + - - +
277A ALA* 3.5 5.7 + - - +
278A GLU* 3.4 24.4 + - - +
305A LEU* 3.9 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.8 38.2 - - + +
264A CYS* 4.0 16.4 - - + +
265A ILE 3.7 27.4 - - - +
267A GLU* 3.9 22.4 - - + +
270A TYR* 3.4 32.5 - - + -
271A SER 2.8 18.0 + - - +
272A GLY 3.8 2.9 - - - +
274A GLU* 1.3 72.9 - - - +
276A MSE 1.3 67.5 + - - +
278A GLU* 3.0 12.2 + - - +
279A PHE 3.0 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASP* 4.0 15.9 - - - +
263A PRO* 3.5 31.4 - - - -
264A CYS* 3.3 19.3 - - - +
265A ILE* 5.1 0.2 - - + -
272A GLY 2.7 26.6 + - - +
273A ARG 3.9 1.3 - - - +
275A ILE* 1.3 72.8 - - - +
277A ALA* 1.3 62.2 + - - +
279A PHE* 3.2 9.3 + - - +
280A ARG* 3.0 24.3 + - - +
287A THR* 3.7 25.1 - - + +
288A ALA 3.4 24.9 - - - +
289A THR* 4.0 9.0 - - - -
292A ILE* 3.8 22.9 - - + -
307A SER 4.0 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG 3.0 18.1 + - - +
274A GLU* 3.5 6.7 - - - +
275A ILE 3.2 0.2 - - - -
276A MSE 1.3 74.9 - - - +
278A GLU* 1.3 64.7 + - + +
280A ARG* 3.1 4.6 + - - +
281A ARG* 3.0 35.7 + - - +
305A LEU* 3.2 32.8 - - + +
306A GLN* 4.0 5.2 - - + +
307A SER* 3.8 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.4 27.6 - - + +
270A TYR* 3.9 28.1 - - - -
274A GLU 3.4 11.0 + - - +
275A ILE* 3.0 11.9 + - - +
277A ALA* 1.3 79.9 - - + +
279A PHE* 1.3 63.0 + - - +
281A ARG* 3.3 15.2 + - - +
282A ARG* 2.9 56.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.8 8.6 - - + +
246A ALA* 3.8 38.4 - - + -
247A ILE* 4.5 3.6 - - + -
250A CYS* 4.0 15.3 - - + -
260A ALA* 3.9 16.4 - - + -
263A PRO* 3.6 22.2 - - + -
264A CYS* 3.7 20.9 - - - -
275A ILE 3.0 8.0 + - - +
276A MSE 3.3 9.0 - - - +
278A GLU* 1.3 75.4 - - - +
280A ARG* 1.3 56.3 + - - +
282A ARG* 3.3 2.7 + - - -
283A THR* 2.7 71.3 + - + +
285A ILE* 4.0 8.3 - - + -
287A THR* 3.6 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A MSE 3.0 12.5 + - - +
277A ALA* 3.1 9.4 + - - +
279A PHE* 1.3 83.3 - - - +
281A ARG* 1.3 57.7 + - - +
283A THR* 3.9 2.7 - - - -
284A GLY* 3.1 27.6 + - - -
285A ILE 4.3 9.9 - - - +
287A THR* 3.8 18.8 - - + +
306A GLN* 3.4 43.5 + - - +
307A SER 4.5 1.6 - - - +
308A VAL 4.5 5.1 + - - -
309A ASP* 2.7 44.1 + - - +
280C ARG* 3.5 39.4 + - - +
281C ARG* 5.2 11.9 - - - +
306C GLN* 5.5 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ALA* 3.0 25.7 + - - +
278A GLU* 3.6 19.8 - - - +
280A ARG* 1.3 80.5 - - - +
282A ARG* 1.3 61.0 + - + +
284A GLY* 4.7 2.1 + - - -
305A LEU* 4.1 15.6 + - - +
306A GLN* 5.8 0.4 - - - +
280C ARG* 5.9 9.0 - - - +
306C GLN* 3.2 28.8 - - - +
333C TRP* 2.6 31.4 + - - +
334C GLY* 3.4 29.7 - - - +
335C LEU* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 5.7 0.4 - - - -
247A ILE* 3.7 35.0 - - + -
251A LYS* 3.4 27.2 + - - -
278A GLU* 2.9 56.7 + - - +
279A PHE 3.3 2.4 + - - +
281A ARG* 1.3 82.2 - - + +
283A THR* 1.3 59.2 + - - +
331C ASN 3.9 11.3 + - - -
332C GLU 4.1 7.7 + - - -
333C TRP 4.6 3.0 + - - -
334C GLY* 3.8 36.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 4.0 29.4 - - + +
250A CYS* 4.8 4.3 - - + -
251A LYS* 4.4 19.6 + - + +
254A ASN* 4.4 4.9 + - - -
279A PHE* 2.7 58.2 + - + +
280A ARG* 3.8 1.0 + - - -
282A ARG* 1.3 81.6 - - - +
284A GLY* 1.3 63.4 + - - +
285A ILE* 3.3 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASN* 3.3 17.4 - - - +
280A ARG* 3.1 14.0 + - - -
281A ARG 4.7 2.3 + - - -
282A ARG 3.9 0.6 - - - -
283A THR* 1.3 77.9 + - - +
285A ILE* 1.3 59.5 + - - +
286A PRO* 3.8 5.9 - - - +
284C GLY 5.6 2.3 - - - +
----------------------------------------------------------
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