Contacts of the helix formed by residues 385 - 408 (chain B) in PDB entry 3R29
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 385 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 5.3 2.1 - - - +
293B PRO* 5.6 6.5 - - + -
296B ASP* 2.9 10.0 + - - +
383B LEU* 4.2 1.1 - - - -
384B SER* 1.3 82.8 + - - +
386B PRO* 1.4 61.1 - - - +
387B ALA* 3.3 8.8 + - - +
388B GLU* 3.2 38.6 + - - +
389B VAL* 3.1 19.8 + - - +
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Residues in contact with PRO 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B PRO* 4.1 14.5 - - + +
380B SER 5.6 0.2 - - - +
383B LEU* 3.2 40.8 - - + +
384B SER 3.5 4.3 - - - +
385B ASN* 1.4 84.4 - - - +
387B ALA* 1.3 61.6 + - + +
388B GLU 2.7 6.5 + - - -
389B VAL* 2.5 40.1 + - + +
390B GLU* 3.3 5.2 + - - +
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Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ASN* 3.3 5.9 + - - +
386B PRO* 1.3 80.8 - - + +
388B GLU* 1.3 57.5 + - - +
390B GLU* 4.4 16.7 - - - +
391B ALA* 4.8 2.8 + - - +
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Residues in contact with GLU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 3.2 28.0 - - - +
293B PRO* 5.4 0.9 - - - +
385B ASN* 3.2 31.7 + - - +
386B PRO 2.7 4.8 + - - -
387B ALA* 1.3 74.8 - - - +
389B VAL* 1.3 60.2 + - - +
390B GLU 3.0 2.7 - - - -
391B ALA* 2.5 38.7 + - + +
392B LEU* 2.8 31.2 - - + +
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 4.7 11.7 - - + -
296B ASP* 5.2 0.9 - - + +
300B LEU* 4.2 15.5 - - + -
376B PHE* 3.8 36.3 - - + +
377B ASN 4.0 7.4 - - - +
378B PRO* 4.4 3.6 - - + -
383B LEU* 3.8 18.4 - - + -
385B ASN 3.1 22.4 - - - +
386B PRO* 2.5 25.7 + - + +
388B GLU* 1.3 81.9 + - - +
390B GLU* 1.3 59.8 + - - +
392B LEU* 3.2 13.8 + - - +
393B ARG* 3.3 11.4 + - - +
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Residues in contact with GLU 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 2.6 38.1 + - - +
417A LYS* 3.4 40.1 - - - +
378B PRO* 3.7 20.3 - - + +
386B PRO 3.3 3.9 + - - +
387B ALA* 4.4 15.8 - - - +
388B GLU 4.4 0.4 - - - +
389B VAL* 1.3 77.8 - - - +
391B ALA* 1.3 50.1 + - - +
393B ARG* 3.2 8.8 - - + +
394B GLU* 2.7 38.4 + - - +
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Residues in contact with ALA 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ALA 4.8 2.4 + - - +
388B GLU* 2.5 29.5 + - + +
390B GLU* 1.3 69.7 - - - +
392B LEU* 1.3 56.0 + - + +
393B ARG 3.0 1.1 - - - -
394B GLU* 3.4 19.0 + - - +
395B LYS* 2.6 45.6 + - + +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B MET* 4.4 3.4 - - - +
287B PRO 4.0 0.7 - - - +
288B HIS* 3.3 56.1 - - + +
292B LEU* 4.5 4.9 - - + -
376B PHE* 3.1 47.8 - - + -
388B GLU* 2.8 36.3 + - + +
389B VAL* 3.2 9.8 + - - +
391B ALA* 1.3 79.4 - - + +
393B ARG* 1.3 55.8 + - - +
395B LYS* 3.6 9.5 - - + +
396B VAL* 2.9 34.1 + - - +
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Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LYS* 6.2 1.6 - - - +
420A LEU* 4.7 17.8 + - - +
421A ARG* 4.2 17.6 - - - +
373B ILE* 2.7 48.4 + - + +
374B VAL* 4.1 4.2 - - - +
376B PHE* 3.1 32.8 + - + +
377B ASN* 4.1 20.6 + - - +
378B PRO* 3.6 22.7 - - - +
