Contacts of the helix formed by residues 368 - 383 (chain A) in PDB entry 6O0Z
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 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A TYR* 3.4 8.2 - - - -
366A GLY 3.9 0.4 + - - -
367A ALA* 1.3 77.2 - - - +
369A GLN* 1.3 64.2 + - - +
370A GLU* 4.0 6.6 + - - +
371A GLU* 2.4 42.1 + - - +
372A PHE* 3.4 20.6 + - - +
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Residues in contact with GLN 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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362A TYR* 3.9 27.4 + - + +
368A SER* 1.3 74.6 - - - +
370A GLU* 1.3 76.0 + - - +
372A PHE* 3.4 2.8 + - - +
373A TYR* 2.9 68.2 + - + -
396A GLU* 4.2 10.3 + - - +
398A LEU 5.6 0.2 - - - -
400A ARG* 3.1 38.7 + - - +
401A LYS 5.6 0.2 + - - -
404A THR* 5.5 3.8 - - - +
405A PHE* 4.6 15.0 - - + -
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Residues in contact with GLU 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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368A SER* 3.4 7.0 + - - +
369A GLN* 1.3 98.2 + - - +
371A GLU* 1.3 62.8 + - + +
373A TYR* 3.3 13.0 + - - +
374A LYS* 2.9 30.0 + - - +
396A GLU* 5.1 10.7 - - - +
405A PHE* 4.6 15.7 - - + -
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Residues in contact with GLU 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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357A ASN* 3.4 32.2 + - - +
366A GLY 4.5 5.4 - - - +
367A ALA* 4.4 5.7 - - + -
368A SER* 2.4 40.6 + - - +
369A GLN 3.4 0.2 - - - -
370A GLU* 1.3 76.4 - - + +
372A PHE* 1.3 57.1 + - - +
374A LYS* 3.5 7.0 + - - +
375A PHE* 2.9 29.8 + - - +
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Residues in contact with PHE 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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357A ASN* 3.6 12.5 - - - +
358A GLY* 3.2 35.7 - - - -
359A TYR* 3.7 14.6 - + + -
362A TYR* 3.8 28.9 - + + -
367A ALA* 5.1 2.4 - - + +
368A SER 3.4 18.9 + - - +
369A GLN 3.4 3.1 + - - +
370A GLU 3.3 0.2 - - - -
371A GLU* 1.3 78.6 - - - +
373A TYR* 1.3 80.7 + + - +
375A PHE* 3.3 1.0 + - - +
376A ILE* 2.9 62.2 + - + +
398A LEU* 5.5 1.6 - - + -
399A LEU* 3.7 32.3 - - + -
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Residues in contact with TYR 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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362A TYR* 6.1 0.2 - - - -
369A GLN* 2.9 52.5 + - + +
370A GLU* 3.7 13.5 - - - +
372A PHE* 1.3 97.6 - + - +
374A LYS* 1.3 56.9 + - - +
376A ILE* 3.3 4.6 + - + +
377A LYS* 3.0 33.3 + - - +
393A LEU* 4.4 32.1 - - + +
396A GLU* 3.9 24.0 - - + -
397A ASP* 3.9 2.3 + - - -
398A LEU* 2.5 56.0 + - + -
399A LEU 5.0 0.2 - - - -
400A ARG* 5.5 0.7 - - - +
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Residues in contact with LYS 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 GLU 2.9 17.6 + - - +
371A GLU* 3.9 7.2 - - - +
373A TYR* 1.3 76.7 - - - +
375A PHE* 1.3 61.4 + - - +
377A LYS* 4.4 5.6 - - - +
378A PRO* 3.6 16.3 - - - +
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Residues in contact with PHE 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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346A LYS* 5.6 2.2 - - - -
349A GLU* 4.1 25.4 - - + -
350A ILE* 4.7 16.8 - - + -
356A LYS* 4.8 13.2 - - + -
357A ASN* 3.3 35.9 - - + +
358A GLY* 3.7 21.3 - - - -
371A GLU 2.9 18.6 + - - +
372A PHE 3.7 1.3 - - - +
373A TYR 3.2 0.2 - - - -
374A LYS* 1.3 79.2 - - - +
376A ILE* 1.3 66.9 + - + +
377A LYS 3.4 0.2 - - - -
378A PRO* 3.6 5.7 - - - +
