Contacts of the helix formed by residues 273 - 289 (chain A) in PDB entry 6F0X
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 ALA 273 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PHE* 4.4 10.9 - - + -
260A ALA* 4.9 8.5 - - + -
268A THR* 5.5 1.6 - - - +
269A GLU 4.5 2.2 + - - +
270A PRO* 2.9 14.3 + - + +
272A ASP* 1.3 76.6 - - - +
274A ILE* 1.3 70.2 + - + +
275A ARG 3.1 1.1 - - - -
276A VAL* 2.9 7.1 + - - +
277A VAL* 2.9 30.1 + - + +
222B PHE* 4.1 29.4 - - + -
275B ARG* 5.6 2.0 - - - +
7Z ARG* 6.1 0.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
260A ALA* 3.5 39.3 - - + +
262A ASN* 5.3 8.5 - - + -
270A PRO* 3.2 34.2 + - + +
273A ALA* 1.3 74.6 - - + +
275A ARG* 1.3 54.5 + - - +
277A VAL* 2.9 10.0 + - + -
278A ASN* 2.7 56.8 + - + +
261F ARG 5.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A PHE* 3.3 40.9 - - - -
270A PRO 4.1 3.6 + - - +
271A SER* 3.0 30.8 + - - +
272A ASP* 3.4 24.1 + - - +
274A ILE* 1.3 77.8 - - - +
276A VAL* 1.3 64.3 + - + +
278A ASN* 2.8 18.5 - - - +
279A ALA* 3.1 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 5.1 6.1 - - + -
218A PHE* 5.2 5.2 - - + -
222A PHE* 5.2 3.6 - - + -
225A SER* 4.1 23.6 - - - +
228A LEU* 4.4 11.9 - - + -
229A VAL* 3.9 27.1 - - + -
272A ASP 3.6 16.4 - - - +
273A ALA 2.9 7.5 + - - +
275A ARG* 1.3 88.3 - - + +
277A VAL* 1.3 53.3 + - - +
278A ASN 3.4 0.4 - - - -
279A ALA* 2.9 8.1 + - + +
280A VAL* 2.5 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PHE* 3.6 28.7 - - + -
256A SER 5.9 0.2 - - - +
257A LEU* 3.5 39.0 - - + +
259A ALA* 6.5 0.9 - - + -
260A ALA* 5.2 9.6 - - + +
273A ALA* 2.9 27.6 + - + +
274A ILE* 2.9 13.1 + - + +
276A VAL* 1.3 76.4 - - - +
278A ASN* 1.3 57.7 + - - +
280A VAL* 2.8 33.9 + - - +
281A LEU* 2.9 16.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 2.7 42.4 + - + +
275A ARG* 2.8 14.6 - - - +
277A VAL* 1.3 72.9 - - - +
279A ALA* 1.3 72.7 + - - +
281A LEU* 2.9 25.1 + - + +
282A THR* 2.6 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 5.8 3.6 - - + -
275A ARG 3.1 16.4 - - - +
276A VAL* 2.9 19.5 + - + +
278A ASN* 1.3 79.8 + - - +
280A VAL* 1.3 51.2 + - - +
282A THR* 2.2 31.6 + - - +
283A GLN* 2.4 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ILE* 6.2 4.3 - - + -
217A LEU* 4.4 18.6 - - + -
218A PHE* 6.1 0.4 - - + -
233A PHE* 3.6 29.4 - - + -
251A ILE* 6.2 2.7 - - + -
257A LEU* 4.7 19.1 - - + -
276A VAL* 2.5 32.1 + - + +
277A VAL* 2.8 15.0 - - - +
279A ALA* 1.3 70.3 - - - +
281A LEU* 1.3 48.5 + - + +
283A GLN* 2.8 13.3 - - - +
284A ILE* 2.3 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 5.0 8.7 - - + -
277A VAL* 2.9 18.8 + - + +
278A ASN* 2.9 29.8 + - + +
280A VAL* 1.3 76.6 - - + +
282A THR* 1.3 48.0 + - + +
284A ILE* 2.9 22.4 - - + +
285A ASP* 2.3 42.3 + - - +
308A ALA* 5.9 1.8 - - + -
309A PHE* 3.5 22.9 - - + -
312A ARG* 3.1 39.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASN* 2.6 26.2 + - + +
279A ALA* 2.2 33.7 + - - +
281A LEU* 1.3 68.1 - - + +
283A GLN* 1.3 59.9 + - - +
285A ASP* 2.9 18.0 + - - +
286A GLN* 2.3 50.6 + - - +
289A ARG* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 3.8 18.4 - - + +
233A PHE* 3.1 62.8 - - + +
279A ALA* 2.4 43.0 + - + +
280A VAL* 2.8 13.2 - - - +
282A THR* 1.3 68.7 + - - +
284A ILE* 1.3 48.1 + - - -
286A GLN* 2.9 14.8 + - - +
287A ILE* 2.6 45.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A VAL* 4.7 3.8 - - + -
233A PHE* 5.9 1.1 - - + -
251A ILE* 5.8 5.8 - - + -
257A LEU* 4.9 5.8 - - + -
280A VAL* 2.3 39.6 + - + +
281A LEU* 2.9 40.9 + - + +
283A GLN* 1.3 64.3 - - - +
285A ASP* 1.3 52.4 + - - +
287A ILE* 2.9 17.2 - - + +
288A LYS* 2.5 59.8 + - - +
295A ILE* 3.6 22.7 - - + -
309A PHE* 4.0 18.8 - - + -
312A ARG* 5.3 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 2.3 29.8 + - - +
282A THR* 2.9 29.5 + - - +
284A ILE* 1.3 65.5 - - - +
286A GLN* 1.3 65.6 + - - +
288A LYS* 3.0 30.0 + - - +
289A ARG* 2.8 43.3 + - - +
312A ARG* 4.4 12.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLN* 4.7 8.5 - - - +
282A THR* 2.3 39.6 + - - +
283A GLN* 3.1 17.9 - - - +
285A ASP* 1.3 65.4 - - - +
287A ILE* 1.3 62.4 + - + +
289A ARG* 2.7 66.5 + - - +
290A HIS* 3.6 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 5.5 4.7 - - + -
236A ILE* 4.1 15.7 - - + -
237A GLN* 4.3 9.9 - - + +
240A ILE* 3.6 26.5 - - + -
249A VAL* 4.6 16.8 - - + -
283A GLN* 2.6 27.7 + - + +
284A ILE* 2.9 34.5 - - + +
286A GLN* 1.3 74.1 - - + +
288A LYS* 1.3 57.9 + - - +
290A HIS* 2.8 32.4 + - - -
293A VAL* 3.1 22.8 - - + +
295A ILE* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ASN* 3.9 18.0 - - + +
173A ARG* 3.1 24.3 + - + +
174A VAL* 3.9 19.8 - - + +
284A ILE* 2.5 37.2 + - - +
285A ASP* 3.0 33.6 + - - +
287A ILE* 1.3 74.6 - - - +
289A ARG* 1.3 55.6 + - + +
290A HIS 2.8 18.6 - - - +
293A VAL* 4.6 8.1 - - - -
295A ILE* 4.4 9.2 - - + -
312A ARG* 3.4 31.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A THR* 6.2 0.6 - - - -
285A ASP* 2.8 31.2 + - - +
286A GLN* 2.7 58.2 + - - +
288A LYS* 1.3 75.5 - - + +
290A HIS* 1.3 64.5 + - + +
291A SER* 5.2 0.5 + - - -
----------------------------------------------------------
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