Contacts of the helix formed by residues 316 - 339 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ASP* 5.2 0.5 - - - +
312B LEU* 3.2 16.5 + - + +
315B SER* 1.3 88.0 + - - +
317B HIS* 1.3 62.8 + - - +
318B GLN* 3.0 16.0 + - - +
319B ARG* 3.3 36.0 + - + +
320B TYR 3.1 16.6 + - - -
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Residues in contact with HIS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ASP 6.0 0.2 - - - -
150B ASP* 3.0 39.8 + - - -
151B LEU 4.5 1.0 + - - -
159B VAL* 3.1 39.1 - - + +
160B GLU 3.2 22.2 + - - +
161B GLU 4.4 2.6 + - - -
162B TRP* 4.1 10.5 - - + -
313B ARG* 2.9 41.4 + - - +
314B GLU 3.8 3.2 + - - +
316B ASN* 1.3 71.6 - - - +
318B GLN* 1.3 67.5 + - - +
320B TYR* 3.3 8.3 - + - +
321B ILE* 3.3 25.1 + - + +
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Residues in contact with GLN 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLU 4.1 4.6 + - - -
162B TRP* 3.4 24.9 - - - +
163B SER* 2.9 48.0 - - - +
166B ILE* 3.7 18.9 - - + +
167B ALA 3.6 4.3 + - - -
176B ASP* 3.0 24.6 - - - +
316B ASN* 3.0 13.1 - - - +
317B HIS* 1.3 83.4 + - - +
319B ARG* 1.3 66.4 + - - +
321B ILE 3.1 7.8 + - - -
322B SER* 3.3 12.6 + - - -
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Residues in contact with ARG 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLN* 3.0 22.4 + - - +
175B GLY 3.5 10.1 + - - -
176B ASP* 2.6 45.5 + - + +
303B LEU* 2.9 48.9 + - + +
304B LYS 4.4 2.2 + - - -
305B TYR* 3.6 37.8 - - + +
306B ASP* 5.3 1.6 - - - +
312B LEU* 4.9 4.9 - - + -
316B ASN* 3.1 29.7 + - + +
318B GLN* 1.3 78.2 - - - +
320B TYR* 1.3 54.5 + - - +
321B ILE 3.1 0.3 + - - -
322B SER* 3.1 2.6 + - - -
323B TYR* 2.8 41.7 + - + +
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Residues in contact with TYR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU* 3.0 42.0 - - + +
117B VAL 3.9 2.4 + - - -
118B THR* 3.5 12.3 + - - -
134B ASP* 3.0 25.7 + - - -
135B ALA* 4.6 3.6 - - + -
309B ILE* 4.4 20.3 - - + +
312B LEU* 3.8 22.8 - - + +
313B ARG* 3.3 52.0 - - + -
316B ASN 3.1 11.8 + - - +
317B HIS* 3.3 17.0 - + - +
318B GLN 3.1 0.2 - - - -
319B ARG* 1.3 76.8 - - - +
321B ILE* 1.3 70.3 + - + +
323B TYR* 3.4 16.1 - + - +
324B ASN* 3.5 6.6 + - - +
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Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA* 3.5 27.6 - - + -
148B VAL* 4.0 24.7 - - + -
149B PHE 5.2 0.7 - - - +
150B ASP* 3.0 34.5 - - + +
162B TRP* 3.8 31.6 - - + -
188B TYR* 4.8 2.5 - - + -
317B HIS* 3.3 23.3 + - + +
318B GLN 3.1 2.8 + - - +
320B TYR* 1.3 80.4 - - + +
322B SER* 1.3 66.8 + - - +
323B TYR 3.0 1.3 - - - -
324B ASN* 2.9 14.9 + - + +
325B ILE* 3.0 14.4 + - + +
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Residues in contact with SER 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B TRP* 2.7 27.6 + - - +
167B ALA* 3.7 1.9 - - - +
176B ASP* 2.9 39.6 + - - +
178B VAL* 3.7 10.8 - - - -
318B GLN 3.3 1.8 + - - -
319B ARG* 3.1 6.6 + - - -
321B ILE* 1.3 77.4 - - - +
323B TYR* 1.3 58.0 + - - +
325B ILE* 3.2 10.5 + - - +
326B ILE* 2.9 37.7 + - - +
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Residues in contact with TYR 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU* 3.1 30.5 - - - -
