Contacts of the helix formed by residues 261 - 283 (chain A) in PDB entry 1ZDT
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 ALA 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A GLN* 6.1 0.2 - - - +
259A PRO 3.5 3.4 + - - +
260A ALA* 1.3 70.5 - - - +
262A PHE* 1.3 62.6 + - - +
263A GLY 3.5 1.8 - - - -
264A LEU* 3.2 18.0 + - + -
265A LEU* 2.9 31.0 + - + +
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Residues in contact with PHE 262 (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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260A ALA 3.0 11.7 + - - +
261A ALA* 1.3 69.9 - - - +
263A GLY* 1.3 66.2 + - - +
265A LEU* 3.1 5.4 + - - +
266A CYS* 2.9 45.1 + - - -
436A TYR* 3.7 22.0 - + - -
440A LYS* 3.7 25.8 - - - -
445A GLU* 3.2 24.2 - - + -
446A MET* 3.8 16.4 - - - -
447A PRO* 4.2 4.0 - - + -
1001A PEF 3.5 44.6 - - + +
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Residues in contact with GLY 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ALA 3.5 0.6 - - - -
262A PHE* 1.3 83.1 - - - +
264A LEU* 1.3 57.2 + - - +
266A CYS* 3.4 8.2 + - - +
267A ARG* 3.0 54.3 + - - -
447A PRO* 4.5 4.5 - - - -
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Residues in contact with LEU 264 (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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246A GLY* 4.7 25.4 - - - +
247A SER 5.1 1.3 - - - +
248A LEU 5.8 3.4 - - - +
261A ALA* 3.2 21.5 + - + +
262A PHE 3.2 0.4 - - - -
263A GLY* 1.3 73.0 - - - +
265A LEU* 1.3 63.0 + - + +
267A ARG* 3.3 27.1 + - + +
268A MET* 2.9 31.7 + - + +
327A THR* 5.7 7.4 - - + -
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Residues in contact with LEU 265 (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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260A ALA* 4.2 10.3 - - + -
261A ALA* 2.9 26.5 + - + +
262A PHE 3.5 6.5 - - - +
264A LEU* 1.3 78.8 - - + +
266A CYS* 1.3 60.5 + - - +
268A MET* 3.4 21.5 + - + +
269A ALA* 3.1 22.3 + - - +
325A LEU* 3.8 28.7 - - + -
329A GLN* 4.7 6.7 - - - +
331A VAL* 6.1 0.7 - - + -
1001A PEF 3.2 63.8 - - + +
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Residues in contact with CYS 266 (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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262A PHE* 2.9 43.7 + - - -
263A GLY 3.4 9.2 - - - +
265A LEU* 1.3 74.7 - - - +
267A ARG* 1.3 65.4 + - - +
269A ALA* 3.2 5.2 + - - +
270A ASP* 3.0 27.5 + - - +
446A MET* 3.9 11.7 - - - -
447A PRO* 3.7 20.6 - - + -
450A ASN* 3.7 14.5 + - - +
452A LEU* 5.7 0.2 - - - +
1001A PEF 3.7 22.2 - - - -
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Residues in contact with ARG 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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246A GLY* 4.9 16.8 - - - +
263A GLY* 3.0 44.4 + - - +
264A LEU* 3.3 31.5 + - + +
266A CYS* 1.3 75.1 - - - +
268A MET* 1.3 63.1 + - - +
270A ASP* 3.2 10.3 + - + +
271A GLN* 3.0 34.2 + - + +
447A PRO* 4.2 19.2 - - - +
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Residues in contact with MET 268 (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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244A ILE* 4.3 9.1 - - + +
246A GLY* 6.0 2.2 - - - +
264A LEU* 2.9 21.1 + - + +
265A LEU* 3.5 29.2 - - + +
267A ARG* 1.3 75.1 - - - +
269A ALA* 1.3 61.2 + - - +
271A GLN* 3.5 6.7 + - - +
272A THR* 2.9 29.5 + - - +
325A LEU* 3.9 32.5 - - + -
326A VAL* 3.4 26.2 - - + +
327A THR* 3.5 28.7 - - + -
1001A PEF 4.3 22.0 - - + -
