Contacts of the helix formed by residues 257 - 279 (chain A) in PDB entry 3QI6
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 THR 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A HIS* 4.5 6.6 - - - -
254A GLY* 2.9 8.2 + - - -
256A LYS* 1.3 84.6 - - - +
258A LEU* 1.3 65.4 + - - +
259A VAL 3.3 2.9 + - - -
260A LEU* 3.4 6.5 + - - +
261A ARG* 2.9 52.2 + - - +
213C HIS* 3.7 25.8 + - + +
257C THR* 4.5 6.2 - - - +
261C ARG* 4.0 14.4 - - + -
340C VAL* 3.8 15.9 - - + -
373C ILE* 3.9 13.9 - - + -
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 5.8 0.2 - - + -
74A VAL* 5.9 0.4 - - + -
188A SER* 3.8 7.2 - - - +
189A PRO* 3.7 31.0 - - + -
190A ALA* 4.1 10.5 - - + +
209A TYR* 3.6 27.1 - - + +
210A ILE* 4.2 4.3 - - + +
254A GLY 3.2 3.2 + - - -
255A LEU* 3.2 35.6 + - + +
257A THR* 1.3 78.2 - - - +
259A VAL* 1.3 57.1 + - + +
261A ARG* 3.4 13.4 - - - +
262A MET* 2.8 69.3 + - + +
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.9 32.3 - - + +
15A ALA* 3.9 32.5 - - + +
18A ALA* 5.3 4.5 - - + -
190A ALA* 4.0 21.3 - - + +
255A LEU 4.9 0.6 + - - -
256A LYS 5.6 0.4 - - - -
257A THR 3.3 0.8 - - - -
258A LEU* 1.3 79.4 - - + +
260A LEU* 1.3 62.6 + - - +
262A MET* 3.5 2.4 + - - +
263A GLN* 3.3 25.8 + - - +
375C ASP* 5.5 4.0 - - - +
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Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 5.6 1.6 - - - +
257A THR* 3.8 9.4 - - - +
259A VAL* 1.3 75.9 - - - +
261A ARG* 1.3 65.6 + - - +
263A GLN* 3.4 21.7 - - - +
264A ARG* 3.4 5.5 + - - +
260C LEU* 3.5 43.4 - - + +
261C ARG* 3.7 20.0 - - + +
264C ARG* 3.7 51.1 - - + +
373C ILE* 3.9 30.1 - - + +
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Residues in contact with ARG 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 2.7 32.9 + - - +
210A ILE 3.2 9.7 + - - -
212A GLY* 3.3 18.2 + - - -
213A HIS* 4.1 5.7 - - - -
254A GLY 2.8 24.5 + - - -
257A THR* 2.9 38.9 + - - +
258A LEU* 3.4 19.3 - - - +
260A LEU* 1.3 73.9 - - - +
262A MET* 1.3 57.0 + - - +
264A ARG* 3.1 3.1 + - - +
265A HIS* 2.9 49.2 + - + +
338A GLY 4.5 0.2 + - - -
340A VAL* 3.9 23.3 - - - -
373A ILE* 4.0 6.5 - - + +
257C THR* 4.0 11.0 - - + -
260C LEU* 3.6 18.4 - - + -
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Residues in contact with MET 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PHE 3.8 8.5 - - - +
187A ALA 3.6 20.0 - - - +
188A SER* 3.5 9.6 - - - +
190A ALA* 3.7 13.7 - - + -
191A LEU* 3.8 23.8 - - + -
209A TYR* 3.1 48.9 - - + -
258A LEU* 2.8 47.7 + - + +
259A VAL 4.1 1.6 - - - +
261A ARG* 1.3 72.5 - - - +
263A GLN* 1.3 56.6 + - - +
265A HIS* 3.7 6.5 - - + +
266A SER* 2.8 36.6 + - - -
307A GLY* 4.9 0.2 - - - -
308A GLY 4.8 7.2 - - - +
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Residues in contact with GLN 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 5.7 2.0 - - - +
259A VAL* 3.3 13.1 + - - +
260A LEU* 3.4 23.2 - - - +
262A MET* 1.3 79.3 - - - +
264A ARG* 1.3 57.4 + - + +
