Contacts of the helix formed by residues 342 - 366 (chain B) in PDB entry 2VF8
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 ARG 342 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TYR* 5.9 1.0 - - - -
338B ARG* 2.7 28.2 + - - +
339B VAL 3.1 4.1 - - - +
340B LYS 3.1 1.6 - - - -
341B ASN* 1.3 92.7 - - - +
343B PRO* 1.4 62.3 - - - +
344B GLU* 2.8 44.3 + - - -
345B GLN* 3.5 37.2 + - + +
346B ALA* 3.3 17.2 + - - +
1848B SO4 2.6 32.1 + - - -
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Residues in contact with PRO 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B VAL* 3.0 18.2 - - + +
340B LYS* 3.5 11.7 - - - +
341B ASN 4.0 2.0 - - - +
342B ARG* 1.4 85.4 - - - +
344B GLU* 1.3 78.4 + - + +
345B GLN 3.4 0.8 + - - -
346B ALA* 4.6 1.1 - - + +
347B ILE* 3.7 28.8 + - + +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN 4.8 0.5 - - - +
342B ARG* 2.8 47.7 + - - -
343B PRO* 1.3 92.1 - - + +
345B GLN* 1.3 68.0 + - - +
347B ILE* 4.2 2.8 + - - +
348B ALA* 3.7 16.5 + - - +
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Residues in contact with GLN 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ARG 4.5 11.4 - - - +
127B ALA* 3.9 22.7 - - - +
128B GLY 4.6 1.9 + - - +
338B ARG* 3.0 37.6 + - - +
342B ARG* 3.5 49.1 + - + +
344B GLU* 1.3 86.1 + - - +
346B ALA* 1.3 73.5 + - - +
347B ILE 3.3 0.2 - - - -
348B ALA* 3.1 8.2 + - - +
349B LEU* 2.7 35.6 + - - +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B GLU* 5.5 0.6 - - - +
335B HIS* 5.1 5.1 + - + +
338B ARG* 4.2 7.0 - - + +
339B VAL* 3.5 32.3 - - + +
342B ARG 3.3 20.0 + - - +
343B PRO 3.9 2.0 + - - +
344B GLU 3.6 0.2 - - - -
345B GLN* 1.3 89.7 - - - +
347B ILE* 1.3 62.3 + - + +
349B LEU* 3.3 11.7 + - + +
350B GLN* 3.2 23.7 + - - +
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Residues in contact with ILE 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B VAL* 5.9 3.8 - - + -
343B PRO* 3.7 18.3 + - + +
344B GLU 4.5 2.9 - - - +
345B GLN 3.3 0.4 - - - -
346B ALA* 1.3 78.3 - - + +
348B ALA* 1.3 63.0 + - - +
349B LEU 3.2 0.2 + - - -
350B GLN* 4.1 5.0 - - - +
351B ARG* 3.2 27.1 + - + +
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ARG* 5.2 9.4 - - + +
127B ALA* 5.7 0.9 - - + -
344B GLU 3.7 13.5 + - - +
345B GLN* 3.1 11.9 + - - +
347B ILE* 1.3 77.8 - - - +
349B LEU* 1.3 50.6 + - - +
351B ARG* 4.0 17.3 - - - +
352B MET* 2.8 56.4 + - + +
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 4.5 7.6 - - + -
127B ALA* 4.3 22.2 - - + -
304B PHE* 3.9 30.3 - - + -
327B TYR* 3.9 23.3 - - + +
332B GLU* 3.5 24.7 - - - +
338B ARG* 3.9 22.2 - - - +
345B GLN* 2.7 20.0 + - - +
346B ALA* 3.5 13.5 - - + +
347B ILE 3.1 0.4 - - - -
348B ALA* 1.3 72.0 - - - +
350B GLN* 1.3 62.3 + - + +
352B MET* 3.9 3.7 - - - +
353B ALA* 3.0 29.0 + - + +
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Residues in contact with GLN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR 4.1 13.7 - - - +
328B ALA 3.2 28.6 + - - +
330B GLU* 3.6 31.7 - - + +
332B GLU* 5.6 0.7 - - - +
335B HIS* 6.2 0.2 - - - +
346B ALA 3.2 15.0 + - - +
347B ILE* 4.1 5.1 - - - +
349B LEU* 1.3 73.3 - - + +
351B ARG* 1.3 83.2 + - - +
352B MET 3.0 1.6 - - - -
353B ALA* 2.9 2.5 + - - +
354B ALA* 2.7 53.6 + - - +