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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 LEU 3.1 10.0 + - - +
266A CYS 3.2 8.5 + - - +
268A MET* 1.3 79.2 - - + +
270A ASP* 1.3 60.0 + - - +
272A THR* 3.3 9.0 + - - -
273A PHE* 3.0 26.7 + - - +
306A LEU* 3.8 5.6 - - - +
452A LEU* 4.1 16.6 - - + +
1001A PEF 3.9 40.2 - - + -
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Residues in contact with ASP 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 CYS 3.0 16.0 + - - +
267A ARG* 3.2 13.0 + - + +
269A ALA* 1.3 75.6 - - - +
271A GLN* 1.3 63.2 + - - +
273A PHE* 3.2 9.5 + - - +
274A ILE* 3.0 31.1 + - - +
449A ASN 4.5 1.0 - - - +
450A ASN* 3.4 20.8 + - - -
451A LEU* 3.0 47.6 + - + +
452A LEU* 3.3 18.9 + - - +
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Residues in contact with GLN 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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243A ARG 4.9 1.7 - - - +
244A ILE* 3.9 22.9 - - + +
245A LEU* 3.7 44.1 + - + +
246A GLY 4.8 4.0 - - - +
267A ARG* 3.0 26.6 + - + +
268A MET 3.8 5.2 - - - +
270A ASP* 1.3 78.2 - - - +
272A THR* 1.3 60.3 + - - +
274A ILE* 3.3 27.6 - - - +
275A SER* 3.1 26.3 + - - -
451A LEU* 5.4 2.0 - - - +
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Residues in contact with THR 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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240A VAL* 6.1 0.9 - - + -
244A ILE* 3.6 14.8 - - + +
268A MET* 2.9 16.6 + - - +
269A ALA* 3.5 11.0 - - - -
270A ASP 3.2 0.2 - - - -
271A GLN* 1.3 73.4 - - - +
273A PHE* 1.3 66.3 + - - +
275A SER* 2.9 24.0 + - - +
276A ILE* 3.0 12.9 + - + +
306A LEU* 3.9 15.7 - - + -
309A ASP* 3.5 28.7 - - - +
313A ARG* 5.0 4.5 - - - +
326A VAL* 3.7 12.1 - - + +
1001A PEF 6.0 3.1 - - + +
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Residues in contact with PHE 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 3.0 13.7 + - - +
270A ASP 3.2 10.1 + - - +
272A THR* 1.3 77.6 - - - +
274A ILE* 1.3 64.4 + - - +
276A ILE* 3.1 21.2 + - + +
277A VAL* 3.1 31.1 + - + +
298A LEU* 5.7 2.7 - - + -
302A TRP* 3.5 28.3 - + + -
306A LEU* 4.0 22.0 - - + +
451A LEU* 4.7 10.5 - - + -
452A LEU* 3.9 17.7 - - + -
455A MET* 3.7 43.5 - - + -
744P LEU* 4.3 2.7 - - + -
745P LEU* 4.0 5.2 - - + -
748P LEU* 4.0 23.3 - - + -
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Residues in contact with ILE 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 ASP 3.0 16.5 + - - +
271A GLN* 3.3 30.3 - - - +
273A PHE* 1.3 79.7 - - + +
275A SER* 1.3 57.3 + - - +
277A VAL* 3.3 8.6 + - - +
278A ASP* 3.1 38.0 + - - +
451A LEU* 3.7 24.2 - - + -
748P LEU* 3.9 25.8 - - + -
752P ASP 4.1 20.0 - - - +
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Residues in contact with SER 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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235A PRO* 5.8 3.0 - - - +
240A VAL* 4.4 23.8 - - - +
244A ILE* 5.2 3.6 - - - -
271A GLN 3.1 10.0 + - - -
272A THR* 2.9 23.3 + - - +
273A PHE 3.2 0.2 - - - -
274A ILE* 1.3 80.5 - - - +
276A ILE* 1.3 59.0 + - - +
278A ASP* 3.4 13.4 - - - +
279A TRP* 3.0 26.2 + - - +
282A ARG* 4.9 1.7 + - - -
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Residues in contact with ILE 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 THR* 3.0 20.9 + - + +
273A PHE* 3.1 16.6 + - + +
275A SER* 1.3 78.6 - - - +
277A VAL* 1.3 60.4 + - + +
279A TRP* 3.4 14.4 + - + +
280A ALA* 3.0 23.9 + - - +
298A LEU* 5.4 2.5 - - + -
302A TRP* 5.6 0.9 - - - +
