Contacts of the helix formed by residues 278 - 300 (chain D) in PDB entry 6S6A
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 278 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D LYS* 5.3 0.4 - - - +
276D PRO 3.8 5.1 + - - -
277D VAL* 1.3 77.3 - - - +
279D MET* 1.3 57.4 + - - +
280D GLN* 3.2 29.4 + - - +
281D SER* 3.1 37.2 + - - +
282D TYR 3.4 3.3 + - - -
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Residues in contact with MET 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D GLU* 3.1 46.1 - - + +
231D LYS* 4.3 23.1 - - - +
269D TYR* 3.3 27.1 - - + +
277D VAL* 3.4 29.3 + - + +
278D ASP* 1.3 69.4 + - - +
280D GLN* 1.3 61.3 + - + +
281D SER 3.3 0.9 - - - -
282D TYR* 3.8 15.1 - - - +
283D GLU* 3.4 25.5 + - - +
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Residues in contact with GLN 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LYS 4.9 2.6 - - - +
245B LEU* 3.1 57.0 - - + +
278D ASP* 3.2 17.7 + - - +
279D MET* 1.3 77.9 - - + +
281D SER* 1.3 61.1 + - - +
283D GLU* 3.6 6.9 - - - +
284D LEU 3.5 8.8 + - - -
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Residues in contact with SER 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 5.3 0.7 - - - -
258D LYS* 5.1 3.8 - - - +
260D PHE* 4.0 13.0 - - - -
278D ASP* 3.1 31.3 + - - +
280D GLN* 1.3 76.8 - - - +
282D TYR* 1.3 61.9 + - - +
284D LEU* 3.1 19.1 + - - +
285D CYS* 3.2 17.0 + - - -
340D ILE* 2.9 28.8 - - - +
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Residues in contact with TYR 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D HIS* 3.9 12.8 - + - -
226D PHE* 3.8 10.8 + - + +
227D GLU* 3.8 33.9 - - + -
230D SER* 3.2 14.3 + - - -
260D PHE* 3.9 21.0 - + + -
262D PHE* 3.3 31.4 - + - -
267D LYS 2.4 24.3 + - - -
268D ILE* 3.4 1.2 - - - -
269D TYR* 3.3 31.4 - + + -
277D VAL* 4.6 0.4 - - + -
278D ASP 3.4 3.2 + - - +
279D MET* 3.8 22.6 - - - +
280D GLN 3.5 0.4 - - - -
281D SER* 1.3 78.1 - - - +
283D GLU* 1.3 61.5 + - - +
285D CYS* 3.6 1.6 + - - +
286D CYS* 3.1 42.1 + - - -
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Residues in contact with GLU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 4.3 12.7 - - + +
222D ASP 5.7 0.3 - - - -
223D HIS* 3.3 53.0 + - + +
227D GLU* 5.1 0.9 - - - +
279D MET 3.4 16.0 + - - +
280D GLN* 3.6 12.6 - - - +
282D TYR* 1.3 78.9 - - - +
284D LEU* 1.3 55.0 - - - +
286D CYS* 3.6 2.8 - - - +
287D ASP* 3.2 41.2 + - - +
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Residues in contact with LEU 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PHE* 3.9 3.9 - - + -
241B SER* 3.5 38.6 - - - +
242B CYS* 3.9 16.8 - - - +
245B LEU* 3.7 13.7 - - + -
246B ALA* 5.2 1.8 - - + -
280D GLN 3.5 9.8 + - - +
281D SER* 3.1 13.7 + - - +
283D GLU* 1.3 75.9 - - - +
285D CYS* 1.3 57.1 - - - +
287D ASP* 3.1 7.9 + - - +
288D MET* 2.9 30.5 + - - +
320D LEU* 4.1 13.0 - - + -
326D LEU* 3.6 38.6 - - + -
340D ILE* 6.1 1.8 - - + -
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Residues in contact with CYS 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D PHE* 3.5 32.8 - - + -
262D PHE* 3.3 28.3 - - + -
281D SER 3.5 6.1 - - - -
282D TYR 3.8 4.3 - - - +
284D LEU* 1.3 76.4 - - - +
286D CYS* 1.3 52.6 + - - +
287D ASP 3.0 1.1 - - - -
288D MET* 2.7 29.0 + - - +
289D ILE* 2.9 20.0 + - - +
