Contacts of the helix formed by residues 309 - 335 (chain D) in PDB entry 4WLU
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 309 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D SER* 4.0 10.7 + - - -
223D LEU* 5.9 0.9 - - - +
308D VAL* 1.3 75.7 - - - +
310D SER* 1.3 59.7 + - - +
311D PHE* 3.5 10.6 + - - +
312D GLU* 3.0 36.8 + - - +
313D GLU* 2.8 27.4 + - - +
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Residues in contact with SER 310 (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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309D SER* 1.3 71.2 - - - +
311D PHE* 1.3 60.0 + - - +
313D GLU* 3.7 10.8 - - - +
314D LYS* 2.9 31.5 + - - +
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Residues in contact with PHE 311 (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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220D GLN* 3.6 26.5 - - - +
223D LEU* 3.6 31.2 - - + -
224D THR* 4.2 17.0 - - + -
227D THR* 3.7 24.5 - - + -
309D SER* 3.5 8.6 + - - +
310D SER* 1.3 79.8 + - - +
312D GLU* 1.3 66.4 + - + +
314D LYS* 3.4 25.7 + - + +
315D MET* 3.2 54.4 + - + +
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Residues in contact with GLU 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ILE* 4.3 1.3 - - + +
207D PRO 4.3 8.5 - - - +
208D LEU* 3.8 22.8 - - + +
209D ILE* 3.1 11.3 + - - +
210D SER* 2.6 48.9 + - - -
223D LEU* 6.1 0.7 - - - +
308D VAL* 3.2 16.4 - - + +
309D SER* 3.0 27.2 + - - +
311D PHE* 1.3 78.2 - - + +
313D GLU* 1.3 66.7 + - - +
315D MET* 3.3 18.4 + - + +
316D ILE* 3.0 28.3 + - - +
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Residues in contact with GLU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D VAL* 4.2 9.9 - - + +
309D SER 2.8 16.9 + - - +
310D SER* 3.7 10.8 - - - +
312D GLU* 1.3 75.8 - - - +
314D LYS* 1.3 65.3 + - - +
316D ILE* 3.2 20.6 + - - +
317D SER* 2.9 24.3 + - - -
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Residues in contact with LYS 314 (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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310D SER 2.9 19.1 + - - +
311D PHE* 3.5 26.1 - - + +
312D GLU 3.3 0.2 - - - -
313D GLU* 1.3 76.4 - - - +
315D MET* 1.3 55.1 + - + +
317D SER* 3.3 8.4 + - - -
318D ASP* 2.7 56.6 + - - +
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Residues in contact with MET 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D LYS 4.7 3.6 - - - +
206D ILE* 3.8 26.5 - - + +
207D PRO* 4.4 8.1 - - + +
227D THR* 3.6 27.4 - - + -
231D GLN* 4.0 13.9 - - - +
311D PHE* 3.2 49.4 + - + +
312D GLU* 3.3 22.6 + - + +
314D LYS* 1.3 75.8 - - + +
316D ILE* 1.3 65.5 + - - +
318D ASP* 3.2 11.0 + - - +
319D ALA* 2.9 25.5 + - - +
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Residues in contact with ILE 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ILE* 3.7 32.1 - - + -
206D ILE* 3.6 15.9 - - + +
208D LEU* 5.1 1.1 - - + -
283D THR* 4.8 8.5 - - + -
288D PHE* 4.5 12.1 - - + -
305D ILE* 3.9 20.2 - - + -
308D VAL* 4.5 9.2 - - + -
312D GLU 3.0 22.4 + - - +
313D GLU* 3.5 20.6 - - - +
315D MET* 1.3 73.5 - - - +
317D SER* 1.3 60.4 + - - +
319D ALA* 3.0 12.1 + - - +
320D ILE* 2.8 38.2 + - + +
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Residues in contact with SER 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D GLU* 2.9 20.5 + - - -
314D LYS* 3.4 11.7 - - - -
316D ILE* 1.3 79.4 - - - +
318D ASP* 1.3 63.6 + - - +
319D ALA 3.3 0.3 + - - -
320D ILE* 3.6 15.9 + - - +
321D PRO* 3.6 9.4 - - - +
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Residues in contact with ASP 318 (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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203D LYS* 3.7 33.1 + - + +
314D LYS* 2.7 45.1 + - - +
315D MET* 3.2 9.6 + - - +
