Contacts of the helix formed by residues 364 - 380 (chain A) in PDB entry 6B5G
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 ASP 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A GLN* 3.4 31.3 + - + +
362A GLN 3.4 0.8 - - - -
363A ILE* 1.3 91.9 + - + +
365A LYS* 1.3 64.9 + - - +
366A LYS* 3.5 10.2 + - - +
367A GLN* 3.1 21.5 + - - +
368A TYR* 3.1 23.4 + - - +
397A PHE* 3.6 20.0 - - + +
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Residues in contact with LYS 365 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A ASP* 1.3 75.9 - - - +
366A LYS* 1.3 60.0 + - - +
368A TYR* 3.4 25.2 + - + -
369A ASN* 2.9 60.9 + - - +
397A PHE* 3.8 30.3 - - + -
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Residues in contact with LYS 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A ASP* 3.4 11.4 + - - +
365A LYS* 1.3 79.7 - - - +
367A GLN* 1.3 63.8 + - + +
369A ASN* 3.4 8.0 + - - +
370A LYS* 3.1 55.9 + - + +
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Residues in contact with GLN 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TRP* 3.8 15.8 + - + +
214A GLN* 6.1 0.9 - - - +
318A GLN* 4.8 5.4 - - - +
362A GLN* 4.9 0.2 - - + -
363A ILE* 3.6 29.6 - - + +
364A ASP* 3.1 16.0 + - - +
366A LYS* 1.3 77.6 + - + +
368A TYR* 1.3 65.2 + - - +
370A LYS* 3.1 34.8 + - - +
371A ILE* 3.0 34.6 + - + +
419A PHE* 3.6 34.7 + - - +
601A NAD 3.9 12.0 + - - +
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Residues in contact with TYR 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A GLN* 4.7 3.7 - - + +
364A ASP 3.1 18.9 + - - +
365A LYS* 3.5 37.5 - - + +
367A GLN* 1.3 77.0 - - - +
369A ASN* 1.3 66.4 + - - +
371A ILE* 3.3 5.0 + - - +
372A LEU* 3.1 46.9 + - + +
391A GLY* 3.2 21.5 + - - -
392A LEU 5.4 0.5 + - - -
393A GLY 5.3 3.6 + - - -
396A GLY 5.5 2.0 - - - -
397A PHE* 3.7 29.8 - + + -
398A PHE 3.3 22.7 + - - -
399A ILE* 3.5 27.7 - - + +
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Residues in contact with ASN 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A LYS* 2.9 54.8 + - - +
366A LYS* 3.8 7.4 - - - +
367A GLN 3.2 0.2 - - - -
368A TYR* 1.3 80.6 - - - +
370A LYS* 1.3 57.0 + - - +
372A LEU* 3.4 6.9 + - - +
373A GLU* 3.0 30.7 + - - +
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Residues in contact with LYS 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A LYS* 3.1 46.3 + - + +
367A GLN* 3.1 37.3 + - - +
369A ASN* 1.3 76.0 - - - +
371A ILE* 1.3 64.1 + - + +
373A GLU* 3.5 5.9 + - - +
374A LEU* 3.1 36.4 + - + +
601A NAD 4.9 5.5 + - - -
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Residues in contact with ILE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A GLN* 3.7 19.5 - - + +
367A GLN* 3.0 21.4 + - - +
368A TYR 3.7 4.0 - - - +
370A LYS* 1.3 78.4 - - + +
372A LEU* 1.3 57.9 + - - +
374A LEU* 3.2 2.9 + - - +
375A ILE* 2.9 38.1 + - + +
399A ILE* 3.8 24.2 - - + -
418A ILE* 3.9 24.9 - - + +
419A PHE 3.3 29.6 - - - +
420A GLY* 3.6 12.8 - - - -
421A PRO* 4.5 2.0 - - + -
422A VAL* 3.9 17.7 - - + -
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A TYR* 3.1 54.1 + - + +
369A ASN* 3.9 7.0 - - - +
