Contacts of the helix formed by residues 363 - 379 (chain M) in PDB entry 6CET
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 363 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361M LEU* 3.9 2.0 + - - -
362M PRO* 1.3 76.7 - - - +
364M VAL* 1.3 76.7 + - - +
365M LEU* 3.2 25.9 - - - +
366M ALA* 3.1 7.3 + - - +
367M LYS* 3.0 36.5 + - - +
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Residues in contact with VAL 364 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363M SER* 1.3 85.8 + - - +
365M LEU* 1.3 55.2 + - + +
367M LYS* 3.3 10.4 + - + +
368M PHE* 2.8 25.8 + - - +
398M LEU* 4.5 29.1 - - + +
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Residues in contact with LEU 365 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335M MET* 3.7 40.8 - - + -
361M LEU* 3.7 31.2 - - + -
363M SER* 3.2 23.7 - - - +
364M VAL* 1.3 76.1 - - + +
366M ALA* 1.3 61.3 + - - +
368M PHE* 3.3 13.7 - - + +
369M SER* 2.9 25.6 + - - -
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Residues in contact with ALA 366 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356M PHE* 5.9 7.0 - - + -
361M LEU* 3.3 27.6 - - - +
362M PRO* 4.0 3.6 - - + -
363M SER 3.1 17.2 + - - +
365M LEU* 1.3 82.3 - - - +
367M LYS* 1.3 62.8 + - - +
369M SER* 2.5 26.3 + - - +
370M LEU* 2.9 15.1 + - - +
371M PRO* 3.8 2.4 - - - +
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Residues in contact with LYS 367 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362M PRO* 5.6 4.6 - - - +
363M SER* 3.0 22.3 + - - +
364M VAL* 3.3 11.6 + - + +
366M ALA* 1.3 79.4 - - - +
368M PHE* 1.3 64.8 + - - +
371M PRO* 3.2 34.7 - - + +
372M VAL* 3.9 9.7 - - - +
391M ILE* 5.1 20.4 - - + -
394M VAL* 5.1 17.3 - - + -
398M LEU* 6.1 3.6 - - + -
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Residues in contact with PHE 368 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335M MET* 4.6 17.9 - - + -
339M ASN* 3.3 32.5 - - + -
364M VAL* 2.8 14.7 + - + +
365M LEU* 3.3 15.7 - - + +
367M LYS* 1.3 78.5 - - - +
369M SER* 1.3 65.9 + - - +
372M VAL* 3.3 34.3 - - + +
398M LEU* 5.6 13.4 - - + +
402M LEU* 3.6 35.2 - - + -
404M ILE* 5.4 10.1 - - + -
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Residues in contact with SER 369 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356M PHE* 4.6 24.4 - - - +
365M LEU 2.9 11.8 + - - -
366M ALA* 2.5 27.3 + - - +
368M PHE* 1.3 86.8 - - - +
370M LEU* 1.3 65.8 + - - +
372M VAL* 4.0 0.7 - - - +
373M SER* 3.1 27.6 + - - -
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Residues in contact with LEU 370 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356M PHE* 4.6 29.2 - - + -
366M ALA* 2.9 9.0 + - + +
369M SER* 1.3 80.8 + - - +
371M PRO* 1.4 66.8 - - + +
373M SER* 3.1 12.3 + - - +
374M LEU* 2.9 27.7 + - + +
377M PHE* 6.3 1.6 - - + -
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Residues in contact with PRO 371 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366M ALA 3.8 0.2 - - - +
367M LYS* 3.2 47.8 - - + +
370M LEU* 1.4 85.9 - - + +
372M VAL* 1.3 58.6 + - - +
374M LEU* 3.9 7.0 - - + +
375M SER* 2.9 36.2 + - - +
387M GLU* 5.7 4.9 - - - +
391M ILE* 4.9 22.9 - - + -
395M VAL* 6.5 1.3 - - + -
