Contacts of the strand formed by residues 462 - 470 (chain A) in PDB entry 3VOQ
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 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458A LEU* 3.5 6.0 - - - +
459A SER 2.8 33.3 + - - +
460A ASN 3.8 9.0 - - - +
461A HIS* 1.3 87.6 - - - +
463A TYR* 1.3 65.1 + - - +
464A LYS* 3.5 9.4 + - + +
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Residues in contact with TYR 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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438A CYS* 3.7 30.3 - - + -
456A THR* 4.3 7.6 - - + -
457A TYR 3.3 3.8 - - - +
458A LEU* 3.7 26.4 - - + +
462A ASP* 1.3 72.9 - - - +
464A LYS* 1.3 61.9 + - - +
465A HIS* 4.1 26.7 + - + +
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Residues in contact with LYS 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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456A THR* 3.3 5.9 - - - +
457A TYR* 2.7 63.7 + - + +
459A SER* 3.6 37.5 + - - -
460A ASN* 6.4 0.2 - - - -
462A ASP* 4.0 9.4 - - + +
463A TYR* 1.3 78.2 - - - +
465A HIS* 1.3 65.7 + - - +
466A LEU* 6.0 0.9 - - + -
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Residues in contact with HIS 465 (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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454A LYS* 3.5 30.1 - - - -
455A LEU 3.3 4.7 - - - +
456A THR* 3.0 40.4 + - + +
463A TYR* 4.1 20.8 + + + +
464A LYS* 1.3 77.6 - - - +
466A LEU* 1.3 68.8 + - - +
467A TYR* 4.4 14.5 - - + +
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Residues in contact with LEU 466 (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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390A MET* 3.8 25.8 - - + -
411A ILE* 4.0 19.3 - - + -
430A ILE* 4.3 14.4 - - + -
432A ILE* 4.5 3.6 - - + -
453A PHE 3.8 0.3 - - - +
454A LYS* 3.3 5.4 - - - +
455A LEU* 2.7 43.3 + - + +
457A TYR* 3.8 30.7 - - + +
464A LYS* 6.2 0.7 - - + -
465A HIS* 1.3 80.6 - - - +
467A TYR* 1.3 64.4 + - - +
468A PHE* 3.7 31.3 - - + -
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Residues in contact with TYR 467 (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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390A MET* 3.6 5.8 - - - +
391A ILE* 2.9 53.3 + - + +
394A LEU* 4.1 30.0 - - + +
443A ALA* 4.7 8.1 - - + -
452A ILE* 4.2 12.3 - - + -
453A PHE 3.4 10.5 - - - +
454A LYS* 3.2 44.8 + - + -
465A HIS* 4.4 16.8 - - + +
466A LEU* 1.3 76.6 - - - +
468A PHE* 1.4 68.1 + - - +
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Residues in contact with PHE 468 (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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388A VAL* 3.8 20.6 - - + -
389A SER 3.2 6.7 - - - +
390A MET* 3.8 29.8 - - + -
391A ILE* 4.1 4.0 - - - -
400A VAL* 4.2 7.4 - - + -
402A LEU* 4.4 9.0 - - + -
411A ILE* 3.8 31.4 - - + -
452A ILE* 3.1 5.5 - - - +
453A PHE* 2.9 70.7 + + + -
455A LEU* 4.3 14.4 - - + -
466A LEU* 3.7 37.5 - - + -
467A TYR* 1.4 78.6 - - - +
469A GLU* 1.3 61.4 + - - +
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Residues in contact with GLU 469 (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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388A VAL* 3.8 2.0 - - - +
389A SER* 2.8 49.5 + - - +
391A ILE* 4.2 8.5 - - + +
397A THR* 4.0 14.8 - - + +
450A HIS* 4.0 19.6 + - - +
451A ALA 3.0 13.5 - - - +
452A ILE* 3.7 18.2 - - + +
453A PHE* 5.5 0.2 - - - -
468A PHE* 1.3 76.3 - - - +
470A SER* 1.3 64.8 + - - +
475A VAL* 4.5 1.6 - - - -
394B LEU* 4.3 5.7 - - - +
395B ARG* 3.0 41.9 + - - -
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Residues in contact with SER 470 (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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387A LYS 4.1 7.3 + - - -
388A VAL* 3.9 21.2 - - - +
449A SER 3.9 4.9 - - - -
450A HIS* 3.5 5.2 - - - -
451A ALA 2.8 28.5 + - - +
453A PHE* 5.7 0.2 - - - -
469A GLU* 1.3 79.7 - - - +
471A ASP* 1.3 78.6 + - - +
474A THR* 3.6 18.2 - - - +
475A VAL* 3.8 9.7 - - - +
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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