Contacts of the helix formed by residues 363 - 371 (chain T) in PDB entry 2P8Z
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 363 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357T TYR* 3.1 16.8 + - + -
360T PRO* 2.8 40.6 + - + +
361T ALA 3.3 0.2 - - - -
362T ASP* 1.3 83.9 + - - +
364T ALA* 1.3 65.7 + - - +
365T ASN* 2.6 44.9 + - - +
366T CYS* 3.0 6.1 + - - +
367T ILE* 3.1 26.0 + - - +
474T THR* 4.0 15.9 - - - +
476T HIS* 5.8 0.2 + - - -
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Residues in contact with ALA 364 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362T ASP 3.8 1.2 + - - -
363T ASP* 1.3 77.8 + - - +
365T ASN* 1.3 62.1 + - - +
367T ILE* 3.8 7.4 + - - +
368T ALA* 3.2 24.8 + - - +
376T ALA* 5.4 0.5 - - - +
474T THR* 6.4 0.9 - - + -
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Residues in contact with ASN 365 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357T TYR* 3.6 18.4 + - + +
363T ASP* 2.6 29.9 + - - +
364T ALA* 1.3 76.8 - - - +
366T CYS* 1.3 62.8 + - - +
368T ALA* 3.2 7.8 + - - +
369T ILE* 3.0 28.6 + - - +
377T ASP* 4.2 11.9 + - - +
378T LEU 4.8 0.2 + - - -
379T MET* 3.7 30.4 - - + +
472T SER* 3.8 16.8 + - - -
474T THR* 4.3 3.8 - - - +
475T ALA* 3.8 24.2 + - - +
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Residues in contact with CYS 366 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353T ALA* 4.3 18.2 - - - -
354T GLU* 4.3 5.6 - - - -
357T TYR* 3.5 19.2 - - + -
360T PRO 3.3 20.4 - - - +
361T ALA* 3.6 26.7 - - - +
363T ASP* 3.0 10.2 + - - +
365T ASN* 1.3 76.3 - - - +
367T ILE* 1.3 57.5 + - - +
369T ILE* 3.0 10.4 + - - +
370T LYS* 2.9 47.6 + - - +
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Residues in contact with ILE 367 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361T ALA 4.1 15.9 - - - +
362T ASP* 4.1 11.2 - - - +
363T ASP 3.1 17.1 + - - +
364T ALA* 3.9 7.4 - - - +
366T CYS* 1.3 77.4 - - - +
368T ALA* 1.3 57.6 + - - +
370T LYS* 3.1 17.1 + - + +
371T ASN* 2.9 49.1 + - - +
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Residues in contact with ALA 368 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364T ALA 3.2 15.7 + - - +
365T ASN* 3.2 8.7 + - - +
367T ILE* 1.3 79.9 - - - +
369T ILE* 1.3 57.4 + - - +
371T ASN* 4.8 0.9 - - - +
372T CYS* 2.9 21.7 + - - -
373T ASP* 2.9 20.6 + - + +
376T ALA* 3.4 33.4 - - + -
377T ASP 5.1 0.7 - - - +
401T PHE 3.9 2.3 - - - +
402T ALA* 3.8 13.4 - - + +
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Residues in contact with ILE 369 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349T GLN* 2.9 39.7 + - + +
353T ALA* 3.9 23.8 - - + +
356T LEU* 4.6 5.8 - - + -
357T TYR* 5.1 6.5 - - + -
365T ASN 3.0 15.9 + - - +
366T CYS* 3.0 11.2 + - - +
368T ALA* 1.3 75.9 - - - +
370T LYS* 1.3 64.5 + - - +
372T CYS 3.0 2.6 + - - -
379T MET* 3.4 40.2 - - + -
401T PHE* 3.4 29.6 - - + -
402T ALA* 3.7 4.5 - - + -
478T MET* 4.7 10.3 - - + -
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Residues in contact with LYS 370 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346T VAL* 4.4 5.5 - - - +
349T GLN* 3.3 11.6 - - - +
350T ALA* 3.6 36.8 + - + +
353T ALA* 3.1 15.3 - - + -
354T GLU* 3.4 41.7 + - - +
361T ALA 4.3 7.7 + - - -
366T CYS* 2.9 29.7 + - - +
367T ILE* 3.1 17.4 + - + +
369T ILE* 1.3 77.5 - - - +
371T ASN* 1.3 67.0 + - - +
372T CYS 3.7 0.2 + - - -
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Residues in contact with ASN 371 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346T VAL* 5.4 6.7 - - - +
367T ILE* 2.9 40.2 + - - +
368T ALA* 4.9 1.0 - - - +
370T LYS* 1.3 83.4 - - - +
372T CYS* 1.3 72.3 + - - +
373T ASP* 3.0 17.1 + - + +
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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