266A SER* 3.3 5.4 + - - -
267A GLU* 3.0 50.1 + - - +
264C ARG* 2.9 33.2 + - - +
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Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU 3.4 0.8 + - - -
261A ARG 3.1 7.2 + - - +
263A GLN* 1.3 79.0 - - + +
265A HIS* 1.3 64.3 + - - +
267A GLU* 3.1 22.4 + - - -
268A ASN* 3.0 44.4 + - - +
373A ILE* 3.8 30.0 + - + +
374A GLU 5.5 0.4 - - - -
375A ASP* 5.8 1.8 + - - -
259C VAL* 5.8 5.5 - - - +
260C LEU* 3.4 46.2 - - + +
263C GLN* 2.8 36.2 + - - +
264C ARG* 6.0 0.8 - - - +
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Residues in contact with HIS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 3.6 34.7 - + + -
261A ARG* 2.9 43.4 + - + +
262A MET* 3.7 11.0 - - + +
264A ARG* 1.3 73.0 - - - +
266A SER* 1.3 57.8 + - - +
268A ASN* 4.0 3.0 - - - +
269A ALA* 2.9 32.4 + - - +
308A GLY* 3.6 18.2 - - - +
338A GLY* 4.6 0.9 - - - -
339A SER 3.1 33.1 + - - -
340A VAL* 4.8 0.8 + - - -
370A SER* 5.7 0.7 - - - -
371A VAL* 2.7 26.8 + - - +
372A GLY* 3.8 10.2 - - - -
373A ILE* 4.0 11.6 - - + +
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 4.0 8.5 - - - +
262A MET 2.8 20.9 + - - -
263A GLN* 3.8 5.4 - - - -
264A ARG 3.1 0.2 - - - -
265A HIS* 1.3 76.4 - - - +
267A GLU* 1.3 65.0 + - - +
270A ALA* 3.1 21.7 + - - +
287A TYR* 3.5 8.8 + - - -
305A GLY* 5.1 3.6 - - - -
306A PHE 4.2 6.9 + - - -
307A GLY* 3.2 37.7 + - - -
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Residues in contact with GLU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A GLN* 3.0 38.8 + - + +
264A ARG* 3.1 34.2 + - - +
266A SER* 1.3 77.5 - - - +
268A ASN* 1.3 63.3 + - - +
270A ALA* 3.2 7.7 + - - +
271A ALA* 3.1 22.2 + - - +
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Residues in contact with ASN 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG* 3.0 31.7 + - - +
265A HIS 4.0 0.7 - - - +
267A GLU* 1.3 78.2 - - - +
269A ALA* 1.3 59.6 + - - +
271A ALA* 3.2 4.9 + - - +
272A VAL* 2.8 31.0 + - - +
371A VAL* 3.4 18.6 - - + -
372A GLY 2.9 21.5 + - - +
373A ILE* 3.7 8.3 - - - +
374A GLU 3.1 23.4 + - - +
376A VAL* 3.5 29.6 + - + +
379A LEU* 4.1 3.5 - - + +
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A HIS 2.9 21.1 + - - +
266A SER 3.9 0.4 - - - +
268A ASN* 1.3 79.3 - - - +
270A ALA* 1.3 56.0 + - - +
272A VAL 4.3 0.4 - - - +
273A ALA* 2.8 27.2 + - - +
287A TYR* 3.8 10.9 - - + -
307A GLY 3.3 20.2 - - - +
308A GLY* 3.7 19.5 - - - +
310A VAL* 3.5 12.8 - - + +
371A VAL* 3.8 11.2 - - + +
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A SER 3.1 13.9 + - - +
267A GLU* 3.2 10.7 + - - +
269A ALA* 1.3 75.1 - - - +
271A ALA* 1.3 58.2 + - - +
273A ALA* 3.4 2.8 + - - +
274A GLU* 2.9 31.2 + - - +
287A TYR* 4.0 20.4 + - + +
290A LEU* 5.8 1.0 - - - +
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLU 3.1 8.9 + - - +
268A ASN 3.4 8.5 - - - +
270A ALA* 1.3 78.5 - - - +
272A VAL* 1.4 59.7 + - - +
274A GLU* 3.9 10.7 - - - +
275A PHE* 2.9 31.0 + - - +
376A VAL* 3.7 24.2 - - + -
