Contacts of the helix formed by residues 367 - 381 (chain D) in PDB entry 6F0X
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 367 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D GLN 6.1 0.2 - - - -
351D LEU* 3.9 28.9 - - - -
356D LEU* 4.6 7.8 - - - +
359D ILE* 4.6 5.6 - - - +
361D PHE 5.9 0.2 - - - -
362D ILE 3.9 9.0 + - - -
364D ASN* 2.5 29.7 + - - -
366D VAL* 1.3 73.5 - - - +
368D LYS* 1.3 64.7 + - - +
369D LEU 3.0 3.8 + - - -
370D SER* 3.1 11.3 + - - +
371D LEU* 2.9 31.0 + - - +
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Residues in contact with LYS 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D GLU* 2.9 28.0 - - - +
364D ASN 2.9 14.6 + - - +
365D ASN* 4.1 23.8 + - - +
366D VAL 3.3 1.0 - - - -
367D SER* 1.3 77.6 + - - +
369D LEU* 1.3 66.8 + - + +
371D LEU* 3.0 10.6 + - + +
372D LEU* 2.8 28.0 + - + +
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Residues in contact with LEU 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D GLN* 4.7 14.8 - - + +
349D GLN 5.7 5.4 - - - +
350D LEU* 6.0 1.6 - - + -
365D ASN 5.1 6.3 - - - +
366D VAL 4.6 11.7 - - - +
367D SER 3.0 1.0 + - - -
368D LYS* 1.3 87.3 - - + +
370D SER* 1.3 65.8 + - - +
372D LEU* 3.0 21.9 + - + +
373D LEU* 3.0 12.6 + - - +
408D GLU* 3.3 54.5 - - + +
411D LEU* 4.3 4.8 - - - +
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Residues in contact with SER 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D PHE* 4.2 16.0 - - - -
332D LEU* 5.2 0.5 - - - +
349D GLN 4.4 1.7 + - - -
350D LEU* 3.7 20.5 - - - +
351D LEU* 3.6 22.4 + - - -
356D LEU* 4.4 18.7 - - - +
366D VAL 5.2 0.4 + - - -
367D SER* 3.1 14.1 + - - +
369D LEU* 1.3 78.4 - - - +
371D LEU* 1.3 58.3 + - - +
373D LEU* 3.3 13.2 + - - +
374D ASN* 2.8 25.6 + - - +
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Residues in contact with LEU 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D LEU* 4.6 11.2 - - + -
361D PHE* 4.2 36.8 - - + +
362D ILE 4.7 0.7 - - - +
363D GLU* 3.1 30.3 - - - +
367D SER* 2.9 30.9 + - - +
368D LYS* 3.0 16.1 + - + +
370D SER* 1.3 77.2 - - - +
372D LEU* 1.3 58.6 + - - +
374D ASN* 3.0 21.1 + - - +
375D ASP* 2.9 32.0 + - - +
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Residues in contact with LEU 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368D LYS* 2.8 14.7 + - + +
369D LEU* 3.0 15.2 + - + +
371D LEU* 1.3 73.7 - - - +
373D LEU* 1.3 65.4 + - - +
375D ASP* 3.2 19.6 + - + +
376D ILE* 2.9 30.7 + - + +
408D GLU* 4.8 12.3 - - + +
411D LEU* 4.1 28.5 - - + -
412D GLN* 5.2 6.5 - - + +
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Residues in contact with LEU 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D PHE* 3.7 27.4 - - + -
331D TYR* 3.5 43.7 - - + -
332D LEU* 4.3 8.1 - - + -
335D LEU* 3.7 30.5 - - + -
350D LEU* 6.1 0.4 - - + -
369D LEU 3.0 11.4 + - - +
370D SER* 3.3 12.1 - - - +
372D LEU* 1.3 76.6 - - - +
374D ASN* 1.3 56.7 + - - +
376D ILE* 3.1 22.5 + - + +
377D SER* 2.9 27.4 + - - -
411D LEU* 4.6 14.2 - - + +
414D LEU* 4.9 3.8 - - + -
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Residues in contact with ASN 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D ALA* 5.7 2.9 - - - +
328D PHE* 5.0 9.5 - - + +