326D LEU* 6.0 5.4 - - - -
338D VAL* 3.8 20.8 - - + +
340D ILE* 4.4 14.4 - - - -
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Residues in contact with CYS 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D HIS* 3.6 22.2 - - + +
226D PHE* 5.2 0.4 - - + -
262D PHE* 3.6 3.1 - - - -
267D LYS* 3.4 34.0 - - + +
282D TYR* 3.1 58.1 + - - +
283D GLU 3.6 6.5 - - - +
285D CYS* 1.3 76.3 - - - +
287D ASP* 1.3 63.4 + - - +
289D ILE* 3.5 4.2 + - - +
290D ASP* 3.2 29.1 + - - +
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Residues in contact with ASP 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLN 6.3 0.2 - - - -
238B PHE* 3.7 9.6 - - + -
241B SER* 2.2 42.3 + - - +
245B LEU* 5.8 0.3 - - - +
223D HIS* 4.8 2.4 + - - -
283D GLU* 3.2 34.6 + - - +
284D LEU 3.3 12.1 - - - +
285D CYS 3.0 0.2 - - - -
286D CYS* 1.3 78.6 - - - +
288D MET* 1.3 58.0 + - - +
290D ASP* 3.4 15.9 - - - +
291D VAL* 2.9 29.8 + - - +
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Residues in contact with MET 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PHE* 3.9 11.7 - - + -
284D LEU 2.9 10.9 + - - +
285D CYS* 2.7 12.3 + - - +
287D ASP* 1.3 74.6 - - - +
289D ILE* 1.3 59.0 + - - +
290D ASP 3.1 1.8 - - - -
291D VAL* 3.2 4.8 + - - +
292D VAL* 2.9 32.9 + - + +
316D ALA* 3.5 32.1 - - + +
318D ILE* 3.4 33.7 - - + -
326D LEU* 3.8 38.1 - - + +
327D TYR 3.9 0.2 - - - +
328D LEU* 3.8 17.0 - - + -
338D VAL* 4.0 16.6 - - + -
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Residues in contact with ILE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D PHE* 3.4 54.7 - - + -
263D ASP 5.3 0.9 - - - +
264D VAL* 3.8 28.7 - - + +
267D LYS* 4.2 13.0 - - + -
285D CYS 2.9 15.6 + - - +
286D CYS* 3.8 8.3 - - - +
288D MET* 1.3 75.9 - - - +
290D ASP* 1.3 53.0 + - - +
292D VAL* 3.8 6.6 - - - +
293D ILE* 2.8 45.0 + - + +
328D LEU* 3.9 20.2 - - + -
336D ALA* 5.5 4.7 - - + -
338D VAL* 4.1 2.2 - - + -
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Residues in contact with ASP 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE* 5.5 0.4 - - - -
267D LYS* 3.1 34.5 + - - +
286D CYS 3.2 12.6 + - - +
287D ASP* 3.4 22.3 - - - +
288D MET 3.1 0.4 - - - -
289D ILE* 1.3 74.5 - - - +
291D VAL* 1.3 54.8 + - + +
293D ILE* 3.4 1.7 + - - -
294D ASP* 2.8 50.7 + - - +
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Residues in contact with VAL 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE* 4.1 27.1 - - + +
235B ILE* 5.1 4.7 - - + -
238B PHE* 3.5 34.8 - - + -
252B MET* 3.6 37.9 - - + -
287D ASP 2.9 19.3 - - - +
288D MET* 3.2 9.6 + - + +
290D ASP* 1.3 76.0 - - + +
292D VAL* 1.3 55.4 + - + +
294D ASP* 4.3 0.2 - - - +
295D VAL* 3.0 41.8 + - + +
318D ILE* 5.5 0.2 - - + -
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Residues in contact with VAL 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B MET* 5.7 1.6 - - - -
254B VAL* 4.1 21.6 - - + +
255B ARG 5.5 2.9 - - - +
288D MET* 2.9 23.3 + - + +
289D ILE* 3.8 7.6 - - + +
291D VAL* 1.3 74.5 - - + +
293D ILE* 1.3 67.7 + - + +
296D SER* 2.6 36.6 + - - +
310D TYR* 5.9 3.1 - - + -
314D SER* 5.5 7.6 - - - -
315D MET 5.4 1.8 - - - +
316D ALA* 3.3 31.9 - - + -
328D LEU* 4.1 25.8 - - + -
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Residues in contact with ILE 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D VAL* 3.5 33.0 - - + +