389B VAL 3.3 3.9 + - - +
390B GLU* 3.2 12.3 - - - +
391B ALA 3.0 0.2 - - - -
392B LEU* 1.3 75.9 - - - +
394B GLU* 1.3 59.7 + - - +
395B LYS 3.0 1.1 - - - -
396B VAL* 2.7 24.8 + - - +
397B TYR* 3.0 36.3 + - + -
422B LEU* 5.7 0.8 - - - +
426B ARG* 5.5 1.4 - - - +
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Residues in contact with GLU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LYS* 2.5 29.1 + - - +
390B GLU* 2.7 26.0 + - - +
391B ALA* 3.4 20.2 - - - +
393B ARG* 1.3 73.4 - - - +
395B LYS* 1.3 62.6 + - + +
397B TYR* 3.3 33.8 - - + +
398B ALA* 3.4 23.4 + - - +
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Residues in contact with LYS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASP* 2.7 58.1 + - + +
230B MET* 3.7 12.6 - - + +
288B HIS* 3.0 28.7 + - + +
391B ALA* 2.6 27.4 + - + +
392B LEU* 3.6 11.2 - - + +
394B GLU* 1.3 74.4 - - + +
396B VAL* 1.3 62.6 + - - +
398B ALA* 3.9 4.2 - - - +
399B SER* 3.3 23.7 + - - -
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Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B MET* 3.6 31.4 - - + -
235B ILE* 4.5 13.2 - - + -
369B CYS* 3.8 30.5 - - + +
372B ALA* 3.9 12.1 - - + -
373B ILE* 4.3 7.4 - - + +
376B PHE* 4.0 16.4 - - + -
392B LEU 2.9 22.6 + - - +
393B ARG* 2.7 13.5 + - - +
395B LYS* 1.3 69.9 - - - +
397B TYR* 1.3 67.6 + - - +
399B SER* 2.9 7.6 + - - -
400B LEU* 2.8 18.1 + - + +
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Residues in contact with TYR 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLY* 4.1 15.9 + - - -
416A ALA* 3.7 25.4 - - + -
417A LYS* 3.5 26.4 - - - +
420A LEU* 3.5 29.2 - - + -
373B ILE* 3.7 17.6 - - + +
393B ARG* 3.0 31.0 + - + -
394B GLU* 3.3 43.6 - - + +
396B VAL* 1.3 76.2 - - - +
398B ALA* 1.3 70.1 + - + +
400B LEU* 2.7 13.4 + - - +
401B GLU* 2.7 32.4 + - - -
415B PHE* 3.7 20.7 - + + -
419B LEU* 4.9 3.1 - - + -
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASN 5.5 2.2 - - - +
394B GLU 3.4 15.5 + - - +
395B LYS* 3.9 7.2 - - - +
397B TYR* 1.3 83.5 - - + +
399B SER* 1.3 56.2 + - - +
401B GLU* 2.6 38.8 + - - +
402B ALA* 3.4 3.6 + - - +
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Residues in contact with SER 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASN 3.2 19.1 + - - +
228B GLU* 3.3 12.7 + - - +
229B ASP* 5.1 0.5 + - - -
230B MET* 2.5 30.9 + - - +
231B PRO 4.9 1.3 - - - -
232B VAL* 4.3 17.2 - - - +
235B ILE* 6.1 0.4 - - - -
395B LYS 3.3 8.7 + - - -
396B VAL* 2.9 13.0 + - - -
398B ALA* 1.3 74.6 - - - +
400B LEU* 1.3 60.8 + - - +
402B ALA* 3.3 9.3 + - - +
403B TYR* 3.3 19.4 + - - +
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B VAL* 5.4 0.4 - - - -
366B GLU* 4.4 10.8 - - + -
369B CYS* 3.6 43.5 - - + -
370B LEU* 4.7 15.7 - - + -
373B ILE* 4.9 2.0 - - + -
396B VAL 2.8 10.7 + - - +
397B TYR* 2.7 15.7 + - - +
399B SER* 1.3 77.1 - - - +
401B GLU* 1.3 66.5 + - - +
403B TYR* 3.6 9.8 + - + +
404B CYS* 3.3 32.2 + - - -
415B PHE* 3.8 22.7 - - + -
418B LEU* 4.1 15.0 - - + -
419B LEU* 4.8 5.4 - - + -
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Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLU* 4.0 13.2 - - - +
405A LYS* 4.7 5.1 + - - -
412A PRO 4.8 9.2 - - - +
