Contacts of the helix formed by residues 311 - 332 (chain B) in PDB entry 6BFN
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 311 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B PRO 3.4 4.0 + - - -
310B LEU* 1.3 75.8 - - - +
312B TRP* 1.3 60.0 + - - +
313B PRO* 3.6 11.4 - - - +
314B GLN* 2.9 38.2 + - - +
315B ARG* 2.9 24.6 + - - +
482B PRO* 4.4 8.7 - - - -
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Residues in contact with TRP 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B SER* 1.3 71.0 - - - +
313B PRO* 1.3 71.7 - - + +
315B ARG* 3.3 28.1 + - + +
316B LEU* 2.9 23.6 + - - +
418B LEU* 3.7 44.0 - - + -
478B LEU* 3.8 18.2 - - + -
479B ASP* 3.4 24.5 - - + -
482B PRO* 3.5 22.5 - - + +
483B GLY 2.8 23.7 + - - -
484B PRO 3.7 9.6 - - - -
485B CYS* 3.4 33.1 - - + +
486B PRO* 5.0 2.9 - - + -
489B LEU* 4.0 33.9 - - + +
493B LEU* 5.2 1.8 - - + -
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Residues in contact with PRO 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B SER* 3.6 13.9 - - - +
312B TRP* 1.3 94.5 - - + +
314B GLN* 1.3 55.7 + - + +
316B LEU* 3.3 9.3 + - + +
317B ASP* 2.9 36.4 + - - +
486B PRO* 6.3 0.4 - - + -
489B LEU* 4.7 4.0 - - + -
525B VAL* 4.6 20.4 - - + -
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Residues in contact with GLN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B PRO 4.0 3.3 - - - +
310B LEU* 3.3 21.0 - - + +
311B SER* 2.9 38.6 + - - +
313B PRO* 1.3 74.8 - - + +
315B ARG* 1.3 66.8 + - - +
317B ASP* 3.1 10.7 + - - +
318B ILE* 2.9 31.0 + - + +
352B LEU* 3.6 28.8 - - + +
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Residues in contact with ARG 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 3.7 20.2 - - - +
309B PRO* 4.7 3.6 - - - +
310B LEU* 2.7 45.0 + - + +
311B SER 2.9 12.7 + - - +
312B TRP* 3.3 30.7 + - + +
314B GLN* 1.3 75.7 - - - +
316B LEU* 1.3 63.4 + - - +
318B ILE* 3.4 8.1 + - - +
319B LEU* 3.0 32.1 + - + +
417B THR* 2.4 56.2 + - + -
418B LEU 4.2 0.6 + - - -
420B GLY* 4.8 0.8 - - - -
479B ASP* 2.8 34.4 + - - +
481B ARG* 4.8 3.2 - - - +
482B PRO* 3.7 15.3 - - - +
493B LEU* 5.7 3.6 - - + -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B TRP 2.9 13.0 + - - +
313B PRO* 3.4 10.8 - - + +
314B GLN 3.2 0.2 - - - -
315B ARG* 1.3 77.3 - - - +
317B ASP* 1.3 58.9 + - - +
319B LEU* 3.3 4.9 + - - +
320B LEU* 2.9 30.1 + - + +
489B LEU* 4.5 11.9 - - + -
493B LEU* 4.1 17.7 - - + +
518B LEU* 4.0 33.4 - - + +
521B LEU* 4.1 7.6 - - + -
522B GLN* 3.6 38.6 - - + +
525B VAL* 3.7 26.2 - - + -
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B PRO* 2.9 22.8 + - - +
314B GLN* 3.1 10.6 + - - +
316B LEU* 1.3 76.8 - - - +
318B ILE* 1.3 58.0 + - + +
320B LEU* 3.1 8.8 + - - +
321B GLY* 2.9 27.0 + - - -
352B LEU 5.8 2.2 - - - +
354B PRO* 4.3 5.1 - - + +
522B GLN* 2.8 34.1 + - - +
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 4.1 31.2 - - + -
310B LEU* 4.0 32.1 - - + -
314B GLN* 2.9 22.2 + - + +
315B ARG* 3.7 7.0 - - - +
317B ASP* 1.3 76.0 - - + +
319B LEU* 1.3 60.2 + - + +
322B THR* 2.9 37.4 + - - +
346B VAL* 4.4 4.3 - - + -
348B LEU* 3.9 20.9 - - + -
352B LEU* 3.8 25.1 - - + +
354B PRO* 3.3 19.7 - - + +
417B THR* 6.1 0.7 - - + -