302B LYS* 3.4 48.6 + - + +
303B LEU* 5.0 5.6 - - + +
305B TYR* 4.4 26.4 + + + -
309B ILE* 3.9 25.1 - - + +
312B LEU* 4.8 7.6 - - + -
319B ARG* 2.8 25.2 + - + +
320B TYR* 3.4 8.7 - + - +
322B SER* 1.3 78.7 - - - +
324B ASN* 1.3 55.6 + - - +
326B ILE* 3.6 6.2 + - - +
327B ALA* 3.1 26.7 + - + +
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Residues in contact with ASN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP* 3.4 36.4 + - - +
116B GLU* 3.9 26.5 + - + +
135B ALA* 3.8 23.8 - - + +
136B ILE 3.8 1.4 + - - -
137B THR* 3.3 23.4 + - - +
148B VAL* 5.7 0.2 - - - +
320B TYR 3.5 5.1 + - - +
321B ILE* 2.9 13.1 + - + +
323B TYR* 1.3 79.3 - - - +
325B ILE* 1.3 64.0 + - - +
327B ALA* 3.2 17.1 - - - +
328B VAL* 3.3 6.6 + - - +
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B THR* 3.9 21.1 - - + +
146B PHE* 4.5 13.8 - - + -
148B VAL* 4.1 22.4 - - + -
162B TRP* 3.6 39.5 - - + -
178B VAL* 4.8 5.2 - - + -
182B ILE* 4.0 23.3 - - + -
186B ILE* 4.2 14.6 - - + -
321B ILE* 3.0 14.9 + - + +
322B SER* 3.6 7.9 - - - +
324B ASN* 1.3 73.1 - - - +
326B ILE* 1.3 66.7 + - + +
328B VAL* 3.2 5.5 + - - +
329B TYR* 3.1 19.1 + - - +
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ASP 5.1 4.0 - - - +
177B GLU 4.6 2.2 - - - +
178B VAL* 3.7 24.9 - - + +
179B PRO* 3.6 31.6 - - + -
182B ILE* 5.1 1.3 - - + -
301B GLY 4.2 3.4 - - - +
302B LYS* 4.4 11.4 - - + -
303B LEU* 5.4 6.5 - - + +
322B SER* 2.9 24.9 + - - +
323B TYR* 3.7 7.0 - - - +
325B ILE* 1.3 72.9 - - - +
327B ALA* 1.3 66.6 + - - +
329B TYR* 3.2 6.2 + - + -
330B ARG* 2.8 65.1 + - + +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP* 4.8 12.6 - - + +
290B LEU* 3.6 29.1 - - + +
302B LYS* 4.7 11.4 - - - +
323B TYR* 3.1 17.6 + - + +
324B ASN* 3.2 18.4 - - - +
325B ILE 3.2 0.2 - - - -
326B ILE* 1.3 78.9 - - - +
328B VAL* 1.3 64.5 + - - +
330B ARG* 3.4 15.4 + - - +
331B VAL* 3.5 6.3 + - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASN* 3.4 39.0 + - + +
113B PHE 4.5 0.7 - - - +
114B ASP* 4.0 19.3 - - + +
137B THR* 3.5 34.8 - - + +
139B TYR* 3.9 14.1 - - + +
146B PHE* 4.5 6.3 - - + -
324B ASN 3.5 14.1 - - - +
325B ILE 3.2 5.5 + - - +
327B ALA* 1.3 77.0 - - - +
329B TYR* 1.3 64.2 + - - +
331B VAL* 3.2 17.8 + - - +
332B LEU* 3.2 11.1 + - + +
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Residues in contact with TYR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B PHE* 4.0 17.2 - + + -
179B PRO* 3.4 35.4 - - + -
181B GLU* 3.1 23.4 + - + +
182B ILE* 3.4 35.2 - - + -
325B ILE 3.1 12.9 + - - +
326B ILE* 3.7 10.3 - - + +
328B VAL* 1.3 75.9 - - - +
330B ARG* 1.3 56.0 + - - +
332B LEU* 3.0 13.9 + - + +
333B GLN* 2.7 83.6 + - + +
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Residues in contact with ARG 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B PRO* 5.4 5.7 - - - +
290B LEU* 4.5 7.0 - - + -
294B SER* 4.3 20.9 - - - +
298B LEU* 3.6 6.1 - - - +
300B VAL* 3.5 35.7 - - - +
301B GLY 2.5 34.9 + - - +
302B LYS* 4.5 8.2 - - + +
303B LEU* 5.5 3.6 - - - +
326B ILE* 2.8 49.8 + - + +
327B ALA* 3.5 9.0 - - - +
328B VAL 3.2 0.2 - - - -
329B TYR* 1.3 79.5 - - - +
331B VAL* 1.3 57.8 + - - +
333B GLN* 3.0 29.1 + - - +
334B ILE* 2.7 33.7 + - - +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASN* 3.4 23.6 - - - +