415A PHE* 5.5 1.2 - - - -
397B TYR 2.7 8.7 + - - +
398B ALA* 2.6 22.5 + - - +
400B LEU* 1.3 74.5 - - - +
402B ALA* 1.3 57.9 + - - +
404B CYS* 3.3 4.7 + - - +
405B LYS* 2.8 57.9 + - + +
415B PHE* 3.8 41.1 - - + +
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Residues in contact with ALA 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASN 5.3 9.9 - - - +
228B GLU* 5.3 7.4 - - - +
232B VAL* 6.4 0.2 - - + -
398B ALA 3.4 3.6 + - - +
399B SER* 3.3 13.1 + - - +
400B LEU 3.2 0.4 - - - -
401B GLU* 1.3 76.5 - - - +
403B TYR* 1.3 69.5 + - - +
405B LYS* 2.7 21.9 + - - -
406B HIS* 2.9 14.3 + - - +
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Residues in contact with TYR 403 (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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232B VAL* 4.3 18.1 - - + +
363B ASP* 2.5 40.2 + - - -
365B THR* 3.6 33.6 + - + -
366B GLU* 4.2 14.8 - - + -
399B SER 3.3 10.4 + - - +
400B LEU* 4.2 9.6 - - + +
401B GLU 3.5 0.6 - - - -
402B ALA* 1.3 77.3 - - - +
404B CYS* 1.3 61.9 + - - +
406B HIS* 3.6 5.1 + - - +
407B LYS* 2.9 67.2 + - + +
408B TYR* 4.3 5.4 - + - -
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Residues in contact with CYS 404 (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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366B GLU* 4.5 9.6 - - - -
400B LEU* 3.3 22.0 - - - -
401B GLU 3.3 7.6 + - - +
402B ALA 2.7 3.0 + - - -
403B TYR* 1.3 77.7 - - - +
405B LYS* 1.3 58.8 + - + +
408B TYR* 2.8 48.4 + - - +
411B GLN 5.7 0.7 - - - +
414B ARG* 4.5 9.0 - - + -
415B PHE* 4.4 21.8 - - + +
418B LEU* 3.6 31.4 - - - -
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Residues in contact with LYS 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLU* 5.1 2.6 + - - -
405A LYS* 4.7 15.6 - - - +
401B GLU* 2.8 50.9 + - + +
402B ALA* 2.7 15.1 + - - +
404B CYS* 1.3 72.7 - - + +
406B HIS* 1.3 58.6 + - - +
408B TYR 4.7 2.2 - - - -
409B PRO* 3.4 24.6 - - - +
411B GLN 6.0 0.2 - - - -
412B PRO* 4.3 22.4 + - + +
415B PHE* 6.3 0.8 - - - +
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Residues in contact with HIS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ALA 2.9 16.0 + - - +
403B TYR* 4.2 4.6 + - - +
405B LYS* 1.3 72.9 - - - +
407B LYS* 1.3 77.6 + - + +
408B TYR 2.7 11.3 + - - -
409B PRO* 3.5 12.0 - - - +
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Residues in contact with LYS 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ASP* 3.7 9.3 + - - +
403B TYR* 2.9 56.2 + - + +
406B HIS* 1.3 89.5 - - + +
408B TYR* 1.3 97.5 + - + +
409B PRO* 4.0 3.3 - - - +
410B GLU* 4.7 1.4 - - - +
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Residues in contact with TYR 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLN* 4.5 18.9 + - - +
363B ASP* 3.3 13.1 + - - +
366B GLU* 3.7 8.1 - - - -
403B TYR* 4.3 3.1 - + - -
404B CYS* 2.8 28.1 + - - +
405B LYS* 4.3 1.0 - - - +
406B HIS 2.7 2.2 + - - -
407B LYS* 1.3 139.5 + - + +
409B PRO* 1.3 58.9 - - - +
410B GLU* 2.9 23.4 - - - +
411B GLN* 2.9 27.6 + - + +
414B ARG* 3.5 51.8 + - - -
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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