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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
----------------------------------------------------------
296B LEU* 5.3 0.7 - - + -
315B ARG 3.0 22.1 + - - +
316B LEU* 3.6 4.7 - - - +
318B ILE* 1.3 80.5 - - + +
320B LEU* 1.3 57.9 + - - +
322B THR* 3.5 3.5 + - - +
323B ALA* 2.9 30.3 + - - +
410B PHE* 3.5 10.8 - - + -
413B VAL* 4.2 13.7 - - + -
414B VAL* 4.1 32.3 - - + +
417B THR* 3.7 31.9 - - + +
493B LEU* 3.9 35.4 - - + -
518B LEU* 3.9 14.4 - - + -
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 2.9 15.2 + - + +
317B ASP* 3.1 9.8 + - - +
319B LEU* 1.3 77.4 - - - +
321B GLY* 1.3 57.3 + - - +
323B ALA* 3.3 4.0 + - - +
324B ARG* 2.9 40.3 + - - +
515B TYR* 3.5 33.8 - - + +
518B LEU* 3.6 17.7 - - + +
519B GLU* 3.4 36.6 - - + +
522B GLN* 3.7 35.0 - - + +
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Residues in contact with GLY 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ASN* 3.3 23.7 - - - +
317B ASP 2.9 12.0 + - - -
320B LEU* 1.3 74.2 - - - +
322B THR* 1.3 65.5 + - - +
324B ARG* 3.1 13.7 + - - -
325B ALA 3.0 18.5 + - - -
354B PRO* 3.5 20.2 - - - -
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Residues in contact with THR 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ASN* 5.4 1.1 - - - -
296B LEU* 5.7 0.3 - - - +
318B ILE* 2.9 20.2 + - - +
319B LEU* 3.8 6.8 - - - +
321B GLY* 1.3 75.2 - - - +
323B ALA* 1.3 63.0 + - - +
325B ALA* 3.2 8.8 + - - +
326B ILE* 3.0 37.4 + - + +
341B ILE* 5.5 2.7 - - + -
346B VAL* 3.6 39.1 - - + +
354B PRO* 3.6 6.3 - - - +
356B LEU* 5.0 11.0 - - + -
410B PHE* 3.9 18.6 - - + -
413B VAL* 5.5 4.2 - - + +
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Residues in contact with ALA 323 (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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319B LEU 2.9 18.6 + - - +
320B LEU 3.4 6.1 - - - +
322B THR* 1.3 78.2 - - - +
324B ARG* 1.3 55.1 + - - +
326B ILE* 3.2 1.7 + - - +
327B GLN* 2.9 35.1 + - - +
410B PHE* 3.8 10.0 - - + -
511B MET* 4.0 19.5 - - + +
515B TYR* 4.2 14.8 - - - +
518B LEU* 3.6 20.0 - - + -
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Residues in contact with ARG 324 (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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233A ASN 3.1 18.2 + - - +
234A THR* 3.6 19.7 - - - +
268B HIS* 3.6 11.7 - - + -
269B PRO* 6.1 0.2 - - - -
270B ASN* 2.9 28.0 + - - +
320B LEU* 2.9 25.4 + - - +
321B GLY* 3.1 19.0 + - - +
323B ALA* 1.3 74.5 - - - +
325B ALA* 1.3 63.3 + - - +
327B GLN* 2.9 33.0 + - - +
328B PHE* 3.0 10.0 + - - +
515B TYR* 2.9 43.0 + - + -
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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
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268B HIS* 4.3 6.7 - - - -
270B ASN* 3.4 37.8 - - + +
271B ILE* 4.1 11.6 - - + +
321B GLY 3.0 6.6 + - - +
322B THR* 3.2 10.1 + - - +
324B ARG* 1.3 77.1 - - - +
326B ILE* 1.3 62.7 + - - +
328B PHE* 3.1 6.8 + - - +
329B LEU* 3.0 27.1 + - - +
356B LEU* 4.3 13.2 - - + -
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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
----------------------------------------------------------