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Residues in contact with ARG 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B MET* 5.4 6.3 - - - +
347B ILE* 3.2 18.2 + - + +
348B ALA* 4.1 13.3 + - - +
350B GLN* 1.3 93.4 + - - +
352B MET* 1.3 93.2 + - - +
354B ALA* 4.3 2.1 - - - +
355B ASP* 3.5 21.3 + - - +
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Residues in contact with MET 352 (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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119B LEU* 4.9 11.8 - - + +
122B MET* 3.4 40.4 - - + +
123B LEU* 3.8 26.2 - - + +
126B ARG* 4.8 16.2 - - + -
127B ALA* 5.4 1.3 - - - -
348B ALA* 2.8 33.6 + - + +
349B LEU* 3.9 5.4 - - - +
351B ARG* 1.3 109.3 - - - +
353B ALA* 1.3 69.1 + - - +
355B ASP* 3.6 6.5 + - - +
356B LEU* 3.6 23.1 + - - +
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Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 4.4 4.7 - - + +
324B LEU* 3.9 27.8 - - + +
327B TYR* 4.3 5.4 - - + -
328B ALA* 3.5 26.2 - - + +
349B LEU* 3.0 20.5 + - + +
350B GLN* 2.9 4.2 + - - +
352B MET* 1.3 76.5 - - - +
354B ALA* 1.3 54.8 + - - +
356B LEU* 2.8 28.2 + - - +
357B VAL* 3.1 11.3 + - - +
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Residues in contact with ALA 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ALA* 3.6 15.5 - - + +
350B GLN* 2.7 39.3 + - - +
351B ARG* 4.3 3.4 - - - +
353B ALA* 1.3 73.4 - - - +
355B ASP* 1.3 56.2 + - - +
357B VAL* 4.0 7.1 - - + +
358B LYS* 3.1 28.4 + - - +
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Residues in contact with ASP 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.9 16.6 - - + +
351B ARG* 3.5 17.3 + - - +
352B MET* 3.8 7.6 - - - +
353B ALA 3.0 1.0 + - - -
354B ALA* 1.3 75.2 - - - +
356B LEU* 1.3 61.3 + - - +
358B LYS* 3.6 15.4 - - - +
359B ARG* 3.1 70.4 + - - -
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Residues in contact with LEU 356 (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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116B LEU* 4.1 31.0 - - + +
119B LEU* 3.6 39.3 - - + +
120B LEU* 4.3 25.6 - - + -
123B LEU* 4.3 16.8 - - + -
320B VAL* 6.4 0.4 - - + -
324B LEU* 4.3 20.0 - - + -
352B MET* 3.6 17.5 + - + +
353B ALA 2.8 10.3 + - - +
355B ASP* 1.3 71.8 - - - +
357B VAL* 1.3 57.3 + - - +
359B ARG* 3.3 4.4 + - - +
360B LEU* 2.8 43.7 + - + +
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Residues in contact with VAL 357 (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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321B SER* 4.4 13.2 - - - +
324B LEU* 4.3 7.4 - - + -
325B ARG* 3.7 53.2 - - + +
328B ALA* 4.5 6.7 - - + -
353B ALA 3.1 14.1 + - - +
354B ALA* 4.0 10.5 - - - +
356B LEU* 1.3 75.4 - - - +
358B LYS* 1.3 55.2 + - - +
360B LEU* 2.9 7.9 + - - -
361B ASP* 2.8 51.0 + - - +
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Residues in contact with LYS 358 (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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354B ALA 3.1 20.6 + - - +
355B ASP* 3.6 20.0 - - - +
357B VAL* 1.3 78.9 - - - +
359B ARG* 1.3 64.6 + - + +
361B ASP* 3.3 15.4 + - - +
362B VAL* 3.7 13.3 + - - +
395B TYR* 5.2 5.2 - - + -
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Residues in contact with ARG 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B THR* 4.2 11.0 + - - +
