Contacts of the helix formed by residues 255 - 276 (chain D) in PDB entry 3QNQ
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 VAL 255 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D ALA* 3.9 15.3 - - + +
240D LEU* 3.5 38.6 - - + -
241D VAL* 3.7 22.2 - - + -
244D LEU* 3.8 19.3 - - + -
251D GLY 3.0 6.0 + - - +
254D ILE* 1.3 71.6 - - + +
256D GLY* 1.3 58.6 + - - +
257D GLY 3.0 3.6 - - - -
258D VAL* 2.9 23.3 + - - +
259D MET* 2.9 20.7 + - + +
263D TRP* 4.0 16.4 - - + -
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Residues in contact with GLY 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D VAL* 4.9 1.0 - - - +
251D GLY 3.8 0.2 + - - -
252D ALA* 3.3 24.1 + - - +
253D THR* 3.6 1.8 - - - -
255D VAL* 1.3 78.6 - - - +
257D GLY* 1.3 56.8 + - - +
258D VAL 3.4 0.2 - - - -
259D MET 3.9 0.9 - - - -
260D SER* 2.9 32.4 + - - -
263D TRP* 3.7 20.1 - - - -
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Residues in contact with GLY 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LEU* 4.8 2.4 - - - +
25D ILE* 4.0 22.7 - - - +
26D ARG* 4.1 22.7 + - - +
29D LEU* 4.5 1.7 - - - +
253D THR 2.7 23.3 + - - -
254D ILE 3.6 2.5 - - - -
255D VAL 3.0 0.6 - - - -
256D GLY* 1.3 73.9 - - - +
258D VAL* 1.3 62.6 + - - +
259D MET 3.4 0.2 - - - -
260D SER* 4.0 10.2 + - - -
261D PRO* 4.5 0.5 - - - +
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Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D VAL* 5.7 0.9 - - + -
22D LEU* 3.3 45.1 - - + -
25D ILE* 6.0 0.2 - - - -
254D ILE* 3.2 12.5 + - + +
255D VAL* 2.9 10.4 + - - +
257D GLY* 1.3 77.4 - - - +
259D MET* 1.3 69.4 + - + +
260D SER 3.7 0.2 - - - -
261D PRO* 3.6 11.4 - - - +
262D ILE* 5.3 4.2 - - - +
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Residues in contact with MET 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D GLY* 4.2 19.7 - - - +
233D GLY* 4.9 7.9 - - - +
237D ALA* 4.9 2.9 - - + -
255D VAL* 2.9 21.4 + - + +
258D VAL* 1.3 85.1 - - + +
260D SER* 1.3 60.2 + - - +
261D PRO* 3.0 6.1 - - - -
262D ILE* 3.1 25.3 + - + +
263D TRP* 2.8 84.8 + - + +
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Residues in contact with SER 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 3.4 27.3 - - - +
33D MET* 6.2 0.7 - - - +
146D LEU* 4.9 0.7 - - - -
256D GLY 2.9 21.6 + - - -
257D GLY* 4.0 4.3 - - - -
259D MET* 1.3 72.3 - - - +
261D PRO* 1.3 70.7 - - - +
263D TRP* 3.7 12.8 - - - -
264D LEU* 3.0 36.7 + - - +
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Residues in contact with PRO 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ILE* 5.0 0.9 - - + -
29D LEU* 4.3 13.0 - - + -
146D LEU* 3.7 26.6 - - + +
147D PHE* 3.6 28.0 - - + -
150D MET* 3.6 26.5 - - + -
257D GLY 4.5 1.8 - - - +
258D VAL 3.6 15.3 - - - +
259D MET 3.2 5.8 - - - -
260D SER* 1.3 100.5 - - - +
262D ILE* 1.3 64.4 + - + +
264D LEU 3.8 0.5 - - - -
265D SER* 3.0 20.5 + - - -
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Residues in contact with ILE 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D PHE* 3.9 23.2 - - + -
224D LEU* 3.6 30.7 - - + +
225D SER* 3.7 33.7 - - - +
228D GLY* 4.0 15.5 - - - -
258D VAL 5.3 2.9 - - - +
259D MET* 3.1 32.2 + - + +
261D PRO* 1.3 78.9 - - + +
