Contacts of the strand formed by residues 464 - 470 (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 GLY 464 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342H TYR* 4.3 3.5 - - - -
343H VAL 2.5 30.9 + - - +
354H GLY 4.0 20.2 + - - -
358H ALA* 6.5 1.1 - - - -
457H ALA 3.5 9.2 - - - -
462H GLY 3.5 1.2 + - - -
463H GLN* 1.3 76.6 - - - +
465H HIS* 1.3 58.9 + - - -
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Residues in contact with HIS 465 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H ASN 6.1 0.9 - - - -
341H MET 4.3 6.3 - - - -
342H TYR* 5.1 0.9 - - - +
354H GLY 5.2 0.2 + - - -
355H PRO* 5.0 5.9 - - - +
358H ALA* 6.5 1.6 - - - -
455H VAL 4.4 0.2 - - - -
456H ALA* 2.9 4.9 - - - -
457H ALA* 2.9 36.4 + - - +
464H GLY* 1.3 74.8 - - - -
466H ALA* 1.3 58.2 + - - +
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Residues in contact with ALA 466 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340H PHE* 3.5 1.9 - - - -
341H MET* 3.1 36.2 + - - +
358H ALA* 6.0 5.6 - - - +
359H THR* 6.2 2.5 - - - +
362H VAL* 6.0 0.7 - - - -
455H VAL 3.2 9.0 - - - -
456H ALA* 4.1 2.0 - - - +
465H HIS* 1.3 74.4 - - - +
467H MET* 1.3 56.8 + - - +
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Residues in contact with MET 467 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339H ASP 3.4 13.7 - - - -
340H PHE* 4.2 2.5 - - - +
454H LEU* 3.4 2.3 - - - +
455H VAL* 2.9 32.4 + - - +
466H ALA* 1.3 75.0 - - - +
468H ILE* 1.3 62.4 + - - +
469H VAL 4.0 0.3 + - - -
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Residues in contact with ILE 468 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337H LEU* 4.4 1.4 - - - -
338H ARG* 3.5 27.2 + - - +
339H ASP 3.4 9.0 + - - +
453H GLY 3.6 7.9 - - - +
454H LEU* 4.1 4.7 - - - +
467H MET* 1.3 75.0 - - - +
469H VAL* 1.3 58.8 + - - +
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Residues in contact with VAL 469 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H TYR 4.3 9.0 - - - -
337H LEU* 5.2 0.4 - - - +
338H ARG 5.1 0.4 - - - +
452H TYR* 3.5 2.2 - - - -
453H GLY* 2.8 37.5 + - - +
467H MET 4.0 0.4 + - - -
468H ILE* 1.3 74.1 - - - +
470H GLU* 1.3 61.4 + - - +
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Residues in contact with GLU 470 (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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335H ALA* 3.6 16.3 - - - -
336H TYR* 3.6 13.2 + - - +
442H ALA* 6.0 1.4 - - - -
451H GLN 3.3 9.0 - - - -
452H TYR* 4.5 2.5 - - - +
468H ILE 4.3 0.2 - - - -
469H VAL* 1.3 75.3 - - - +
471H ALA* 1.3 66.5 + - - +
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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