Contacts of the helix formed by residues 367 - 379 (chain A) in PDB entry 5OAQ
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 CYS 367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A VAL* 4.0 22.9 - - + -
365A PRO 3.5 1.3 + - - -
366A LEU* 1.3 76.1 - - - +
368A GLU* 1.3 67.2 + - - +
369A TYR* 3.2 4.3 - - + +
370A MET* 3.1 22.5 + - - +
371A ILE* 3.0 19.5 + - - +
502A MYR 1.8 59.0 + - - +
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Residues in contact with GLU 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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366A LEU 3.8 1.9 + - - +
367A CYS* 1.3 74.6 - - - +
369A TYR* 1.3 56.9 + - - +
371A ILE* 3.2 29.0 + - - +
372A ASN* 2.8 49.2 + - - +
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Residues in contact with TYR 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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334A VAL* 3.8 30.5 - - + -
336A SER* 4.5 13.3 - - - -
341A VAL* 3.8 25.6 - - + +
342A VAL* 4.3 26.5 - - + -
367A CYS* 3.2 3.6 - - + +
368A GLU* 1.3 78.9 - - - +
370A MET* 1.3 62.2 + - + +
372A ASN* 3.4 8.0 + - - +
373A PHE* 2.8 38.1 + + + +
393A PHE* 4.2 11.6 - + - -
65L LEU* 3.6 45.5 - - + +
68L LEU* 4.8 2.8 - - - +
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Residues in contact with MET 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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334A VAL* 3.9 17.3 - - + -
366A LEU* 3.6 17.7 - - + -
367A CYS* 3.1 25.8 + - - +
369A TYR* 1.3 80.1 - - + +
371A ILE* 1.3 65.9 + - - +
373A PHE* 3.7 7.5 - - + +
374A ILE* 3.0 33.3 + - + +
393A PHE* 3.3 41.1 - - + -
395A ILE* 4.7 1.6 - - - -
502A MYR 3.9 52.7 - - + -
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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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314A TYR* 3.8 53.3 - - + +
366A LEU* 3.7 21.8 - - + +
367A CYS 3.0 10.8 + - - +
368A GLU* 3.7 32.8 - - - +
370A MET* 1.3 76.6 - - - +
372A ASN* 1.3 61.8 + - - +
374A ILE* 3.4 9.1 + - - +
375A HIS* 3.0 46.7 + - + +
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Residues in contact with ASN 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 GLU* 2.8 36.5 + - - +
369A TYR* 3.7 6.9 - - - +
371A ILE* 1.3 78.1 - - - +
373A PHE* 1.3 59.3 + - - +
375A HIS* 3.3 11.6 + - - +
376A LYS* 2.9 37.5 + - + +
65L LEU* 4.6 15.8 - - + +
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Residues in contact with PHE 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 TYR* 2.8 32.9 + - + +
370A MET* 3.7 14.4 - - + +
371A ILE 3.3 0.2 - - - -
372A ASN* 1.3 69.5 - - - +
374A ILE* 1.3 59.8 + - - +
376A LYS* 3.2 5.8 + - - +
377A LEU* 2.9 54.9 + - + +
389A VAL* 3.6 20.6 - - + -
390A LEU* 3.7 12.6 - - + -
393A PHE* 3.5 43.5 - + + -
502A MYR 5.0 2.2 - - + -
65L LEU* 3.9 15.6 - - + +
68L LEU* 3.5 26.9 - - + -
69L PHE* 3.7 15.0 - + - -
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Residues in contact with ILE 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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247A PHE* 4.3 35.0 - - + -
302A LEU* 5.2 5.8 - - + -
314A TYR* 4.5 13.5 - - + +
366A LEU* 3.8 24.0 - - + -
370A MET* 3.0 25.3 + - + +
371A ILE* 3.6 4.5 - - - +
373A PHE* 1.3 75.2 - - - +
375A HIS* 1.3 65.6 + - + +
377A LEU* 3.4 10.2 + - + +
378A LYS* 3.1 41.9 + - + +
502A MYR 4.1 32.5 - - + -
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Residues in contact with HIS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A TYR* 3.8 23.8 + + - -
371A ILE* 3.0 37.2 + - + +
372A ASN* 3.4 15.7 + - - +
373A PHE 3.2 0.2 - - - -
374A ILE* 1.3 79.1 - - + +
376A LYS* 1.3 63.2 + - + +
378A LYS* 3.4 6.6 + - + +
379A HIS* 3.0 47.3 + + - +
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Residues in contact with LYS 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 ASN* 2.9 21.1 + - - +
373A PHE 3.2 0.9 + - - +
375A HIS* 1.3 76.3 - - + +
377A LEU* 1.3 63.5 + - - +
379A HIS* 3.2 15.1 + - - +
380A LEU* 3.3 16.1 + - - +
65L LEU* 4.1 23.8 - - + -
66L GLU* 2.8 39.0 + - - -
69L PHE* 3.5 44.6 - - + +
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Residues in contact with LEU 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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302A LEU* 4.0 25.4 - - + -
373A PHE* 2.9 43.0 + - + +
374A ILE* 3.6 9.2 - - - +
376A LYS* 1.3 76.5 - - - +
378A LYS* 1.3 62.2 + - - +
380A LEU* 3.2 12.5 + - + +
386A MET* 3.2 48.9 - - + +
389A VAL* 4.0 19.5 - - + -
390A LEU* 4.1 14.4 - - + -
502A MYR 4.2 10.8 - - + -
69L PHE* 3.5 18.5 - - + -
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Residues in contact with LYS 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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247A PHE* 5.5 0.4 - - + -
302A LEU* 3.0 40.6 + - + +
303A ASN* 5.0 0.6 - - - +
304A THR* 3.0 33.5 + - + +
305A ASN* 4.8 6.3 - - - +
374A ILE* 3.1 33.7 + - + +
375A HIS* 3.9 8.1 - - + +
377A LEU* 1.3 78.2 - - - +
379A HIS* 1.3 65.4 + - + +
380A LEU 3.3 8.1 + - - +
386A MET* 4.1 11.0 - - + +
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Residues in contact with HIS 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 HIS* 3.0 43.9 + + - +
376A LYS* 3.2 7.4 + - - +
377A LEU 3.1 1.0 - - - -
378A LYS* 1.3 82.2 - - + +
380A LEU* 1.3 62.0 + - - +
381A PRO* 3.8 4.0 - - - +
73L MET* 5.7 3.1 - - - +
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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