Contacts of the helix formed by residues 316 - 340 (chain B) in PDB entry 4O6M
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 LEU 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B CYS* 2.8 23.8 + - - +
314B VAL* 3.8 20.4 - - + +
315B ASN* 1.3 80.8 - - - +
317B PRO* 1.3 64.7 - - - +
318B SER* 3.0 12.3 - - - +
319B LEU* 2.9 41.5 + - + +
408B MPG 5.6 2.9 - - + -
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Residues in contact with PRO 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B PHE* 4.3 20.6 - - + -
200B THR* 4.3 17.9 - - + +
250B ILE* 3.8 24.8 - - + +
254B LEU* 5.1 10.1 - - + -
311B CYS* 3.8 10.0 - - + +
312B SER* 4.3 5.2 - - - +
315B ASN* 3.2 13.7 - - - +
316B LEU* 1.3 89.2 - - - +
318B SER* 1.3 62.8 + - - +
320B ALA* 3.1 20.6 + - + +
321B LEU* 3.4 10.4 + - - +
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Residues in contact with SER 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 3.5 32.6 - - - +
261B TYR* 3.6 28.3 + - - -
316B LEU* 4.2 15.6 + - - +
317B PRO* 1.3 82.9 - - - +
319B LEU* 1.3 64.6 + - - +
321B LEU* 3.2 6.8 + - - +
322B VAL* 3.2 25.6 + - - +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B CYS* 3.8 17.7 - - - -
316B LEU* 2.9 33.8 + - + +
318B SER* 1.3 80.3 + - - +
320B ALA* 1.3 59.4 + - - +
322B VAL* 3.2 5.4 + - + +
323B ILE* 2.9 42.8 + - + +
406B MPG 4.1 42.4 - - + -
408B MPG 4.0 26.5 - - + -
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE* 5.6 1.1 - - + -
307B ILE* 4.0 9.4 - - + +
308B ILE* 3.9 32.1 - - + -
311B CYS* 3.6 27.1 - - + -
316B LEU 3.7 0.4 + - - -
317B PRO* 3.1 13.5 + - + +
319B LEU* 1.3 79.1 - - - +
321B LEU* 1.3 58.1 + - + +
323B ILE* 3.4 1.2 + - - +
324B ILE* 3.0 37.5 + - - +
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 3.9 31.6 - - + -
250B ILE* 3.9 33.2 - - + -
251B THR* 3.6 21.5 - - - +
254B LEU* 3.9 15.7 - - + -
261B TYR* 4.8 7.9 - - + +
264B ILE* 3.9 10.9 - - + +
265B GLY* 4.3 10.1 - - - +
268B ALA* 3.6 12.8 - - + +
308B ILE* 6.2 1.6 - - + -
317B PRO 3.8 9.9 - - - +
318B SER 3.2 7.3 + - - +
320B ALA* 1.3 78.6 - - + +
322B VAL* 1.3 58.0 + - - +
324B ILE* 4.8 2.9 - - + -
325B ALA* 2.9 33.3 + - - +
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B TYR* 5.1 4.5 - - + -
264B ILE* 4.1 28.7 - - + -
318B SER 3.2 15.3 + - - +
319B LEU* 3.2 11.2 + - - +
321B LEU* 1.3 77.7 - - - +
323B ILE* 1.3 62.1 + - - +
325B ALA* 3.4 1.7 + - - +
326B LEU* 3.0 45.2 + - + +
405B MPG 4.3 17.5 - - + -
406B MPG 3.6 35.4 - - + -
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Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ILE* 3.9 28.9 - - + -
311B CYS* 4.4 0.2 - - - -
319B LEU* 2.9 36.9 + - + +
320B ALA 3.9 3.6 - - - +
322B VAL* 1.3 77.1 - - - +
324B ILE* 1.3 58.2 + - - +
326B LEU* 3.3 3.5 + - - +
327B LEU* 2.8 59.2 + - + +
406B MPG 4.1 28.9 - - + -
408B MPG 4.1 25.6 - - + -
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Residues in contact with ILE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B VAL* 5.5 6.7 - - + -
268B ALA* 3.7 15.7 - - + +
