Contacts of the helix formed by residues 270 - 288 (chain A) in PDB entry 4WNG
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 270 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ALA* 3.0 13.5 + - - +
268A LEU* 3.1 16.8 - - + +
269A LYS* 1.3 73.6 - - - +
271A ARG* 1.3 64.4 + - - +
272A ALA* 3.5 7.3 + - - +
273A VAL* 3.2 40.9 + - + +
274A GLU* 3.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LYS 3.4 10.9 + - - +
270A ASP* 1.3 70.6 + - - +
272A ALA* 1.3 65.2 + - - +
274A GLU* 3.3 36.6 + - - +
275A ALA* 3.1 19.6 + - - +
304A ILE* 3.4 36.9 - - + +
307A GLU* 3.3 33.9 + - + +
308A LEU* 5.7 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASP* 3.5 6.6 + - - +
271A ARG* 1.3 76.0 - - - +
273A VAL* 1.3 70.1 + - + +
275A ALA* 2.8 20.2 + - - +
276A GLN* 3.0 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 3.5 52.3 - - + +
265A ALA* 3.7 16.8 - - + -
268A LEU* 5.7 2.5 - - + -
270A ASP* 3.2 33.3 + - + +
272A ALA* 1.3 76.7 - - + +
274A GLU* 1.3 58.7 + - - +
276A GLN* 3.0 12.2 + - - +
277A SER* 2.9 30.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
262A LEU* 3.8 15.0 - - + -
265A ALA* 3.5 15.0 - - + +
266A ARG* 3.0 47.3 + - - +
269A LYS 6.0 0.3 - - - -
270A ASP 3.2 12.7 + - - +
271A ARG* 3.3 42.9 + - - +
272A ALA 3.1 0.8 - - - -
273A VAL* 1.3 80.1 - - - +
275A ALA* 1.3 61.4 + - - +
277A SER* 3.2 4.1 + - - -
278A CYS* 3.1 27.4 + - - -
304A ILE* 5.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ARG 3.1 11.0 + - - +
272A ALA* 2.8 22.3 + - - +
274A GLU* 1.3 70.5 - - - +
276A GLN* 1.3 60.3 + - - +
278A CYS* 3.3 5.1 + - - +
279A TYR* 3.0 22.9 + - - +
301A HIS* 3.9 28.5 - - + +
304A ILE* 4.3 19.7 - - + +
305A ALA* 5.0 4.5 - - + +
310A ASP* 6.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 5.8 4.9 - - - +
272A ALA 3.0 9.2 + - - +
273A VAL* 3.2 13.9 - - + +
275A ALA* 1.3 75.8 - - - +
277A SER* 1.3 64.6 + - - +
279A TYR* 3.2 10.1 + - - +
280A SER* 2.9 27.6 + - - +
996B GLU* 5.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ARG* 5.1 0.2 - - - -
258A TYR* 4.5 2.6 - - - +
261A THR* 3.4 33.3 + - - -
262A LEU* 3.7 28.4 + - - -
265A ALA* 4.1 0.5 - - - +
273A VAL* 2.9 20.0 + - - +
274A GLU* 3.2 8.2 + - - -
276A GLN* 1.3 75.8 - - - +
278A CYS* 1.3 61.8 + - - +
280A SER* 3.5 6.1 + - - -
281A LEU* 3.3 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 3.9 26.5 - - - -
266A ARG* 4.7 1.3 - - - -
274A GLU* 3.1 23.2 + - - -
275A ALA* 3.8 6.5 - - - +
277A SER* 1.3 75.2 - - - +
279A TYR* 1.3 67.1 + - - +
280A SER 3.4 0.2 + - - -
281A LEU* 3.4 2.8 + - - +
282A GLY* 3.3 16.1 + - - -
297A TYR* 3.3 44.6 - - + +
298A HIS 4.7 0.2 + - - -
300A LYS* 3.9 25.1 - - - -
301A HIS* 4.2 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ALA 3.0 16.4 + - - +
276A GLN* 3.5 8.3 - - - +
278A CYS* 1.3 78.9 - - - +
280A SER* 1.3 59.5 + - - +
282A GLY* 3.3 1.9 + - - -
283A ASN* 2.6 55.2 + - - -