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Residues in contact with VAL 372 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315M HIS* 3.4 23.9 + - + +
317M VAL* 3.9 18.4 - - + -
367M LYS 3.9 9.6 - - - +
368M PHE* 3.3 40.8 - - + +
369M SER 4.0 0.7 - - - +
370M LEU 3.3 0.4 - - - -
371M PRO* 1.3 77.5 - - + +
373M SER* 1.3 58.1 + - - +
375M SER* 4.7 0.9 - - - -
376M GLU* 2.9 31.4 + - - +
395M VAL* 6.3 3.1 - - + -
398M LEU* 5.9 6.7 - - + -
404M ILE* 5.4 9.2 - - + -
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Residues in contact with SER 373 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349M ALA* 5.5 3.1 - - - +
369M SER 3.1 17.4 + - - -
370M LEU* 3.1 18.7 + - - +
372M VAL* 1.3 77.0 - - - +
374M LEU* 1.3 56.7 + - - +
376M GLU* 3.3 6.4 + - - +
377M PHE* 2.9 58.8 + - - -
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Residues in contact with LEU 374 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370M LEU* 2.9 19.1 + - + +
371M PRO* 3.3 7.2 + - + +
373M SER* 1.3 74.3 - - - +
375M SER* 1.3 63.1 + - - +
377M PHE* 3.1 26.4 + - + +
378M ARG* 3.0 28.0 + - + +
383M PRO* 4.2 20.0 - - + -
387M GLU* 4.0 30.1 - - - +
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Residues in contact with SER 375 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315M HIS* 3.4 19.5 + - - -
371M PRO* 2.9 20.0 + - - +
372M VAL* 4.7 0.9 - - - -
374M LEU* 1.3 79.6 - - - +
376M GLU* 1.3 57.8 + - - +
378M ARG* 4.4 1.6 - - - +
379M ASN* 2.8 34.9 + - - +
380M PRO 4.8 10.0 + - - -
383M PRO* 4.7 7.8 - - - +
384M ALA* 4.4 23.5 + - - +
395M VAL* 5.2 5.8 - - - +
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Residues in contact with GLU 376 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315M HIS* 3.2 15.8 - - + +
316M LEU* 5.0 0.9 - - - -
317M VAL* 3.8 29.2 - - + +
318M TYR* 2.3 38.9 + - + -
372M VAL 2.9 20.1 + - - +
373M SER* 3.7 5.2 - - - +
375M SER* 1.3 76.0 - - - +
377M PHE* 1.3 76.2 + - - +
379M ASN* 3.0 26.6 + - - +
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Residues in contact with PHE 377 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349M ALA* 5.0 16.2 - - + -
370M LEU* 6.3 1.8 - - + -
373M SER* 2.9 42.5 + - - -
374M LEU* 3.1 29.6 + - + +
376M GLU* 1.3 91.2 - - - +
378M ARG* 1.3 68.1 + - + +
379M ASN* 4.3 1.6 - - - +
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Residues in contact with ARG 378 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191M PHE* 5.2 23.1 - - + +
374M LEU* 3.0 18.1 + - + +
375M SER 4.7 0.2 - - - +
377M PHE* 1.3 87.8 + - + +
379M ASN* 1.3 64.1 + - - +
380M PRO* 3.3 21.9 - - + +
383M PRO* 4.5 15.3 - - + -
412M LEU* 5.0 7.1 - - - +
413M MET* 6.3 0.8 - - - -
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Residues in contact with ASN 379 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314M ALA* 4.0 9.8 - - + +
315M HIS* 3.3 25.7 + - - -
375M SER 2.8 28.2 + - - -
376M GLU* 3.0 27.8 - - - +
377M PHE 4.3 1.6 - - - +
378M ARG* 1.3 72.1 + - - +
380M PRO* 1.3 61.4 + - - +
409M TYR* 2.3 28.1 + - + +
412M LEU* 3.6 10.6 - - + +
365N LEU* 6.0 1.9 - - - +
366N ASP* 5.4 3.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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