Contacts of the helix formed by residues 316 - 339 (chain D) in PDB entry 3RMD
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 ASN 316 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ASP* 5.1 0.3 - - - +
306D ASP* 5.4 6.9 + - + +
312D LEU* 3.5 20.5 + - + +
315D SER* 1.3 80.4 + - - +
317D HIS* 1.3 52.4 + - - +
318D GLN* 2.7 30.4 + - - +
319D ARG* 2.9 44.6 + - + +
320D TYR 3.4 6.1 + - - -
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Residues in contact with HIS 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ASP 5.9 0.2 - - - -
150D ASP* 3.4 33.1 + - - -
152D LEU* 6.2 0.4 - - - +
159D VAL* 3.1 36.4 - - + +
160D GLU 3.1 28.3 + - - -
161D GLU 4.0 10.9 + - - -
162D TRP* 4.4 1.8 - - + +
312D LEU 3.7 4.7 - - - -
313D ARG* 3.1 32.9 + - - +
314D GLU 4.9 0.2 - - - +
315D SER 3.3 7.8 + - - +
316D ASN* 1.3 71.3 - - - +
318D GLN* 1.3 70.6 + - - +
320D TYR* 3.2 12.8 - - - +
321D ILE* 3.5 14.6 + - + +
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Residues in contact with GLN 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D GLU 4.4 4.8 + - - -
162D TRP* 3.2 33.1 + - - +
163D SER* 2.8 44.0 + - - +
166D ILE* 3.6 22.6 - - + +
176D ASP* 3.1 29.7 - - - +
316D ASN* 2.7 15.7 + - - +
317D HIS* 1.3 79.2 - - - +
319D ARG* 1.3 64.6 + - - +
320D TYR 3.0 1.0 + - - -
321D ILE 3.1 8.5 + - - -
322D SER* 3.1 13.6 + - - -
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Residues in contact with ARG 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D GLN* 4.4 18.6 - - - +
175D GLY 2.7 29.1 + - - -
176D ASP* 3.0 11.6 + - - +
303D LEU* 3.2 38.0 - - - +
304D LYS* 3.1 30.2 + - - +
305D TYR* 5.1 4.3 - - - +
306D ASP* 5.3 7.2 + - - +
312D LEU* 4.6 12.3 - - + -
316D ASN* 2.9 36.0 + - + +
318D GLN* 1.3 76.5 - - - +
320D TYR* 1.3 53.8 + - - +
322D SER* 4.2 4.9 - - - -
323D TYR* 2.5 41.9 + - + +
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Residues in contact with TYR 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D GLU* 3.3 28.4 + - + +
117D VAL 3.6 2.4 + - - -
118D THR* 2.9 24.6 + - - -
134D ASP* 2.4 41.8 + - - -
135D ALA* 3.8 8.3 - - + -
309D ILE* 4.6 11.7 - - + -
312D LEU* 3.6 41.3 + - + +
313D ARG* 4.0 18.4 - - - -
316D ASN 3.4 2.6 + - - -
317D HIS* 3.2 14.3 + - - +
318D GLN 3.1 0.2 - - - -
319D ARG* 1.3 77.3 - - - +
321D ILE* 1.3 73.2 + - + +
323D TYR* 3.6 7.2 - + - +
324D ASN* 3.1 26.5 + - - +
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Residues in contact with ILE 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ASP 4.4 0.9 - - - +
135D ALA* 3.9 18.8 - - + -
148D VAL* 3.8 28.3 - - + -
150D ASP* 2.8 37.2 - - + +
162D TRP* 3.8 28.9 - - + -
188D TYR* 4.4 1.1 - - + -
317D HIS* 3.6 19.7 - - + +
318D GLN 3.1 2.0 + - - -
320D TYR* 1.3 89.8 - - + +
322D SER* 1.3 60.8 + - - +
323D TYR 3.1 0.7 - - - -
324D ASN* 3.4 5.4 + - + +
325D ILE* 2.9 37.8 + - + +
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Residues in contact with SER 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D TRP* 2.7 27.3 + - - +
167D ALA* 3.9 0.9 - - - +
176D ASP* 2.4 42.5 + - - -
178D VAL* 4.4 7.7 - - - +
303D LEU* 3.6 5.6 - - - +
318D GLN 3.1 7.1 + - - -
319D ARG* 3.7 3.8 - - - -
321D ILE* 1.3 74.7 - - - +
323D TYR* 1.3 61.9 + - - +
325D ILE* 3.9 8.9 - - - +
326D ILE* 3.1 32.6 + - - +
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Residues in contact with TYR 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D GLU* 3.9 19.5 - - - -
302D LYS* 2.9 46.4 + - + +
303D LEU* 3.7 39.9 - - + +
305D TYR* 4.0 35.0 - + + -
309D ILE* 5.9 3.7 - - + +
312D LEU* 5.4 6.7 - - + -