298A HIS* 4.0 11.1 + + - -
301A HIS* 3.8 36.6 - + + +
316A ARG* 3.5 36.4 + - + +
320A SER* 3.8 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A SER* 5.7 0.2 + - - -
243A ASN* 5.6 0.2 + - - -
258A TYR* 3.8 37.6 - - - -
276A GLN* 2.9 20.0 + - - +
277A SER* 3.8 5.6 - - - -
278A CYS 3.3 0.2 - - - -
279A TYR* 1.3 79.4 - - - +
281A LEU* 1.3 61.7 + - - +
283A ASN* 3.1 17.7 + - - +
284A THR* 2.8 20.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
255A SER* 3.3 43.1 - - - +
258A TYR* 3.5 29.8 - - + +
259A LYS* 4.1 7.0 - - + +
262A LEU* 4.2 13.0 - - + -
277A SER 3.3 16.8 + - - +
278A CYS 3.8 5.6 - - - +
279A TYR 3.4 0.4 - - - -
280A SER* 1.3 78.5 - - - +
282A GLY* 1.3 62.6 + - - +
284A THR* 3.1 6.2 + - - -
285A TYR* 3.1 44.5 + - + +
297A TYR* 4.1 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A CYS 3.3 10.1 + - - -
279A TYR 3.3 2.4 + - - -
280A SER 3.3 0.4 - - - -
281A LEU* 1.3 77.7 - - - +
283A ASN* 1.3 53.2 + - - +
286A THR* 2.7 32.1 + - - -
294A ALA* 3.5 25.7 - - - +
297A TYR* 4.1 3.8 - - - +
298A HIS* 3.7 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 2.6 58.5 + - - -
280A SER* 3.1 10.9 + - - +
282A GLY* 1.3 74.1 - - - +
284A THR* 1.3 63.4 + - - +
286A THR* 3.5 17.7 - - - -
287A LEU* 3.5 17.2 + - + +
298A HIS* 3.6 9.0 + - - -
320A SER* 4.8 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ILE* 3.8 21.0 - - + +
251A PHE* 3.2 33.0 - - + +
255A SER* 4.0 18.2 - - - +
258A TYR* 3.5 18.9 - - - -
280A SER 2.8 15.0 + - - -
281A LEU* 3.1 8.0 + - - -
283A ASN* 1.3 74.7 - - - +
285A TYR* 1.3 66.3 + - - +
286A THR 3.1 1.3 - - - -
287A LEU* 3.0 21.6 + - - +
288A LEU* 3.0 13.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A SER* 4.2 13.0 - - - -
281A LEU* 3.1 43.7 + - + +
282A GLY 4.1 3.6 - - - +
284A THR* 1.3 75.0 - - - +
286A THR* 1.3 50.6 + - - +
288A LEU* 2.8 26.9 + - + +
289A GLN 2.7 30.5 + - - -
290A ASP* 2.9 35.6 + - + +
293A LYS* 3.5 21.8 - - + -
294A ALA 3.9 8.3 - - - +
297A TYR* 3.2 39.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLY 2.7 21.5 + - - -
283A ASN* 3.5 12.0 - - - -
284A THR 3.1 0.4 - - - -
285A TYR* 1.3 78.7 - - - +
287A LEU* 1.3 58.2 + - + +
289A GLN* 3.0 23.3 + - - +
290A ASP 3.9 5.1 + - - -
291A TYR* 4.1 24.1 + - + +
294A ALA* 4.1 8.3 - - - +
298A HIS* 4.8 3.5 - - - -
324A ALA* 5.7 3.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ILE* 4.2 19.7 - - + -
251A PHE* 3.9 53.5 - - + -
283A ASN* 3.5 17.9 + - + +
284A THR* 3.0 13.9 + - - +
286A THR* 1.3 78.0 - - + +
288A LEU* 1.3 59.2 + - - +
289A GLN* 3.3 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 3.9 33.9 - - + +
252A GLU* 4.0 17.5 - - + +
255A SER* 4.4 5.8 - - - +
284A THR* 3.0 12.7 + - + +
285A TYR* 2.8 45.4 + - + +
287A LEU* 1.3 76.7 - - - +
289A GLN* 1.3 71.8 + - - +
290A ASP* 3.5 4.9 + - + +
----------------------------------------------------------
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