353D LEU* 5.2 9.5 - - - +
356D LEU* 5.1 4.8 - - + +
361D PHE* 4.4 18.4 - - - -
370D SER 2.8 14.5 + - - +
371D LEU* 3.0 25.5 + - + +
373D LEU* 1.3 73.9 - - - +
375D ASP* 1.3 61.3 + - - +
377D SER* 3.2 8.6 + - - -
378D ARG* 2.9 64.0 + - - +
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Residues in contact with ASP 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371D LEU* 2.9 17.5 + - - +
372D LEU* 3.5 21.5 - - + +
374D ASN* 1.3 75.1 - - - +
376D ILE* 1.3 65.9 + - + +
378D ARG* 3.2 21.9 + - - +
379D LYS* 3.2 27.4 + - - +
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Residues in contact with ILE 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D TYR* 3.9 15.7 - - + -
372D LEU* 2.9 27.7 + - + +
373D LEU* 3.2 26.7 - - + +
375D ASP* 1.3 75.2 - - - +
377D SER* 1.3 51.4 + - - +
379D LYS* 3.0 25.0 + - - +
380D SER* 2.4 50.2 + - - +
411D LEU* 4.2 31.4 - - + +
414D LEU* 4.3 11.9 - - + -
415D SER* 4.7 7.9 - - - -
418D VAL* 4.6 16.2 - - + -
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Residues in contact with SER 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D ALA* 4.2 13.5 - - - +
327D ILE* 3.2 30.3 - - - +
328D PHE* 3.7 14.7 + - - +
331D TYR* 3.7 8.1 - - - -
373D LEU* 2.9 15.9 + - - +
374D ASN* 3.6 12.6 - - - -
376D ILE* 1.3 74.5 - - - +
378D ARG* 1.3 58.8 + - - +
380D SER* 2.7 29.7 + - - -
381D GLU* 3.1 15.4 + - - +
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Residues in contact with ARG 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D ALA* 5.1 11.9 - - + -
361D PHE* 4.0 21.6 - - - -
374D ASN* 2.9 51.5 + - - +
375D ASP* 3.2 22.7 + - - +
377D SER* 1.3 74.9 - - - +
379D LYS* 1.3 57.4 + - - +
381D GLU* 4.8 4.9 + - - +
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Residues in contact with LYS 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D ASP* 3.2 11.5 + - + +
376D ILE* 3.0 29.7 + - - +
377D SER 3.0 0.4 - - - -
378D ARG* 1.3 75.8 - - - +
380D SER* 1.3 61.0 + - - +
381D GLU 3.4 4.4 - - - +
415D SER* 2.7 34.2 + - - +
418D VAL* 5.1 7.2 - - + -
419D ASP* 4.8 14.3 + - - +
422D PHE* 3.1 31.5 - - + -
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Residues in contact with SER 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D ILE* 4.0 9.9 - - - -
331D TYR* 3.6 18.6 + - - -
376D ILE* 2.4 47.6 + - - +
377D SER* 2.7 16.6 + - - -
379D LYS* 1.3 69.9 - - - +
381D GLU* 1.3 66.6 + - - +
383D LEU* 3.2 32.2 - - - +
388D LEU* 4.3 6.1 - - - +
391D LEU* 5.9 0.2 - - - -
418D VAL* 4.7 8.2 - - - +
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Residues in contact with GLU 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D PRO* 4.7 5.0 - - + +
322D PRO* 2.6 29.4 - - + +
323D SER* 2.9 17.6 - - - -
324D ALA* 3.0 22.8 + - - +
327D ILE* 3.4 14.3 - - + +
377D SER 3.1 8.5 + - - +
378D ARG* 5.3 4.2 - - - +
379D LYS 3.4 7.9 - - - +
380D SER* 1.3 82.3 - - - +
382D GLY* 1.3 62.8 + - - +
383D LEU 4.3 0.7 - - - +
388D LEU* 6.1 0.9 - - - -
422D PHE* 4.3 7.6 - - - -
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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
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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