319D ARG* 2.5 25.2 + - + +
320D TYR* 3.6 7.4 - + - +
322D SER* 1.3 72.3 - - - +
324D ASN* 1.3 71.5 + - - +
326D ILE* 2.9 27.9 - - + +
327D ALA* 3.1 7.5 + - + +
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Residues in contact with ASN 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ASP* 3.3 29.2 + - - +
116D GLU* 3.1 41.1 + - + +
135D ALA* 4.8 2.7 - - + -
136D ILE* 3.8 14.2 - - - +
137D THR* 2.2 37.3 + - - -
148D VAL* 5.8 1.1 - - - -
320D TYR 3.1 14.5 + - - +
321D ILE* 3.6 9.2 - - - +
323D TYR* 1.3 82.2 - - - +
325D ILE* 1.3 62.5 + - - +
327D ALA* 3.1 16.9 + - - +
328D VAL* 3.5 5.4 + - - +
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Residues in contact with ILE 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D THR* 3.7 14.1 - - + +
146D PHE* 4.7 3.8 - - + -
148D VAL* 3.6 31.2 - - + -
162D TRP* 3.7 34.3 - - + -
178D VAL* 5.6 7.9 - - + -
182D ILE* 4.6 14.4 - - + -
186D ILE* 4.4 20.0 - - + -
321D ILE* 2.9 23.9 + - + +
322D SER* 3.9 5.6 - - - +
324D ASN* 1.3 80.5 + - - +
326D ILE* 1.3 62.8 + - + +
327D ALA 2.9 5.7 + - - -
328D VAL* 3.3 3.8 + - - +
329D TYR* 3.1 19.2 + - - +
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Residues in contact with ILE 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ASP 5.9 0.4 - - - +
177D GLU 5.7 1.1 - - - +
178D VAL* 4.8 12.6 - - + -
179D PRO* 4.5 21.8 - - + -
182D ILE* 6.2 0.4 - - + -
302D LYS* 3.8 16.8 - - + -
303D LEU* 3.2 44.9 - - + +
322D SER 3.1 17.0 + - - +
323D TYR* 2.9 29.2 - - + +
325D ILE* 1.3 77.2 - - + +
327D ALA* 1.3 60.7 + - + +
329D TYR* 3.8 8.2 - - + +
330D ARG* 3.0 46.8 + - + +
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Residues in contact with ALA 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ASP* 3.6 17.5 - - - +
290D LEU* 4.1 20.9 - - + +
302D LYS* 4.6 11.0 - - - +
323D TYR* 3.1 12.4 + - + +
324D ASN* 3.1 13.4 + - - +
325D ILE 2.9 1.6 + - - -
326D ILE* 1.3 78.5 - - - +
328D VAL* 1.3 59.8 + - - +
329D TYR 3.0 0.9 - - - -
330D ARG* 2.6 32.6 + - - +
331D VAL* 3.2 9.7 + - - +
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Residues in contact with VAL 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ASN* 2.9 32.3 - - - +
113D PHE 3.6 4.0 - - - -
114D ASP* 3.4 25.7 - - + +
137D THR* 3.1 37.0 - - + +
139D TYR* 3.9 18.6 - - + -
146D PHE* 4.3 7.0 - - + -
324D ASN 4.1 3.1 - - - +
325D ILE 3.3 5.6 + - - +
327D ALA* 1.3 78.9 - - - +
329D TYR* 1.3 65.3 + - - +
331D VAL* 3.1 14.4 + - - +
332D LEU* 3.2 19.2 - - + +
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Residues in contact with TYR 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D PHE* 3.5 20.6 - + + -
179D PRO* 3.7 27.6 - - + +
181D GLU* 3.9 20.9 + - - -
182D ILE* 3.3 37.0 - - + -
325D ILE 3.1 14.4 + - - +
326D ILE* 3.8 5.6 - - - +
327D ALA 3.0 0.4 - - - -
328D VAL* 1.3 81.3 - - - +
330D ARG* 1.3 72.7 + - - +
332D LEU* 3.1 10.8 + - + +
333D GLN* 2.6 70.9 + - + +
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Residues in contact with ARG 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D PRO* 5.1 5.3 - - - +
290D LEU* 4.2 13.7 - - + -
294D SER* 3.2 21.1 + - - +
298D LEU* 3.6 8.8 - - - +
300D VAL* 3.0 35.9 - - - +
301D GLY 2.9 26.6 + - - +
302D LYS* 4.9 3.1 - - + -
303D LEU 5.6 0.6 - - - +
326D ILE* 3.0 44.0 + - + +
327D ALA* 2.6 20.3 + - - +
329D TYR* 1.3 84.1 - - - +
331D VAL* 1.3 60.0 + - - +
333D GLN* 3.2 25.7 + - - +
334D ILE* 3.0 28.5 + - - +
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Residues in contact with VAL 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ASN* 3.0 36.1 - - - +