263D TRP* 1.3 65.3 + - + +
265D SER* 3.0 23.1 + - - -
266D LEU* 3.2 17.2 + - + +
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Residues in contact with TRP 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D GLY 4.0 4.7 + - - -
233D GLY 4.8 1.3 + - - -
234D ALA* 5.4 0.2 - - - +
237D ALA* 3.3 35.7 - - + -
241D VAL* 5.8 0.2 - - + -
255D VAL* 4.0 6.1 - - + -
256D GLY* 3.7 24.0 - - - -
259D MET* 2.8 63.1 + - + +
260D SER* 3.9 9.2 - - - -
261D PRO 3.2 0.2 - - - -
262D ILE* 1.3 76.7 - - + +
264D LEU* 1.3 59.1 + - + +
265D SER 3.3 0.4 - - - -
266D LEU* 4.0 2.0 + - - +
267D MET 3.3 10.9 + - - -
284D ILE* 3.9 24.5 - - + +
285D THR* 3.5 7.7 - - - -
286D ALA* 3.2 32.4 + - + +
289D PHE* 3.4 37.0 - + - -
294D TYR* 4.8 12.6 - + - -
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Residues in contact with LEU 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D LEU* 6.4 1.8 - - + -
32D THR* 5.4 4.9 - - - +
36D LEU* 3.7 24.2 - - + -
80D MET* 3.2 35.0 - - + -
143D SER* 3.6 8.2 - - - -
146D LEU* 3.2 17.5 - - + -
260D SER* 3.0 31.6 + - - +
263D TRP* 1.3 75.6 - - + +
265D SER* 1.3 62.5 + - - +
267D MET* 3.3 27.1 - - + +
268D ASP 3.3 12.0 + - - -
286D ALA* 4.7 9.2 - - + -
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Residues in contact with SER 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D SER* 4.2 22.3 + - - -
144D GLN* 5.3 1.7 - - - -
147D PHE* 6.4 0.4 - - - -
221D GLN* 4.9 14.6 + - - +
225D SER* 4.4 8.6 + - - -
261D PRO 3.0 12.7 + - - -
262D ILE* 3.2 14.1 - - - -
264D LEU* 1.3 76.8 - - - +
266D LEU* 1.3 64.9 + - - +
268D ASP* 2.9 19.8 + - - +
269D GLN* 3.2 22.2 + - - +
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Residues in contact with LEU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D SER* 3.3 32.8 - - - +
228D GLY 4.2 2.0 - - - -
229D ALA* 3.7 24.7 - - + +
262D ILE* 3.3 16.2 - - + +
263D TRP* 4.0 5.2 - - + +
265D SER* 1.3 72.1 - - - +
267D MET* 1.3 68.2 + - - +
268D ASP 3.1 0.3 + - - -
269D GLN* 3.2 26.6 + - - +
270D ASN* 3.2 16.8 - - - +
282D ASN* 3.8 18.6 - - - +
284D ILE* 3.0 47.6 - - + +
285D THR* 4.1 1.8 - - - -
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Residues in contact with MET 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 4.5 11.7 - - + -
77D PHE* 3.3 31.4 - - + -
80D MET* 4.9 3.6 - - - -
263D TRP 3.3 7.4 + - - +
264D LEU* 3.3 41.7 - - + +
265D SER 3.1 0.4 - - - -
266D LEU* 1.3 80.4 - - - +
268D ASP* 1.3 73.0 + - + +
270D ASN* 3.5 1.0 + - - +
271D ARG 3.3 13.7 + - - -
285D THR* 3.8 12.3 - - - -
286D ALA* 4.4 1.8 - - - +
287D GLN* 3.0 25.6 - - - +
377D GLY* 3.3 21.8 - - - +
379D ALA* 3.3 28.5 - - - -
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Residues in contact with ASP 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D PHE* 3.9 8.5 - - - +
78D ASN* 4.8 2.3 - - - +
80D MET* 5.4 0.2 - - - -
142D GLY* 5.2 0.2 - - - -
143D SER* 2.6 44.4 + - - +
264D LEU 3.3 3.0 + - - +
265D SER 2.9 7.1 + - - +
267D MET* 1.3 84.2 - - + +
269D GLN* 1.3 71.6 + - - +
271D ARG* 2.4 53.0 + - - +
272D ILE* 3.0 21.2 + - + +
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Residues in contact with GLN 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D SER* 5.1 2.6 + - - -
265D SER* 3.2 18.0 + - - +