379A ILE* 3.3 34.3 - - + +
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Residues in contact with ILE 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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335A LEU* 3.8 28.0 - - + -
350A ILE* 5.2 13.9 - - + -
359A TYR* 6.1 0.2 - - + -
372A PHE* 2.9 55.2 + - + +
373A TYR* 3.7 8.1 - - + +
375A PHE* 1.3 82.4 - - + +
377A LYS* 1.3 66.3 + - - +
378A PRO 3.6 0.4 - - - -
379A ILE* 3.7 12.5 + - + -
380A LEU* 3.1 36.2 + - + +
393A LEU* 4.0 18.4 - - + -
398A LEU* 5.0 3.8 - - + -
399A LEU* 5.3 0.9 - - + -
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Residues in contact with LYS 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 TYR 3.0 18.0 + - - +
374A LYS* 4.4 4.9 - - - +
376A ILE* 1.3 78.9 - - - +
378A PRO* 1.3 65.1 - - + +
380A LEU* 3.3 5.8 + - - +
381A GLU* 2.9 51.7 + - + +
390A LEU* 3.5 26.4 - - + +
393A LEU* 3.9 24.1 - - + +
394A ASN* 4.2 12.1 + - - -
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Residues in contact with PRO 378 (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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374A LYS 3.6 15.3 - - - +
375A PHE 3.6 9.4 - - - +
377A LYS* 1.3 90.9 - - + +
379A ILE* 1.3 68.1 + - + +
381A GLU* 3.2 11.3 + - + +
382A LYS* 2.9 32.2 + - - +
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Residues in contact with ILE 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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339A VAL* 6.0 2.7 - - + -
343A LEU* 5.0 11.4 - - + -
346A LYS* 5.5 19.1 - - + +
350A ILE* 4.4 24.2 - - + -
375A PHE* 3.3 42.2 - - + +
376A ILE* 3.7 12.5 + - + +
377A LYS 3.3 0.4 - - - -
378A PRO* 1.3 83.4 - - + +
380A LEU* 1.3 62.9 + - + +
382A LYS* 3.3 23.0 + - - +
383A MET* 3.4 28.6 + - - +
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Residues in contact with LEU 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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335A LEU* 3.9 26.5 - - + -
376A ILE* 3.1 30.6 + - + +
377A LYS* 3.8 4.7 - - - +
379A ILE* 1.3 77.4 - - + +
381A GLU* 1.3 60.6 + - - +
382A LYS 3.5 0.2 + - - -
383A MET* 3.6 16.5 + - - +
386A THR* 3.1 51.9 + - + +
389A LEU* 4.1 26.7 - - + -
390A LEU* 4.0 16.4 - - + +
393A LEU* 4.5 9.0 - - + -
398A LEU* 4.4 17.3 - - + -
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Residues in contact with GLU 381 (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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377A LYS* 2.9 50.9 + - + +
378A PRO* 3.2 9.8 + - + +
380A LEU* 1.3 75.6 - - - +
382A LYS* 1.3 63.8 + - - +
383A MET 3.5 6.6 - - - +
390A LEU* 4.6 15.8 - - + +
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Residues in contact with LYS 382 (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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343A LEU* 4.1 27.8 - - + -
378A PRO* 2.9 17.7 + - - +
379A ILE* 3.3 17.2 + - - +
381A GLU* 1.3 79.5 - - - +
383A MET* 1.3 60.4 + - + +
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Residues in contact with MET 383 (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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335A LEU* 5.4 4.3 - - + -
338A LEU* 3.4 50.3 - - + +
339A VAL* 4.0 11.2 - - + +
342A GLN* 3.4 32.5 - - + +
343A LEU* 4.5 15.9 - - + +
379A ILE* 3.4 30.0 + - - +
380A LEU* 3.6 19.1 + - + +
381A GLU 3.3 10.0 - - - +
382A LYS* 1.3 84.2 - - - +
384A ASP* 1.3 64.6 + - - +
386A THR* 4.2 10.9 + - + -
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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