113D PHE 5.7 0.7 - - - +
215D GLY* 4.3 8.7 - - - +
216D TRP* 4.4 20.0 - - + +
273D TYR* 3.7 36.6 - - + -
290D LEU* 4.9 6.3 - - + -
327D ALA 3.2 10.1 + - - +
328D VAL* 3.1 13.2 + - - +
330D ARG* 1.3 74.6 - - - +
332D LEU* 1.3 54.3 + - - +
334D ILE* 3.0 10.6 + - - +
335D ASP* 2.7 36.1 + - - +
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Residues in contact with LEU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ASN* 3.3 35.2 - - + +
139D TYR* 3.5 41.5 - - + +
146D PHE* 3.7 26.7 - - + -
328D VAL* 3.2 15.5 - - + +
329D TYR* 3.1 12.7 + - + +
331D VAL* 1.3 75.2 - - - +
333D GLN* 1.3 56.5 + - - +
335D ASP* 3.8 9.4 - - + +
336D ALA* 2.9 29.1 + - - +
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Residues in contact with GLN 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D LEU* 3.4 27.3 - - + +
300D VAL* 4.8 1.0 - - - +
329D TYR* 2.6 62.5 + - + +
330D ARG* 3.2 37.8 + - - +
331D VAL 3.0 0.4 - - - -
332D LEU* 1.3 77.7 - - - +
334D ILE* 1.3 61.8 + - - +
336D ALA* 3.4 7.2 - - - +
337D LYS* 3.3 16.1 + - - +
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Residues in contact with ILE 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D TRP* 4.3 11.7 - - + -
273D TYR* 4.0 9.6 - - + -
277D TYR* 4.5 13.9 - - + -
290D LEU* 4.9 2.9 - - + -
293D ILE* 3.5 31.2 - - + -
294D SER* 4.1 13.0 - - - -
297D GLU* 3.4 28.5 - - + +
298D LEU* 4.0 17.0 - - + -
330D ARG 3.0 20.0 - - - +
331D VAL* 3.0 5.8 + - - +
333D GLN* 1.3 75.1 - - - +
335D ASP* 1.3 55.4 + - - +
336D ALA 3.0 4.7 - - - -
337D LYS* 3.1 2.6 + - - +
338D ARG* 2.7 44.5 + - + +
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Residues in contact with ASP 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D VAL* 5.8 0.7 - - - +
112D ASN* 5.7 2.3 + - - +
273D TYR* 2.8 31.9 + - + +
331D VAL* 2.7 16.6 + - + +
332D LEU* 3.8 11.6 - - - +
334D ILE* 1.3 75.1 - - - +
336D ALA* 1.3 56.6 + - - +
339D GLN* 2.6 29.3 + - - +
340D PHE 3.3 1.7 + - - -
341D ILE* 3.3 42.7 + - - +
342D ASN 4.6 0.3 + - - -
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Residues in contact with ALA 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D LEU 2.9 19.5 + - - +
333D GLN* 3.4 11.2 - - - +
335D ASP* 1.3 79.7 - - - +
337D LYS* 1.3 62.6 + - - +
339D GLN* 4.2 7.3 + - - +
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Residues in contact with LYS 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D PHE 4.4 3.4 + - - -
297D GLU* 2.9 56.7 + - + +
298D LEU* 4.6 2.9 - - + -
299D ASN* 5.9 2.2 - - - +
333D GLN 3.3 10.4 + - - +
334D ILE* 3.1 8.1 + - - +
336D ALA* 1.3 83.6 - - - +
338D ARG* 1.3 65.9 + - + +
339D GLN* 4.9 1.2 - - - +
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Residues in contact with ARG 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D TYR* 4.3 1.3 - - - +
277D TYR* 4.4 1.9 + - + -
280D PHE 5.1 1.0 + - - -
281D SER* 4.0 26.7 + - - +
283D THR* 5.8 1.8 - - - +
296D PHE* 5.2 6.1 - - - -
297D GLU* 3.1 40.9 + - + +
334D ILE* 2.7 23.2 + - + +
337D LYS* 1.3 82.1 - - + +
339D GLN* 1.3 72.5 + - - +
340D PHE* 3.4 52.0 - - + -
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Residues in contact with GLN 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D ASP* 2.6 29.1 + - - +
336D ALA 4.5 8.1 - - - +
337D LYS 4.9 0.9 - - - +
338D ARG* 1.3 79.2 - - - +
340D PHE* 1.3 61.2 + - - +
341D ILE 3.6 1.3 - - - -
342D ASN* 3.1 30.0 + - + -
343D LEU* 3.5 17.5 + - - +
550D VAL* 3.5 23.4 - - - +
554D THR* 3.0 29.1 + - - +
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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