116B LEU* 3.6 25.8 - - + -
119B LEU* 4.5 15.2 - - - +
355B ASP* 3.1 58.6 + - - +
356B LEU* 3.3 4.5 + - - +
358B LYS* 1.3 78.7 - - + +
360B LEU* 1.3 59.1 + - - +
362B VAL* 3.5 1.6 - - - +
363B LEU* 3.1 22.8 + - - +
395B TYR* 3.2 75.6 + - + +
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Residues in contact with LEU 360 (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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116B LEU* 3.7 15.7 - - + -
317B LEU* 3.4 53.8 - - + +
320B VAL* 4.0 16.6 - - + -
321B SER* 3.6 32.3 - - - -
324B LEU* 4.6 2.7 - - + -
356B LEU* 2.8 36.7 + - + +
357B VAL* 2.9 5.3 + - - +
359B ARG* 1.3 73.3 - - - +
361B ASP* 1.3 60.6 + - - +
363B LEU* 3.2 8.9 + - + +
364B LEU* 2.7 31.1 + - + +
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Residues in contact with ASP 361 (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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321B SER* 4.4 8.0 + - - -
325B ARG* 3.7 22.7 + - - -
357B VAL* 2.8 33.9 + - - +
358B LYS* 3.3 7.6 + - - +
359B ARG 3.3 0.2 - - - -
360B LEU* 1.3 75.3 - - - +
362B VAL* 1.3 60.9 + - - +
364B LEU* 2.8 10.4 + - + +
365B HIS* 2.5 54.7 + - + +
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B LYS 3.7 11.1 + - - +
359B ARG 3.5 7.8 + - - +
361B ASP* 1.3 78.1 - - - +
363B LEU* 1.3 67.1 + - - +
364B LEU 2.9 0.2 + - - -
365B HIS* 3.4 10.0 + - - +
366B LEU* 3.5 17.8 + - + +
391B ALA* 3.2 32.8 - - - +
394B LEU* 3.7 29.6 - - + -
395B TYR* 4.2 17.3 - - + +
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Residues in contact with LEU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 3.7 18.4 - - + -
116B LEU* 5.0 3.4 - - + -
317B LEU* 4.2 19.7 - - + -
359B ARG 3.1 13.6 + - - +
360B LEU* 3.2 15.9 - - + +
361B ASP 3.1 0.8 - - - -
362B VAL* 1.3 79.6 - - - +
364B LEU* 1.3 52.9 + - + +
366B LEU 2.6 23.7 - - - +
368B LEU* 3.0 35.6 - - + +
369B GLY 4.9 0.2 - - - -
388B LEU* 3.5 28.7 - - + -
391B ALA* 3.9 16.2 - - + -
392B THR 4.8 0.2 - - - +
395B TYR* 3.4 27.1 - - + +
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 3.9 25.6 - - + +
318B ALA* 4.0 9.6 - - + +
321B SER* 4.3 15.7 - - - +
322B GLU* 6.3 0.7 - - + -
325B ARG* 5.3 5.6 - - - +
360B LEU* 2.7 27.6 + - + +
361B ASP* 2.8 15.9 + - + +
363B LEU* 1.3 68.8 - - - +
365B HIS* 1.3 62.8 + - + +
366B LEU 2.6 16.3 - - - +
367B GLY* 3.7 1.7 - - - -
369B GLY* 3.8 18.6 - - - -
1849B SO4 2.8 38.7 + - - +
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Residues in contact with HIS 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ASP* 2.5 45.2 + - + +
362B VAL* 4.2 4.3 - - - +
364B LEU* 1.3 74.3 - - + +
366B LEU* 1.3 62.2 + - + +
367B GLY* 3.4 3.3 + - - -
419B ALA* 3.8 13.7 - - - +
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B VAL* 3.5 26.5 - - + +
363B LEU 2.6 11.2 - - - +
364B LEU 2.6 11.8 - - - +
365B HIS* 1.3 73.0 - - + +
367B GLY* 1.3 52.2 + - - +
368B LEU* 2.4 33.7 + - + -
387B ARG* 3.4 49.6 - - + +
390B LEU* 4.3 6.5 - - + -
391B ALA* 4.6 3.8 - - + +
394B LEU* 4.7 2.2 - - + -
419B ALA* 4.1 17.9 - - - +
420B LEU* 5.1 3.6 - - - -
423B ALA* 3.7 32.5 - - + -
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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