114B ASP* 5.0 2.5 - - - +
215B GLY* 4.3 5.2 - - - +
216B TRP* 3.9 21.8 - - + +
273B TYR* 3.9 37.0 - - + -
290B LEU* 3.6 25.8 - - + -
327B ALA 3.8 9.2 - - - +
328B VAL* 3.2 5.5 + - - +
330B ARG* 1.3 75.4 - - - +
332B LEU* 1.3 64.4 + - - +
334B ILE* 2.9 10.9 + - - +
335B ASP* 2.8 23.3 + - + +
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASN* 3.8 20.4 - - - +
139B TYR* 3.4 47.8 - - + -
146B PHE* 3.5 34.8 - - + -
328B VAL 3.2 10.0 + - - +
329B TYR* 3.0 18.8 + - + +
331B VAL* 1.3 79.2 - - - +
333B GLN* 1.3 52.3 + - - +
335B ASP* 3.3 7.8 + - + +
336B ALA* 2.7 35.1 + - - +
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Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLU* 5.2 1.2 + - - -
298B LEU* 3.2 25.0 - - + +
300B VAL* 5.2 0.2 - - - +
329B TYR* 2.7 66.2 + - + +
330B ARG* 3.0 39.6 + - - +
332B LEU* 1.3 70.3 - - - +
334B ILE* 1.3 67.4 + - - +
336B ALA* 2.9 19.3 + - - +
337B LYS* 3.0 14.2 + - - +
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TRP* 4.2 12.1 - - + -
273B TYR* 3.9 22.0 - - + -
277B TYR* 4.4 11.9 - - + -
290B LEU* 4.7 5.4 - - + -
293B ILE* 3.7 28.0 - - + +
294B SER* 4.0 18.6 - - - +
297B GLU* 4.4 6.5 - - + -
298B LEU* 3.9 23.1 - - + +
330B ARG 2.7 20.4 + - - +
331B VAL* 3.4 12.6 - - - +
333B GLN* 1.3 73.4 - - - +
335B ASP* 1.3 58.1 + - - +
337B LYS* 3.2 2.7 + - - +
338B ARG* 2.7 39.5 + - + +
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Residues in contact with ASP 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TYR* 2.8 41.9 + - + +
331B VAL* 2.8 16.2 + - + +
332B LEU* 3.7 7.9 - - + +
334B ILE* 1.3 72.1 - - - +
336B ALA* 1.3 62.6 + - - +
339B GLN* 2.5 51.6 + - - +
340B PHE 3.0 3.6 + - - -
341B ILE* 3.3 24.1 + - - +
342B ASN 5.3 0.2 + - - -
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Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU 2.7 19.1 + - - +
333B GLN* 3.1 15.7 - - - +
335B ASP* 1.3 72.7 - - - +
337B LYS* 1.3 61.3 + - + +
339B GLN* 3.9 17.3 - - - +
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Residues in contact with LYS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PHE 4.7 1.4 + - - -
297B GLU* 2.5 56.9 + - + +
298B LEU* 4.4 11.4 - - + -
299B ASN* 5.5 0.8 - - - +
333B GLN 3.0 9.8 + - - +
334B ILE 3.5 7.4 - - - +
335B ASP 3.0 0.2 - - - -
336B ALA* 1.3 79.9 - - - +
338B ARG* 1.3 70.8 + - - +
339B GLN* 4.2 5.0 - - - +
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Residues in contact with ARG 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TYR* 3.9 2.7 - - - +
277B TYR* 4.3 2.7 + - + -
280B PHE 5.0 1.2 + - - -
281B SER* 2.9 35.4 + - - +
283B THR* 4.6 2.6 - - - +
296B PHE* 4.6 6.5 - - - -
297B GLU* 2.7 39.5 + - - +
334B ILE* 2.7 34.3 + - + +
337B LYS* 1.3 82.0 - - + +
339B GLN* 1.3 69.6 + - - +
340B PHE* 3.4 50.3 + - + -
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Residues in contact with GLN 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ASP* 2.5 38.8 + - - +
336B ALA* 3.9 16.8 - - - +
337B LYS 4.2 4.5 - - - +
338B ARG* 1.3 75.2 - - - +
340B PHE* 1.3 62.6 + - - +
341B ILE 3.5 0.9 - - - -
342B ASN* 3.7 29.4 + - - +
343B LEU* 3.4 18.4 + - - +
550B VAL* 5.3 11.7 - - + +
554B THR* 5.4 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