380A LEU* 4.0 9.3 - - + +
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASN 2.8 20.6 + - - +
269A ALA 3.9 3.1 - - - +
271A ALA* 1.4 75.6 - - - +
273A ALA* 1.3 58.9 + - - +
275A PHE* 3.3 1.7 + - - +
276A LEU* 2.9 41.0 + - + +
310A VAL* 4.6 4.5 - - + -
331A PHE* 4.7 3.6 - - + -
369A LEU* 4.2 11.7 - - + -
371A VAL* 4.0 29.4 - - + -
376A VAL* 5.1 1.6 - - + -
379A LEU* 4.6 11.9 - - + -
380A LEU* 3.9 21.3 - - + -
383A LEU* 3.6 26.9 - - + -
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ALA 2.8 17.3 + - - +
270A ALA 3.8 3.4 - - - +
272A VAL* 1.3 77.3 - - - +
274A GLU* 1.3 61.1 + - - +
276A LEU* 3.4 2.0 + - - +
277A ALA* 2.9 26.7 + - - +
285A VAL* 3.8 17.0 - - + +
287A TYR* 3.8 34.3 - - + -
290A LEU* 4.6 8.5 - - + -
310A VAL* 4.1 7.8 - - + +
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Residues in contact with GLU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ALA 2.9 20.5 + - - +
271A ALA* 3.9 9.7 - - - +
273A ALA* 1.3 73.8 - - - +
275A PHE* 1.3 65.6 + - - +
277A ALA* 3.4 14.0 + - - +
278A GLU* 3.4 20.3 + - + +
290A LEU* 5.3 5.5 - - + +
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ALA 2.9 19.4 + - - +
272A VAL 3.5 3.6 - - - +
274A GLU* 1.3 80.4 + - - +
276A LEU* 1.3 81.7 + - + +
278A GLU* 3.2 11.2 + - - +
279A HIS* 3.4 32.0 + + + +
380A LEU* 3.8 32.5 - - + -
383A LEU* 4.0 28.9 - - + -
384A LYS* 4.0 25.4 - - + -
387A LEU* 4.5 0.4 - - + -
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A VAL* 2.9 30.4 + - + +
273A ALA* 4.0 1.3 - - - +
275A PHE* 1.3 89.0 - - + +
277A ALA* 1.3 57.4 + - - +
278A GLU 3.1 0.4 - - - -
279A HIS* 3.1 16.9 + - + +
282A ILE* 3.3 36.2 - - + +
285A VAL* 3.8 14.6 - - + -
310A VAL* 4.9 1.6 - - + -
312A VAL* 3.4 26.7 - - + -
324A LEU* 5.9 1.6 - - + -
369A LEU* 3.7 24.0 - - + -
383A LEU* 4.4 9.6 - - + -
387A LEU* 3.7 29.8 - - + -
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ALA 2.9 19.3 + - - +
274A GLU* 3.6 10.3 - - - +
275A PHE 3.4 0.2 - - - -
276A LEU* 1.3 73.9 - - - +
278A GLU* 1.3 72.6 + - - +
279A HIS 4.8 1.8 - - - +
282A ILE* 5.2 1.6 - - - +
285A VAL* 3.4 19.2 - - + +
290A LEU* 5.3 8.5 - - + -
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A GLU* 3.4 19.0 + - + +
275A PHE* 3.2 6.9 + - - +
276A LEU 3.1 0.6 - - - -
277A ALA* 1.3 91.5 - - - +
279A HIS* 1.3 62.9 + - - +
280A PRO* 3.6 6.1 - - - +
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Residues in contact with HIS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A PHE* 3.4 29.2 + + + +
276A LEU* 3.1 22.2 + - + +
277A ALA 4.8 1.6 - - - +
278A GLU* 1.3 79.4 - - - +
280A PRO* 1.4 79.8 - - + +
281A ALA* 3.0 40.3 + - + +
282A ILE* 3.3 20.7 + - + +
384A LYS* 5.0 4.5 + - - -
387A LEU* 3.6 36.9 - - + +
388A GLY 3.9 14.5 + - - -
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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) + - + + + + + -
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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