Contacts of the helix formed by residues 271 - 297 (chain D) in PDB entry 6Q3W
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D GLN* 5.1 3.1 + - - +
267D ARG 5.1 0.2 - - - +
270D VAL* 1.3 80.9 - - - +
272D LYS* 1.3 64.1 + - - +
273D GLU* 3.7 3.8 + - - +
274D GLY* 2.8 31.6 + - - -
275D PHE* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D SER* 1.3 75.6 - - - +
273D GLU* 1.3 62.0 + - - +
275D PHE* 3.7 6.1 - - - +
276D ARG* 3.3 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D GLN* 3.2 25.0 + - - +
271D SER* 3.3 3.4 + - - +
272D LYS* 1.3 78.7 - - - +
274D GLY* 1.3 58.8 + - - +
276D ARG* 3.2 26.2 + - - +
277D ARG* 2.9 69.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D GLN* 4.2 19.4 - - - +
246D VAL* 3.4 19.4 - - - +
271D SER* 2.8 19.4 + - - -
273D GLU* 1.3 73.4 - - - +
275D PHE* 1.3 65.2 + - - +
277D ARG* 3.1 8.8 + - - +
278D ALA 3.0 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D VAL* 4.6 2.7 - - - -
263D LEU* 3.3 44.6 - - + +
264D GLU* 3.8 26.5 - - - -
267D ARG* 4.3 26.9 - - + +
270D VAL* 3.7 16.6 - - + +
271D SER 3.1 20.2 + - - +
272D LYS* 3.7 6.1 - - - +
274D GLY* 1.3 76.5 - - - +
276D ARG* 1.3 68.0 + - + +
278D ALA* 3.3 3.1 + - - +
279D ARG* 2.8 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D LYS* 3.3 25.0 + - - +
273D GLU* 3.2 34.2 + - - +
275D PHE* 1.3 88.3 - - + +
277D ARG* 1.3 80.1 + - - +
279D ARG* 3.0 33.6 + - - +
280D HIS* 3.1 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D ARG* 3.4 53.4 - - + +
242D GLN* 3.3 29.9 + - + +
243D CYS* 3.7 13.7 - - - -
273D GLU* 2.9 49.6 + - - +
274D GLY* 3.1 12.1 + - - +
276D ARG* 1.3 99.0 - - - +
278D ALA* 1.3 59.4 + - - +
280D HIS* 3.7 8.5 + - - +
281D VAL* 3.6 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D CYS* 4.2 2.2 - - - -
246D VAL* 3.5 35.7 - - + -
255D LEU* 3.7 24.0 - - + -
263D LEU* 3.7 9.2 - - + -
274D GLY 3.0 11.3 + - - +
275D PHE 3.8 3.6 - - - +
277D ARG* 1.3 74.9 - - - +
279D ARG* 1.3 60.9 + - - +
280D HIS 3.2 0.2 - - - -
281D VAL* 3.2 1.7 + - - +
282D VAL* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D LEU* 4.2 13.4 - - + +
263D LEU* 3.7 12.8 - - + +
264D GLU* 3.3 38.4 + - - -
275D PHE* 2.8 43.1 + - + +
276D ARG* 3.0 26.3 + - - +
278D ALA* 1.3 74.5 - - - +
280D HIS* 1.3 64.8 + - - +
282D VAL* 4.9 0.4 - - - -
283D GLY* 3.0 21.1 + - - -
287D ARG* 5.2 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D HIS* 4.6 29.9 + + - -
45D THR* 5.1 0.4 - - - +
276D ARG 3.1 11.4 + - - +
277D ARG* 3.9 8.3 - - - +
278D ALA 3.2 0.2 - - - -
279D ARG* 1.3 79.2 - - - +
281D VAL* 1.3 65.4 + - + +
284D GLU* 2.7 75.3 + - + +
287D ARG* 3.6 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D HIS 4.1 12.3 - - - +
45D THR* 3.9 11.8 - - - +
47D TYR* 6.0 0.9 - - - +
48D ASN* 3.6 37.2 - - + +
243D CYS* 3.9 16.8 - - - -
255D LEU* 3.7 20.6 - - + -
277D ARG 3.6 14.6 - - - +
278D ALA 3.2 1.7 + - - +
280D HIS* 1.3 86.0 - - + +
282D VAL* 1.3 57.9 + - - +
284D GLU* 3.3 4.3 + - - +
285D ILE* 3.0 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D LEU* 3.6 33.2 - - + +
258D VAL* 3.3 28.0 - - + +
259D GLN 3.9 1.1 - - - +
260D LEU* 3.4 33.2 - - + +
263D LEU* 3.9 17.3 - - + -
278D ALA 3.0 18.6 + - - +
279D ARG 4.4 0.9 - - - +
281D VAL* 1.3 75.5 - - - +
283D GLY* 1.3 62.2 + - - +
285D ILE* 3.5 9.2 + - - +
286D ARG* 3.3 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D LEU* 4.2 17.9 - - - +
279D ARG 3.0 18.1 + - - -
280D HIS 3.8 0.2 - - - -
282D VAL* 1.3 78.3 - - - +
284D GLU* 1.3 56.3 + - - +
286D ARG* 3.4 7.8 + - - +
287D ARG* 3.0 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ILE* 3.3 15.9 - - - +
42D GLY* 2.9 39.4 + - - -
43D GLU 4.6 0.5 + - - -
44D HIS* 5.2 4.9 - - - +
45D THR* 3.6 13.9 - - + -
280D HIS* 2.7 43.2 + - + +