317D SER* 1.3 74.8 + - - +
319D ALA* 1.3 60.7 + - - +
321D PRO* 3.5 12.1 - - - +
322D GLU* 5.0 1.6 + - - +
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Residues in contact with ALA 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D LYS* 3.9 9.0 - - - +
204D THR* 3.9 24.9 - - + -
206D ILE* 3.8 19.1 - - + -
288D PHE* 6.0 0.2 - - + -
315D MET 2.9 16.3 + - - +
316D ILE 3.0 5.3 + - - +
318D ASP* 1.3 77.9 - - - +
320D ILE* 1.3 64.8 + - + +
321D PRO 3.4 0.2 - - - -
322D GLU* 3.2 7.0 + - - +
323D LEU* 3.1 29.2 + - + +
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Residues in contact with ILE 320 (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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283D THR* 5.1 7.6 - - - +
284D GLU* 3.8 25.6 - - + +
285D CYS* 3.8 21.1 - - - -
288D PHE* 4.9 9.0 - - + -
316D ILE* 2.8 47.3 + - + +
317D SER* 4.0 8.7 - - - +
318D ASP 3.5 0.2 - - - -
319D ALA* 1.3 75.7 - - + +
321D PRO* 1.3 67.0 - - + +
323D LEU* 3.3 1.5 + - - +
324D LYS* 2.9 52.5 + - + +
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Residues in contact with PRO 321 (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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317D SER 3.6 8.3 - - - +
318D ASP* 3.5 14.4 - - - +
319D ALA 3.4 4.3 - - - -
320D ILE* 1.3 100.2 - - + +
322D GLU* 1.3 60.3 + - - +
324D LYS* 3.6 9.2 + - + +
325D ALA* 3.1 23.2 + - - +
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Residues in contact with GLU 322 (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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145D ASN* 5.1 0.8 + - - +
201D ALA* 3.9 20.5 - - - +
202D GLY* 5.5 0.6 - - - -
203D LYS* 3.3 35.5 + - + +
204D THR* 3.7 17.4 - - + +
318D ASP 5.0 1.3 + - - +
319D ALA 3.2 8.9 + - - +
321D PRO* 1.3 76.3 - - - +
323D LEU* 1.3 67.9 + - - +
325D ALA* 3.1 7.4 + - + +
326D SER* 3.0 33.3 + - - +
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Residues in contact with LEU 323 (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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145D ASN* 3.6 32.0 - - + +
198D GLY* 4.1 10.5 - - - +
199D GLY* 3.9 9.4 - - - +
204D THR* 3.8 17.0 - - + -
277D PHE* 4.1 12.1 - - + -
285D CYS* 3.8 13.7 - - - -
287D TYR 4.8 1.6 - - - +
288D PHE* 3.6 38.4 - - + -
319D ALA* 3.1 24.6 + - + +
320D ILE* 3.7 3.8 - - - +
322D GLU* 1.3 76.9 - - - +
324D LYS* 1.3 63.5 + - - +
326D SER* 3.3 4.7 + - - -
327D ILE* 3.0 33.0 + - + +
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Residues in contact with LYS 324 (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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284D GLU* 3.4 33.5 + - + +
285D CYS* 4.2 15.0 - - - -
320D ILE* 2.9 33.2 + - + +
321D PRO* 3.7 7.8 - - + +
323D LEU* 1.3 76.0 - - - +
325D ALA* 1.3 57.4 + - - +
327D ILE* 3.4 9.9 + - + +
328D LYS* 2.9 31.3 + - - +
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Residues in contact with ALA 325 (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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321D PRO 3.1 14.2 + - - +
322D GLU* 3.1 9.7 + - + +
324D LYS* 1.3 78.3 - - - +
326D SER* 1.3 58.6 + - - +
328D LYS* 3.4 7.4 + - - +
329D LYS* 3.0 29.4 + - - +
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Residues in contact with SER 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ASP* 5.0 9.3 + - - +
143D PRO* 6.0 0.7 - - - +
145D ASN* 3.7 30.2 + - - +
146D SER* 2.7 32.3 + - - -
322D GLU* 3.0 20.4 + - - +
323D LEU* 3.7 6.7 - - - -
325D ALA* 1.3 71.8 - - - +
327D ILE* 1.3 66.3 + - - +
329D LYS* 3.4 6.9 - - - +
330D GLY 3.2 12.1 + - - -
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Residues in contact with ILE 327 (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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145D ASN 3.9 14.6 - - - +