371A ILE* 1.3 76.6 - - - +
373A GLU* 1.3 60.3 + - - +
375A ILE* 3.5 14.7 + - + +
376A GLN* 3.2 28.2 + - - +
389A GLY 3.8 22.2 - - - +
390A LYS* 4.1 4.7 - - + -
391A GLY 4.1 17.0 - - - +
399A ILE* 4.5 11.2 - - + -
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Residues in contact with GLU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A ASN 3.0 17.8 + - - +
370A LYS* 3.8 6.0 - - - +
372A LEU* 1.3 75.7 - - - +
374A LEU* 1.3 62.9 + - - +
376A GLN* 3.2 10.6 + - + +
377A SER* 3.0 24.6 + - - -
412A ARG* 3.0 39.1 + - - -
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LYS* 3.1 29.1 + - + +
371A ILE 3.8 3.8 - - - +
373A GLU* 1.3 75.2 - - - +
375A ILE* 1.3 64.6 + - - +
377A SER* 2.9 23.9 + - - +
378A GLY 3.0 6.2 + - - -
412A ARG* 3.3 33.7 - - + +
413A ILE* 3.1 14.8 - - + +
416A GLU* 3.5 21.3 - - + +
417A GLU 4.1 8.1 - - - +
418A ILE* 3.5 46.7 - - + -
422A VAL* 6.5 0.2 - - - -
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Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A ILE* 2.9 35.1 + - + +
372A LEU* 3.7 16.4 - - + +
373A GLU 3.2 0.2 - - - -
374A LEU* 1.3 76.6 - - + +
376A GLN* 1.3 68.9 + - - +
378A GLY 3.0 2.1 + - - -
379A VAL* 3.0 25.1 + - + +
385A LEU* 4.9 1.6 - - + -
389A GLY* 3.7 35.2 - - - +
399A ILE* 4.6 4.5 - - + -
402A THR* 4.0 21.3 - - + +
404A PHE* 3.5 27.6 - - + -
418A ILE* 5.6 0.2 - - + -
422A VAL* 4.0 18.2 - - + -
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Residues in contact with GLN 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A LEU 3.2 16.4 + - - +
373A GLU* 3.2 13.4 + - + +
375A ILE* 1.3 86.7 - - - +
377A SER* 1.3 56.9 + - - +
379A VAL* 3.1 18.1 + - - +
380A ALA* 2.8 29.9 + - - +
389A GLY 4.6 6.2 - - - +
390A LYS* 4.6 14.8 + - - +
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Residues in contact with SER 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A GLU* 3.0 12.8 + - - -
374A LEU* 2.9 17.0 + - - +
376A GLN* 1.3 75.0 - - - +
378A GLY* 1.3 62.7 + - - +
380A ALA* 3.3 8.8 + - - +
381A GLU* 3.3 31.6 + - - +
412A ARG* 3.3 44.9 + - - +
413A ILE* 3.8 8.3 - - - +
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Residues in contact with GLY 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A LEU 3.0 6.3 + - - -
375A ILE 3.0 4.6 + - - -
377A SER* 1.3 79.9 + - - +
379A VAL* 1.3 64.5 + - - +
381A GLU* 3.2 8.7 + - - -
383A ALA* 3.3 26.2 + - - +
404A PHE* 4.1 4.7 - - - -
411A MET* 3.8 5.3 - - - +
413A ILE* 3.7 30.3 - - - -
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Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A ILE* 3.0 16.6 + - + +
376A GLN* 3.5 19.7 - - - +
378A GLY* 1.3 74.6 - - - +
380A ALA* 1.3 59.1 + - - +
381A GLU 3.0 5.2 + - - -
382A GLY* 3.6 8.0 + - - -
383A ALA 4.5 8.6 - - - +
385A LEU* 3.9 31.4 - - + -
404A PHE* 4.0 9.3 - - + -
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A GLN 2.8 19.2 + - - +
377A SER* 3.3 10.1 + - - +
378A GLY 3.2 0.6 - - - -
379A VAL* 1.3 72.7 - - + +
381A GLU* 1.3 64.3 + - + +
382A GLY 3.9 0.4 - - - -
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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