305A LEU* 3.7 54.1 - - + +
306A LEU* 3.9 28.9 - - + +
309A ASP* 4.2 14.8 - - + +
372A LYS* 5.8 5.8 - - - +
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Residues in contact with VAL 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 PHE* 3.1 44.6 + - + +
274A ILE 3.7 6.7 - - - +
276A ILE* 1.3 73.0 - - + +
278A ASP* 1.3 61.0 - - - +
280A ALA* 3.3 5.4 + - - +
281A ARG* 3.0 29.6 + - - +
298A LEU* 4.1 26.7 - - + -
745P LEU* 4.6 2.7 - - + -
748P LEU* 3.8 39.0 - - + +
749P LEU* 4.2 11.0 - - + -
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Residues in contact with ASP 278 (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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274A ILE* 3.1 28.1 + - - +
275A SER* 3.4 14.5 - - - +
277A VAL* 1.3 74.2 - - - +
279A TRP* 1.3 66.0 + - - +
281A ARG* 3.5 24.5 + - - +
282A ARG* 3.4 36.3 + - - +
748P LEU 4.8 2.9 - - - +
751P LYS* 5.7 2.8 + - - -
752P ASP* 5.9 3.3 + - - -
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Residues in contact with TRP 279 (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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230A LEU* 4.7 12.4 + - + +
233A LEU* 4.7 11.8 - - + +
234A GLU* 4.2 10.4 + - - -
235A PRO* 4.7 7.0 - - + -
275A SER 3.0 15.4 + - - +
276A ILE* 3.4 21.1 - - + +
278A ASP* 1.3 76.8 - - - +
280A ALA* 1.3 73.1 + - + +
282A ARG* 3.1 37.0 + - - +
283A CYS* 3.3 30.4 + - - -
305A LEU* 4.1 23.8 - - + -
369A VAL* 5.0 1.0 - - + +
372A LYS* 3.5 67.5 - - + +
373A PHE* 4.1 6.1 - - - -
376A LEU* 3.8 25.4 - - + -
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Residues in contact with ALA 280 (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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276A ILE 3.0 16.8 + - - +
277A VAL* 3.3 4.7 + - - +
279A TRP* 1.3 90.1 - - + +
281A ARG* 1.3 61.9 + - - +
283A CYS* 3.1 17.2 + - - +
286A PHE* 3.0 28.8 - - + +
298A LEU* 4.1 14.8 - - + -
376A LEU* 4.1 24.0 - - + -
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Residues in contact with ARG 281 (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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277A VAL 3.0 16.2 + - - +
278A ASP* 3.6 27.8 + - - +
279A TRP 3.2 0.2 - - - -
280A ALA* 1.3 77.3 - - - +
282A ARG* 1.3 59.7 + - + +
283A CYS 3.4 0.2 - - - -
286A PHE* 3.9 8.9 - - + -
287A LYS* 3.3 24.4 - - - +
294A GLN* 5.4 2.9 + - - +
748P LEU 2.6 37.1 + - - -
749P LEU* 3.4 41.9 + - + +
750P ASP 4.5 3.6 + - - -
751P LYS* 3.7 37.9 - - - +
752P ASP 4.3 2.8 - - - +
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Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.0 52.9 + - + +
235A PRO* 3.9 27.4 - - - +
275A SER 4.9 1.2 + - - -
278A ASP* 3.4 21.7 + - - +
279A TRP* 3.1 31.4 + - - +
281A ARG* 1.3 81.5 - - + +
283A CYS* 1.3 62.0 + - - +
284A MET 3.6 0.3 + - - -
287A LYS* 3.6 15.3 + - - +
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Residues in contact with CYS 283 (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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230A LEU* 4.2 13.7 - - - -
233A LEU* 3.7 7.6 - - - -
279A TRP* 3.3 57.4 + - - -
280A ALA 3.1 13.3 + - - +
282A ARG* 1.3 75.3 - - - +
284A MET* 1.3 73.5 + - - +
286A PHE* 4.1 6.5 - - + -
287A LYS* 3.1 26.4 + - - +
373A PHE* 4.3 5.2 - - + -
376A LEU* 4.2 8.5 - - + -
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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
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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