271B ALA* 3.7 5.3 - - + +
272B SER* 3.5 24.0 - - - +
299B ILE* 4.3 19.5 - - + -
304B ARG* 3.9 31.4 - - + +
307B ILE* 4.7 7.0 - - + -
308B ILE* 3.9 32.3 - - + -
320B ALA* 3.0 22.2 + - + +
321B LEU* 4.1 4.7 - - + +
323B ILE* 1.3 75.9 - - - +
325B ALA* 1.3 58.5 + - - +
328B GLY* 2.8 28.4 + - - -
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ILE* 4.1 7.9 - - + +
267B LEU* 4.0 8.1 - - + -
268B ALA* 3.8 24.0 - - - +
321B LEU 2.9 21.4 + - - +
322B VAL 3.8 3.6 - - - +
324B ILE* 1.3 77.8 - - - +
326B LEU* 1.3 61.2 + - - +
329B ASN* 2.9 34.1 + - - +
405B MPG 3.9 20.6 - - + +
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL* 3.0 40.4 + - + +
323B ILE* 3.8 2.7 - - - +
325B ALA* 1.3 75.8 - - - +
327B LEU* 1.3 69.2 + - + +
329B ASN* 4.3 0.5 - - - +
330B PHE* 3.1 25.0 + - - +
405B MPG 3.6 37.0 - - + -
406B MPG 4.2 22.2 - - + -
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ILE* 3.9 30.4 - - + +
298B PRO* 4.6 8.7 - - + +
299B ILE* 3.9 21.8 - - + +
307B ILE* 5.0 2.9 - - + -
323B ILE* 2.8 40.3 + - + +
326B LEU* 1.3 76.4 - - + +
328B GLY* 1.3 56.6 + - - +
330B PHE* 3.5 4.4 + - + +
331B GLU* 3.0 30.5 + - - +
406B MPG 5.5 9.2 - - + -
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Residues in contact with GLY 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ALA* 3.7 14.7 - - - +
275B ILE* 3.5 13.5 - - - +
299B ILE* 3.8 19.6 - - - +
304B ARG* 6.3 0.2 - - - -
324B ILE* 2.8 23.9 + - - -
327B LEU* 1.3 74.9 - - - +
329B ASN* 1.3 56.3 + - - +
331B GLU 3.4 0.2 + - - -
332B ALA* 3.0 26.0 + - - +
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Residues in contact with ASN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 4.6 5.0 + - - -
267B LEU* 3.2 42.1 + - - +
270B PHE* 3.4 28.2 - - - -
271B ALA* 3.6 6.5 - - - +
325B ALA 2.9 28.6 + - - +
326B LEU 4.3 1.1 - - - +
328B GLY* 1.3 73.5 - - - +
330B PHE* 1.3 64.9 + - - +
332B ALA* 3.5 5.5 + - - +
333B LEU* 3.2 33.2 + - + +
405B MPG 4.7 9.6 - - + +
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Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B PHE* 5.3 5.2 - + - -
297B ILE* 3.1 26.9 - - + -
326B LEU 3.1 18.4 + - - +
327B LEU* 3.9 4.7 - - + +
329B ASN* 1.3 75.9 - - - +
331B GLU* 1.3 57.6 + - - +
333B LEU* 3.3 10.3 + - + +
334B ARG* 2.9 46.0 + - + -
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Residues in contact with GLU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ILE* 3.5 19.7 - - + -
292B PRO* 5.9 0.2 - - - +
296B ALA* 4.0 4.7 - - - +
297B ILE* 3.0 31.4 + - + +
299B ILE* 3.7 18.6 - - + -
327B LEU 3.0 18.3 + - - +
330B PHE* 1.3 75.5 - - - +
332B ALA* 1.3 62.4 + - - +
334B ARG* 2.8 46.2 + - - +
335B ARG* 2.9 47.8 + - - +
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 3.3 20.9 - - - +
271B ALA* 5.7 0.9 - - - +
274B MET* 4.5 20.0 - - + -
275B ILE* 4.0 8.5 - - + +
278B THR* 4.9 9.4 - - + +
328B GLY 3.0 16.7 + - - +
329B ASN* 3.9 6.3 - - - +
330B PHE 3.3 0.2 - - - -
331B GLU* 1.3 77.2 - - - +
333B LEU* 1.3 62.0 + - - +
335B ARG* 3.2 19.3 + - - +
