Contacts of the strand formed by residues 364 - 371 (chain A) in PDB entry 4ZZH
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 GLY 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A ASN 3.8 0.5 - - - +
347A ILE* 3.3 13.5 - - - +
361A GLN* 2.9 26.9 + - - +
362A CYS 3.2 2.8 + - - -
363A HIS* 1.3 82.4 - - - +
365A SER* 1.3 64.2 + - - -
410A GLU 3.2 17.0 - - - -
411A ILE* 4.0 3.1 - - - -
412A VAL* 3.9 6.1 - - - +
419A PRO* 4.8 3.8 - - - +
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Residues in contact with SER 365 (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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347A ILE 4.6 2.0 - - - -
349A THR* 3.5 13.5 - - - -
361A GLN* 3.3 31.1 + - - +
364A GLY* 1.3 76.9 - - - -
366A PHE* 1.3 59.1 + - - +
367A ALA* 3.2 24.4 + - - +
368A THR 4.0 0.9 + - - +
409A PRO 3.9 0.2 - - - -
410A GLU* 3.3 32.4 + - - +
411A ILE* 3.5 14.4 - - - +
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Residues in contact with PHE 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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309A PHE* 4.4 9.6 - + - -
312A PHE* 4.0 27.1 - + - -
313A ALA* 3.5 32.5 - - + -
316A ILE* 4.7 13.5 - - + -
317A TYR* 3.6 28.7 + + + -
318A PRO* 4.4 13.7 - - + -
347A ILE* 3.5 25.6 - - + -
348A ASP 5.6 0.2 - - - -
349A THR* 3.1 18.7 - - + +
365A SER* 1.3 76.4 - - - +
367A ALA* 1.3 65.0 + - - +
368A THR 3.2 7.0 + - - +
380A CYS* 3.5 19.1 - - - +
409A PRO* 4.0 23.2 - - + +
411A ILE* 3.9 13.9 - - + -
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Residues in contact with ALA 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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349A THR* 4.3 2.9 - - - +
352A GLN* 3.6 29.2 - - + +
365A SER* 3.2 17.1 + - - +
366A PHE* 1.3 78.1 - - - +
368A THR* 1.3 70.6 + - + +
379A ASP* 4.4 1.9 - - - -
380A CYS* 3.1 28.6 + - - +
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Residues in contact with THR 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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365A SER* 4.0 2.5 + - - +
366A PHE 3.2 4.0 - - - -
367A ALA* 1.3 88.1 - - + +
369A ALA* 1.3 62.1 + - - +
377A LYS* 5.1 7.4 + - + +
378A VAL 3.4 17.7 - - - +
379A ASP* 4.4 6.1 - - - +
380A CYS* 5.4 0.4 - - - -
409A PRO* 3.4 4.9 - - - +
410A GLU* 2.9 53.3 + - - +
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Residues in contact with ALA 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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368A THR* 1.3 77.0 - - - +
370A SER* 1.3 61.9 + - - +
377A LYS* 3.4 2.3 - - - +
378A VAL* 2.9 45.8 + - + -
379A ASP 4.4 1.3 + - - +
380A CYS* 6.3 0.2 - - - -
383A VAL* 4.5 19.3 - - + -
407A MET* 3.3 15.1 - - + +
408A LYS 3.3 18.2 - - - +
409A PRO* 3.8 5.4 - - + -
410A GLU* 4.3 2.0 - - - -
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Residues in contact with SER 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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369A ALA* 1.3 76.2 - - - +
371A CYS* 1.3 65.6 + - - +
372A LEU* 3.5 2.3 + - - +
375A LYS* 3.2 33.6 + - - +
376A TYR 3.4 2.2 - - - -
377A LYS* 3.4 12.6 - - - +
407A MET* 3.9 0.7 - - - -
408A LYS* 2.8 35.0 + - - +
410A GLU* 3.5 26.4 + - - +
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Residues in contact with CYS 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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370A SER* 1.3 73.2 + - - +
372A LEU* 1.3 63.5 + - - +
373A ILE* 3.0 22.1 + - - -
374A CYS 3.7 0.9 - - - -
375A LYS* 3.2 29.8 - - - +
376A TYR 3.3 12.1 + - - +
395A CYS* 3.8 9.9 - - - -
405A ALA* 3.9 12.3 - - - -
406A ILE 3.3 9.6 - - - -
407A MET* 3.5 19.2 - - - -
701A ZN 2.3 37.7 - - - -
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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