322B THR* 3.0 23.1 + - + +
323B ALA 3.2 3.8 + - - +
325B ALA* 1.3 76.0 - - - +
327B GLN* 1.3 58.5 + - - +
329B LEU* 3.1 15.0 + - + +
330B HIS* 3.0 41.2 + - + +
338B HIS* 6.0 0.4 - - + -
341B ILE* 3.6 36.1 - - + -
356B LEU* 4.2 13.2 - - + -
406B ASP* 4.3 3.4 - - + +
410B PHE* 3.5 34.5 - - + -
511B MET* 3.6 26.7 - - + -
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Residues in contact with GLN 327 (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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232A ARG 3.0 24.2 + - - -
233A ASN* 3.0 31.7 + - - +
323B ALA 2.9 21.0 + - - +
324B ARG* 2.9 26.1 + - - +
326B ILE* 1.3 73.9 - - - +
328B PHE* 1.3 69.7 + - - +
330B HIS* 3.7 4.4 - - - +
331B GLN* 2.9 49.8 + - - +
511B MET* 3.7 33.0 - - - +
512B THR* 3.6 9.1 - - + +
515B TYR* 4.1 10.5 - - + -
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Residues in contact with PHE 328 (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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198A PHE* 4.3 20.6 - + - -
200A TRP* 4.1 6.7 - + - -
232A ARG* 3.6 41.5 + - + -
236A TYR* 3.3 23.6 - - - -
266B PHE* 3.8 32.0 - + + -
267B ARG 5.0 7.2 - - - -
268B HIS* 3.5 35.0 - + + -
271B ILE* 4.9 1.1 - - + -
324B ARG 3.0 19.4 + - - +
325B ALA 3.3 6.3 - - - +
327B GLN* 1.3 84.1 - - - +
329B LEU* 1.3 68.7 + - + +
331B GLN* 3.3 13.5 + - - +
332B ASP* 3.7 8.0 + - - +
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B PHE* 3.7 36.3 - - + -
271B ILE* 3.9 12.1 - - + -
325B ALA 3.0 15.8 + - - +
326B ILE* 3.1 10.5 + - + +
328B PHE* 1.3 79.4 - - + +
330B HIS* 1.3 62.0 + - + +
331B GLN 3.4 0.2 + - - -
332B ASP* 3.5 11.3 + - - +
336B LEU* 3.2 49.2 + - + +
338B HIS* 4.1 25.1 - - + -
356B LEU* 4.4 8.1 - - + -
359B PHE* 3.6 30.7 - - + -
406B ASP* 5.6 0.2 - - - +
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Residues in contact with HIS 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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326B ILE* 3.0 20.6 + - + +
327B GLN* 3.3 6.7 + - - +
328B PHE 3.2 0.2 - - - -
329B LEU* 1.3 75.0 - - + +
331B GLN* 1.3 63.7 + - + +
332B ASP 3.2 1.1 - - - +
335B SER* 2.5 29.0 + - - +
336B LEU 3.4 17.7 - - - -
403B VAL* 3.6 46.4 - - + +
406B ASP* 3.0 29.4 + - + +
407B THR* 4.5 0.4 - - - -
511B MET* 3.5 39.3 + - + +
512B THR* 6.1 2.2 - - + -
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLU* 5.2 0.3 - - - +
232A ARG* 3.3 53.5 + - + +
233A ASN* 3.7 7.9 - - - +
327B GLN* 2.9 37.9 + - - +
328B PHE* 3.3 7.5 + - - +
330B HIS* 1.3 73.8 - - - +
332B ASP* 1.3 64.0 + - - +
333B SER* 3.7 3.1 + - - -
512B THR* 3.8 19.8 - - + +
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PHE* 3.7 9.6 - - - -
232A ARG* 3.3 17.8 + - - +
265B ARG* 2.7 40.0 + - - -
266B PHE* 3.5 20.1 - - + -
328B PHE 3.7 3.6 + - - +
329B LEU 3.5 15.1 + - - +
330B HIS 3.2 4.3 - - - +
331B GLN* 1.3 83.2 - - - +
333B SER* 1.3 63.3 + - - +
334B PRO* 3.3 12.8 - - - +
335B SER* 3.0 21.8 + - - -
336B LEU 4.7 0.2 - - - +
364B PHE* 4.2 3.6 - - - -
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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) + - + + + + + -
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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