336B ILE* 3.2 16.5 + - - +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A TYR* 3.6 29.8 - - + +
404A MPG 6.4 1.8 - - + -
329B ASN* 3.2 22.2 + - + +
330B PHE* 3.7 8.7 - - + +
332B ALA* 1.3 76.4 - - - +
334B ARG* 1.3 63.1 + - - +
336B ILE* 3.2 24.2 + - + +
337B VAL* 3.2 18.5 + - + +
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Residues in contact with ARG 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B TYR* 4.6 5.1 + - - -
292B PRO* 4.9 8.3 - - - +
295B PHE* 3.4 45.8 + - - -
296B ALA* 3.5 16.1 - - - +
297B ILE 5.0 0.2 - - - +
330B PHE* 2.9 33.3 + - + +
331B GLU* 2.8 44.1 + - - +
333B LEU* 1.3 75.1 - - - +
335B ARG* 1.3 67.9 + - - +
337B VAL* 3.2 9.0 + - + +
338B ALA* 2.8 50.9 + - + +
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Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TRP* 4.0 14.2 - - + -
275B ILE* 2.9 37.3 + - - +
278B THR* 2.9 30.3 + - - +
279B GLY* 4.0 4.2 - - - +
290B TYR* 3.2 43.8 + - + +
292B PRO* 5.9 1.0 - - - +
297B ILE 5.6 1.4 + - - -
299B ILE* 6.0 0.2 - - - +
300B THR* 4.1 16.2 - - - +
331B GLU* 2.9 49.4 + - - +
332B ALA* 3.2 9.8 + - - +
334B ARG* 1.3 80.8 - - - +
336B ILE* 1.3 62.8 + - - +
338B ALA* 4.1 5.1 - - - +
339B LEU* 3.1 29.7 + - + +
419B SO4 5.3 0.8 + - - -
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Residues in contact with ILE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A TYR* 3.0 34.0 + - - +
233A TRP* 3.7 23.1 - - + -
234A LEU* 4.1 9.0 - - + -
237A VAL* 3.9 22.0 - - + -
238A LEU* 4.3 12.6 - - + -
241A TYR* 4.1 18.2 - - + +
404A MPG 4.1 28.9 - - + -
278B THR* 5.7 0.4 - - + -
332B ALA 3.2 14.1 + - - +
333B LEU* 3.2 20.5 + - + +
335B ARG* 1.3 78.5 - - - +
337B VAL* 1.3 67.2 + - + +
340B ARG* 3.7 6.1 + - - +
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Residues in contact with VAL 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A MPG 6.5 0.9 - - + -
333B LEU* 3.2 13.0 + - + +
334B ARG* 3.2 9.1 + - + +
336B ILE* 1.3 81.1 - - + +
338B ALA* 1.3 63.9 + - - +
339B LEU 3.3 0.7 + - - -
340B ARG* 3.3 18.1 + - - +
341B SER* 4.4 2.1 + - - -
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ARG* 2.8 43.0 + - + +
335B ARG* 4.1 4.3 - - - +
337B VAL* 1.3 75.7 - - - +
339B LEU* 1.3 60.1 + - + +
341B SER* 3.1 26.5 + - - -
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A TYR* 3.6 15.5 - - + +
233A TRP* 3.5 42.2 - - + -
282B PHE* 3.7 35.9 - - + -
286B TYR* 3.9 19.8 + - - +
290B TYR* 4.7 12.8 - - + -
335B ARG* 3.1 18.3 + - + +
337B VAL 3.3 0.2 - - - -
338B ALA* 1.3 74.3 - - + +
340B ARG* 1.3 65.1 + - - +
341B SER 3.0 10.6 + - - +
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Residues in contact with ARG 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A TYR* 3.5 38.5 - - + +
404A MPG 5.5 5.2 - - + -
336B ILE 3.7 0.8 + - - +
337B VAL* 3.3 14.5 + - - +
338B ALA 3.2 0.8 - - - -
339B LEU* 1.3 78.6 - - - +
341B SER* 1.3 59.6 + - - +
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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