Contacts of the strand formed by residues 452 - 458 (chain H) in PDB entry 5ZRV
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 TYR 452 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373H ILE* 5.3 2.7 - - - +
374H ASP* 3.5 23.5 + - - +
375H ALA 3.6 6.1 + - - +
450H GLY 5.3 0.2 - - - -
451H GLN* 1.3 78.3 + - - +
453H GLY* 1.3 58.7 + - - +
469H VAL 3.5 7.2 - - - -
470H GLU* 4.5 2.2 - - - +
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Residues in contact with GLY 453 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373H ILE* 5.7 2.0 - - - -
374H ASP 4.9 2.0 - - - -
375H ALA 3.3 19.1 - - - -
452H TYR* 1.3 75.3 - - - +
454H LEU* 1.3 62.7 + - - -
455H VAL 4.0 0.3 + - - -
468H ILE* 4.4 2.2 - - - +
469H VAL* 2.8 37.1 + - - +
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Residues in contact with LEU 454 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375H ALA 3.8 2.5 + - - +
376H PHE* 3.7 6.2 - - - +
377H GLU 3.3 23.9 + - - +
453H GLY* 1.3 74.1 - - - -
455H VAL* 1.3 60.6 + - - +
456H ALA 4.4 0.2 + - - -
467H MET 3.4 9.2 - - - -
468H ILE* 4.1 4.9 - - - +
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Residues in contact with VAL 455 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377H GLU 3.7 8.3 - - - -
453H GLY 4.0 1.0 + - - -
454H LEU* 1.3 73.5 - - - +
456H ALA* 1.3 57.6 + - - +
465H HIS 4.4 0.3 - - - -
466H ALA* 3.2 2.3 - - - -
467H MET 2.9 34.5 + - - +
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Residues in contact with ALA 456 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355H PRO* 5.3 7.2 - - - -
377H GLU 3.7 6.1 + - - +
378H PHE* 3.6 4.8 - - - +
379H HIS* 2.9 25.8 + - - +
455H VAL* 1.3 74.6 - - - +
457H ALA* 1.3 58.3 + - - +
465H HIS 2.9 12.8 - - - -
466H ALA* 4.1 1.8 - - - +
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Residues in contact with ALA 457 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355H PRO* 4.4 9.3 - - - +
379H HIS* 4.6 10.3 - - - +
456H ALA* 1.3 74.8 - - - +
458H CYS* 1.3 60.6 + - - +
464H GLY* 3.5 3.8 - - - -
465H HIS* 2.9 32.4 + - - +
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Residues in contact with CYS 458 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H CYS* 5.3 5.4 - - - -
139H ILE* 5.9 0.8 - - - -
352H LEU* 6.4 1.3 - - - +
354H GLY* 4.2 17.3 - - - -
355H PRO 4.7 1.1 - - - -
379H HIS 5.2 4.6 + - - -
457H ALA* 1.3 75.3 - - - +
459H ALA* 1.3 58.6 + - - +
463H GLN 4.0 3.6 - - - -
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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