Contacts of the helix formed by residues 456 - 464 (chain A) in PDB entry 5VXZ
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 THR 456 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A GLU 3.5 6.7 + - - +
455A ASP* 1.3 74.7 + - - +
457A THR* 1.3 63.4 + - - +
458A ILE 3.4 2.2 - - - -
459A GLN* 3.0 31.3 + - - +
460A GLU* 2.9 50.9 + - + +
48C ARG* 5.8 6.7 - - - +
94C GLN* 5.3 0.2 - - - +
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Residues in contact with THR 457 (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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455A ASP* 2.6 24.7 + - - -
456A THR* 1.3 75.5 - - - +
458A ILE* 1.3 60.1 + - - +
460A GLU* 3.4 10.6 + - - +
461A THR* 2.6 48.3 + - + +
48C ARG* 3.1 23.4 + - - -
50C GLN* 4.1 10.3 - - - +
77C THR* 4.2 19.2 + - + -
79C VAL* 5.4 0.4 - - + -
90C ILE* 4.9 4.3 - - + -
92C ALA* 3.6 25.0 - - + +
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Residues in contact with ILE 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 4.7 12.6 - - + -
307A ILE* 3.8 46.7 - - + -
309A LEU* 4.5 7.4 - - + -
423A VAL* 5.9 0.2 - - + -
448A TRP* 3.4 35.4 - - + +
450A TRP* 3.9 29.4 - - + +
455A ASP* 5.1 3.7 + - - +
456A THR 3.4 0.8 - - - -
457A THR* 1.3 79.0 - - - +
459A GLN* 1.3 56.3 + - - +
461A THR* 3.3 4.5 + - - +
462A VAL* 3.0 29.7 + - + +
468A MET* 5.0 1.0 - - - +
77C THR* 4.3 14.6 - - + +
79C VAL* 5.6 0.7 - - - -
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Residues in contact with GLN 459 (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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292A VAL 5.2 0.9 - - - +
293A LYS* 5.7 12.6 - - + +
447A SER* 5.9 2.8 - - - -
448A TRP* 3.6 30.6 - - + +
455A ASP 5.1 1.4 + - - -
456A THR* 3.0 33.1 + - - +
457A THR 3.3 0.4 - - - -
458A ILE* 1.3 77.3 - - - +
460A GLU* 1.3 65.1 + - + +
461A THR 3.2 0.5 + - - -
462A VAL* 3.7 5.5 - - - +
463A LYS* 3.0 24.9 + - - +
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Residues in contact with GLU 460 (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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456A THR* 2.9 42.9 + - + +
457A THR* 3.8 10.6 - - - +
458A ILE 3.4 0.2 - - - -
459A GLN* 1.3 78.8 - - + +
461A THR* 1.3 58.7 + - + +
463A LYS* 3.3 21.4 - - - +
464A VAL* 3.7 12.1 + - - +
48C ARG* 4.1 16.2 + - - -
50C GLN* 4.9 3.2 - - - +
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Residues in contact with THR 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A THR* 2.6 44.1 + - + +
458A ILE* 4.0 5.4 - - - +
460A GLU* 1.3 74.1 - - + +
462A VAL* 1.3 65.4 + - - +
463A LYS 3.2 1.1 - - - -
464A VAL* 3.4 4.0 + - - +
465A ASN* 2.7 34.8 + - - +
468A MET* 3.8 16.2 - - - +
50C GLN* 5.4 3.8 - - - +
79C VAL* 4.2 13.3 - - + +
81C LEU* 4.9 0.3 - - - +
90C ILE* 4.1 30.8 - - + +
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Residues in contact with VAL 462 (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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292A VAL 3.1 25.6 - - - +
293A LYS* 5.1 0.4 - - - -
294A SER 3.1 25.1 - - - +
295A LEU* 3.8 18.2 - - + -
448A TRP* 5.1 2.0 - - + -
458A ILE* 3.0 20.9 + - + +
459A GLN* 3.7 5.8 - - - +
461A THR* 1.3 78.2 + - - +
463A LYS* 1.3 62.8 + - - +
464A VAL 3.1 0.9 + - - -
465A ASN 3.1 12.0 + - - +
468A MET* 3.4 31.8 - - + +
469A GLN* 2.9 27.5 + - + -
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Residues in contact with LYS 463 (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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292A VAL* 4.5 23.7 - - + +
459A GLN 3.0 13.5 + - - +
460A GLU* 3.3 17.0 - - - +
462A VAL* 1.3 80.7 - - - +
464A VAL* 1.3 68.3 + - - +
466A THR* 4.8 3.3 + - - +
469A GLN* 3.4 15.6 + - - +
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Residues in contact with VAL 464 (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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460A GLU 4.0 13.7 - - - +
461A THR* 3.4 3.4 + - - +
462A VAL 3.1 0.6 - - - -
463A LYS* 1.3 90.8 - - - +
465A ASN* 1.3 74.1 + - - +
466A THR* 3.9 4.0 + - - +
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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