266D LEU* 3.2 29.8 - - - +
268D ASP* 1.3 76.2 - - - +
270D ASN* 1.3 63.5 + - - +
271D ARG 2.8 0.3 + - - -
272D ILE* 2.9 18.0 + - - +
273D ALA* 2.9 12.0 + - - +
281D PRO* 3.8 21.5 - - + -
282D ASN* 3.6 17.6 - - - +
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Residues in contact with ASN 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D LEU 3.2 5.4 + - - +
267D MET 3.7 3.4 - - - +
268D ASP 3.2 0.8 - - - -
269D GLN* 1.3 72.6 - - - +
271D ARG* 1.3 55.8 + - - +
274D PHE* 2.8 34.5 + - - +
280D VAL* 3.1 22.6 - - + +
281D PRO* 3.6 8.7 - - - +
282D ASN* 2.3 49.1 + - - +
285D THR* 3.9 8.0 - - + +
374D ARG* 4.4 0.6 - - - +
375D PRO* 3.0 38.1 + - - +
377D GLY* 3.5 11.9 - - - -
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Residues in contact with ARG 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 4.0 21.3 - - + -
73D VAL* 4.0 14.0 + - - +
77D PHE* 3.6 42.1 - - + +
78D ASN* 3.5 29.7 + - - +
267D MET 3.3 5.7 + - - +
268D ASP* 2.4 53.9 + - - +
269D GLN 2.8 4.4 + - - -
270D ASN* 1.3 73.7 - - - +
272D ILE* 1.3 70.1 + - - +
274D PHE* 3.7 0.7 - - - +
275D GLN* 2.9 58.9 + - - +
376D SER 3.8 3.5 - - - +
377D GLY* 3.3 20.4 - - - +
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Residues in contact with ILE 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ASN* 6.0 0.9 - - - +
268D ASP* 3.0 24.8 + - + +
269D GLN* 2.9 11.1 + - - +
271D ARG* 1.3 99.6 - - - +
273D ALA* 1.3 67.4 - - - +
275D GLN* 3.5 10.7 + - - +
276D ALA* 3.4 21.1 + - + +
278D GLN* 5.2 4.5 - - - +
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D GLN 2.9 10.0 + - - +
270D ASN 3.9 0.9 - - - +
272D ILE* 1.3 81.0 - - - +
274D PHE* 1.3 65.1 + - - +
276D ALA* 3.1 8.5 + - - +
277D GLY 3.2 9.9 + - - -
278D GLN* 3.2 40.1 + - + +
279D ASP 4.2 0.9 - - - +
280D VAL* 4.2 4.7 - - - -
281D PRO* 3.6 32.8 - - + -
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Residues in contact with PHE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 5.3 5.4 - - + -
47D THR* 3.2 37.2 - - + -
49D PRO* 5.3 3.4 - - + -
270D ASN 2.8 24.0 + - - +
271D ARG 3.8 1.3 - - - +
273D ALA* 1.3 73.0 - - - +
275D GLN* 1.3 63.0 + - + +
276D ALA 3.0 5.4 + - - -
277D GLY* 3.0 14.6 + - - -
278D GLN 4.2 7.4 - - - -
280D VAL* 3.6 14.3 - - + +
376D SER* 3.2 34.1 - - - +
395D GLY* 3.5 29.2 - - - -
397D LYS* 4.5 22.7 - - - -
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Residues in contact with GLN 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D LEU* 3.3 30.3 - - + +
47D THR* 4.4 15.8 - - + +
70D GLY* 6.0 0.9 - - - -
73D VAL* 4.6 8.4 - - - +
271D ARG* 2.9 56.7 + - - +
272D ILE* 3.8 9.8 - - - +
274D PHE* 1.3 76.4 - - + +
276D ALA* 1.3 59.1 + - + +
277D GLY 3.6 0.4 - - - -
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Residues in contact with ALA 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ILE* 3.4 16.5 + - + +
273D ALA* 3.1 3.2 + - - +
274D PHE 3.0 0.8 - - - -
275D GLN* 1.3 82.4 - - + +
277D GLY* 1.3 55.8 + - - +
278D GLN* 3.4 13.3 + - + +
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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) + - + + + + + -
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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