149D PRO* 3.9 5.5 - - + +
277D PHE* 4.5 3.4 - - + -
285D CYS* 4.1 11.0 - - + -
286D THR* 4.2 10.1 - - - +
287D TYR* 3.7 57.7 - - + +
323D LEU* 3.0 29.8 + - + +
324D LYS* 3.6 8.3 - - + +
326D SER* 1.3 76.1 - - - +
328D LYS* 1.3 63.3 + - - +
330D GLY* 3.1 3.8 + - - -
331D GLU* 3.0 45.6 + - - +
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Residues in contact with LYS 328 (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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324D LYS 2.9 17.5 + - - +
325D ALA* 3.7 7.4 - - - +
327D ILE* 1.3 75.7 - - - +
329D LYS* 1.3 54.1 + - - +
331D GLU* 3.3 14.5 + - - +
332D ASP* 2.7 66.1 + - - +
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Residues in contact with LYS 329 (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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111D ASP* 2.9 45.2 + - - +
114D PHE* 3.6 36.3 - - + +
115D ASN* 5.8 1.1 - - - -
146D SER* 4.2 2.7 - - - +
325D ALA 3.0 14.7 + - - +
326D SER* 3.4 12.3 - - - +
328D LYS* 1.3 76.6 - - - +
330D GLY* 1.3 63.0 + - - +
332D ASP* 3.9 6.3 - - - +
333D PHE* 3.1 23.2 + - - +
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Residues in contact with GLY 330 (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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114D PHE* 4.1 4.2 - - - -
146D SER 3.7 12.6 - - - -
149D PRO* 4.6 0.4 - - - -
150D ILE* 3.3 42.4 - - - +
326D SER 3.2 4.8 + - - -
327D ILE 3.1 7.5 + - - -
329D LYS* 1.3 75.1 - - - +
331D GLU* 1.3 66.6 + - - +
333D PHE* 3.3 8.5 + - - +
334D VAL* 3.4 8.1 + - - +
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Residues in contact with GLU 331 (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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149D PRO* 4.4 7.1 - - + +
153D GLU* 4.2 32.2 - - + +
286D THR* 4.4 9.0 + - - +
287D TYR* 4.1 10.5 - - + -
327D ILE* 3.0 37.2 + - + +
328D LYS* 3.6 19.0 - - - +
330D GLY* 1.3 74.6 - - - +
332D ASP* 1.3 63.6 + - - +
333D PHE 3.3 0.7 + - - -
334D VAL* 3.3 13.3 + - - +
335D LYS* 3.3 36.1 + - - +
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Residues in contact with ASP 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D LYS* 2.7 59.4 + - - +
329D LYS* 3.9 5.9 + - - +
331D GLU* 1.3 78.2 - - - +
333D PHE* 1.3 60.6 + - - +
335D LYS* 3.5 24.0 + - - +
336D THR* 3.4 21.4 + - - +
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Residues in contact with PHE 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D PHE* 3.8 18.2 - + + -
115D ASN* 6.1 1.6 - - - -
118D ALA* 3.8 33.9 - - + -
119D THR* 3.4 33.7 - - + -
122D ALA* 4.0 14.4 - - + -
150D ILE* 4.2 9.2 - - + -
329D LYS 3.1 12.8 + - - +
330D GLY* 3.5 8.7 - - - +
331D GLU 3.2 0.4 - - - -
332D ASP* 1.3 77.2 - - - +
334D VAL* 1.3 68.4 + - + +
336D THR* 2.7 29.5 + - - -
337D LEU* 3.8 24.4 - - + +
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Residues in contact with VAL 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ILE* 3.6 43.3 - - + +
153D GLU* 3.8 23.6 - - + -
154D VAL* 4.1 9.6 - - + +
157D LYS* 3.5 31.8 + - + -
330D GLY 3.7 9.2 - - - +
331D GLU 3.3 7.7 + - - +
333D PHE* 1.3 80.1 - - + +
335D LYS* 1.3 62.4 + - + +
336D THR 3.1 0.2 - - - -
337D LEU* 3.2 30.7 + - + +
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Residues in contact with LYS 335 (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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153D GLU* 5.1 14.2 + - - +
157D LYS* 5.6 2.2 - - - +
331D GLU* 3.3 40.2 + - - +
332D ASP* 3.7 19.5 + - - +
333D PHE 3.2 0.8 - - - -
334D VAL* 1.3 79.3 - - + +
336D THR* 1.3 59.3 + - + +
337D LEU 3.4 5.1 + - - +
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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