281D VAL 3.6 4.3 - - - +
283D GLY* 1.3 71.4 - - - +
285D ILE* 1.3 65.3 + - - +
287D ARG* 2.7 38.4 + - - +
288D THR* 2.8 30.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D THR* 4.0 9.2 - - - -
48D ASN 4.4 1.6 - - - +
50D GLY* 3.8 26.0 - - - -
51D LEU* 3.6 22.0 - - + +
255D LEU 4.0 9.4 - - - +
256D ARG* 3.7 50.5 - - + +
281D VAL* 3.0 30.3 + - + +
282D VAL* 3.6 6.7 - - - +
284D GLU* 1.3 76.5 - - - +
286D ARG* 1.3 64.4 + - - +
288D THR* 3.3 3.6 + - - -
289D ALA* 3.2 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D GLN* 5.0 3.6 - - - +
260D LEU* 3.6 36.6 - - - +
261D GLU* 2.7 42.4 + - - -
282D VAL 3.3 9.7 + - - +
283D GLY* 3.6 9.2 - - - +
284D GLU 3.2 0.6 - - - -
285D ILE* 1.3 82.1 - - - +
287D ARG* 1.3 63.7 + - + +
289D ALA* 3.3 7.8 + - - +
290D GLN* 3.0 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ILE* 3.9 16.8 - - + +
279D ARG 5.6 0.2 + - - -
280D HIS* 3.6 20.2 + - - +
283D GLY* 3.0 28.3 + - - +
284D GLU* 2.7 46.1 + - - +
286D ARG* 1.3 77.6 - - + +
288D THR* 1.3 52.9 + - - +
290D GLN* 3.2 15.5 + - - +
291D ALA* 2.7 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 288 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ILE* 3.8 25.5 - - + +
42D GLY* 3.2 23.4 + - - -
51D LEU* 3.6 34.7 + - + +
52D VAL 4.2 4.5 - - - +
53D LEU* 4.4 2.5 - - + +
200D LEU* 4.2 11.9 - - + -
284D GLU 2.8 20.7 + - - -
285D ILE 3.6 5.2 - - - -
287D ARG* 1.3 74.5 - - - +
289D ALA* 1.3 64.7 + - - +
291D ALA* 3.3 1.4 + - - +
292D ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 3.9 16.3 - - + +
200D LEU* 5.8 2.0 - - - -
285D ILE 3.2 12.9 + - - +
286D ARG* 3.6 10.5 - - - +
288D THR* 1.3 76.4 - - - +
290D GLN* 1.3 63.4 + - + +
292D ALA* 3.5 5.5 + - - +
293D ALA* 3.2 21.8 + - - +
296D ARG* 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 290 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ARG* 3.0 40.8 + - + +
287D ARG* 3.5 16.0 - - - +
289D ALA* 1.3 76.2 - - + +
291D ALA* 1.3 59.5 + - - +
293D ALA* 3.3 7.8 + - - +
294D ALA* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ILE* 4.1 27.1 - - + -
53D LEU* 4.4 7.4 - - + -
287D ARG 2.7 20.6 + - - +
288D THR 3.3 5.6 + - - +
290D GLN* 1.3 72.6 - - - +
292D ALA* 1.3 59.7 + - - +
294D ALA* 3.2 9.5 + - - +
295D LEU* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D LEU* 4.2 11.4 - - + +
200D LEU* 4.1 27.6 - - + -
211D VAL* 4.8 4.1 - - + +
288D THR 3.0 16.3 + - - +
289D ALA* 3.9 4.7 - - - +
291D ALA* 1.3 76.4 - - - +
293D ALA* 1.3 62.1 + - - +
295D LEU* 3.2 10.2 + - - +
296D ARG* 3.1 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D ALA 3.2 15.8 + - - +
290D GLN* 3.5 11.2 - - - +
292D ALA* 1.3 76.8 - - - +
294D ALA* 1.3 62.9 + - - +
296D ARG* 3.1 26.3 + - - +
297D ARG* 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D GLN 2.9 14.9 + - - +
291D ALA* 3.4 12.3 - - - +
293D ALA* 1.3 76.4 - - - +
295D LEU* 1.3 62.3 + - - +
297D ARG* 3.4 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU* 5.1 5.4 - - + -
53D LEU* 4.0 25.6 - - + -
198D ALA* 4.3 10.3 - - + -
211D VAL* 3.9 23.8 - - + -
212D PRO 4.9 6.8 - - - +
213D LEU* 3.6 33.7 - - + -
291D ALA 2.9 12.9 + - - +
292D ALA* 3.3 10.1 - - - +
294D ALA* 1.3 79.0 - - - +
296D ARG* 1.3 63.0 + - - +
297D ARG 3.2 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D LEU* 3.9 23.8 - - - +
209D SER* 4.5 10.5 + - - -
211D VAL* 4.3 27.7 - - + +
289D ALA 5.1 1.6 + - - -
292D ALA* 3.1 36.6 + - - +
293D ALA* 3.1 16.0 + - - +
295D LEU* 1.3 75.8 - - - +
297D ARG* 1.3 59.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ALA* 3.2 18.2 + - - +
294D ALA* 3.5 22.0 - - - +
295D LEU 3.2 4.7 - - - -
296D ARG* 1.3 80.4 - - - +
----------------------------------------------------------
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