289D ILE* 2.8 30.7 + - + +
290D ASP* 4.2 2.9 - - - +
292D VAL* 1.3 79.5 - - + +
294D ASP* 1.3 61.7 + - - +
296D SER* 3.2 4.7 + - - -
297D CYS* 2.6 50.9 + - - -
309D ALA* 4.1 4.7 - - + +
310D TYR* 4.1 28.5 - - + +
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Residues in contact with ASP 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE* 3.8 31.2 - - + +
290D ASP* 2.8 29.3 + - - +
291D VAL 4.3 1.3 - - - +
293D ILE* 1.3 85.3 - - - +
295D VAL* 1.3 61.6 + - - +
296D SER 3.4 0.2 + - - -
297D CYS* 3.5 16.0 + - - +
298D ILE* 3.6 19.2 + - - +
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Residues in contact with VAL 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 4.4 20.0 - - + -
234B ILE* 4.4 8.5 - - + -
235B ILE* 5.7 1.3 - - + -
254B VAL* 4.8 13.0 - - + -
259B PHE* 4.1 19.7 - - + -
261B ALA* 4.7 2.5 - - + -
263B ILE* 5.2 9.6 - - + -
273B MET* 4.1 25.1 - - + -
291D VAL* 3.0 39.3 + - + +
292D VAL 4.3 2.0 - - - +
294D ASP* 1.3 74.9 - - - +
296D SER* 1.3 57.5 + - - +
298D ILE* 3.2 17.5 + - - +
299D TYR* 3.3 17.8 + - + +
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Residues in contact with SER 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B VAL* 3.9 8.0 - - - +
255B ARG 4.8 4.0 + - - -
256B ASN* 4.8 0.9 - - - -
259B PHE* 3.8 24.8 - - - -
292D VAL* 2.6 26.3 + - - +
293D ILE* 3.2 6.3 + - - -
295D VAL* 1.3 75.5 - - - +
297D CYS* 1.3 58.8 - - - +
298D ILE 3.3 0.7 - - - -
300D GLY* 3.0 29.4 + - - -
301D LEU* 3.9 0.2 - - - +
309D ALA* 3.6 31.8 + - - +
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Residues in contact with CYS 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ILE* 2.6 48.7 + - - -
294D ASP* 3.9 10.3 - - - +
295D VAL 3.4 0.4 - - - -
296D SER* 1.3 75.0 - - - +
298D ILE* 1.3 64.0 + - + +
301D LEU* 3.6 26.3 - - + +
309D ALA* 3.7 13.7 - - + -
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Residues in contact with ILE 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B GLN* 4.6 7.7 - - - +
223B ARG* 5.9 2.8 - - - +
224B ASP* 4.0 22.3 + - + +
227B ARG* 3.7 29.8 - - + -
230B LYS* 4.1 26.0 - - + +
231B ILE* 3.6 29.6 - - + -
234B ILE* 4.2 5.2 - - + -
294D ASP 3.6 15.0 - - - +
295D VAL 3.2 7.0 + - - +
297D CYS* 1.3 82.1 - - + +
299D TYR* 1.3 82.5 + - + +
300D GLY 3.7 0.2 - - - -
301D LEU* 4.8 5.2 + - - +
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Residues in contact with TYR 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU* 2.6 32.5 + - - +
204B LEU* 3.6 18.4 - - - +
222B GLN* 3.6 27.6 - - - -
227B ARG* 3.7 14.9 + - + +
231B ILE* 4.3 8.6 - - + +
258B ASN* 4.9 1.4 - - - +
259B PHE* 3.8 28.1 - + + +
273B MET* 3.5 32.1 - - + -
275B VAL* 3.8 27.1 - - + +
295D VAL* 3.3 15.5 + - + +
298D ILE* 1.3 91.8 - - + +
300D GLY* 1.3 57.0 + - - +
301D LEU 3.4 11.9 + - - +
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Residues in contact with GLY 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ASN* 2.8 23.5 - - - +
258B ASN* 3.3 13.0 + - - -
259B PHE* 3.2 24.9 - - - -
296D SER 3.0 19.8 + - - +
299D TYR* 1.3 75.9 - - - +
301D LEU* 1.3 64.7 + - - +
308D SER 4.0 5.5 - - - +
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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