Contacts of the strand formed by residues 462 - 470 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458B LEU* 3.5 8.2 - - - -
459B SER* 2.9 30.5 + - - +
460B ASN 4.3 6.8 - - - +
461B HIS* 1.4 81.4 - - - +
463B TYR* 1.3 66.0 + - - +
464B LYS* 3.5 21.3 + - - +
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Residues in contact with TYR 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B CYS* 3.8 30.7 - - + -
456B THR* 4.0 18.8 - - + -
457B TYR 3.4 2.5 - - - -
458B LEU* 3.7 23.3 - - + +
462B ASP* 1.3 73.9 - - - +
464B LYS* 1.3 63.7 + - - +
465B HIS* 4.1 16.8 + + + +
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Residues in contact with LYS 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456B THR* 3.2 5.7 - - - +
457B TYR* 2.8 58.7 + - + +
459B SER* 3.6 37.1 + - - +
462B ASP* 4.0 24.0 + - - +
463B TYR* 1.3 78.1 - - - +
465B HIS* 1.3 69.3 + - - +
466B LEU* 5.7 1.1 - - + -
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Residues in contact with HIS 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ARG* 4.6 12.4 + - - -
395A ARG* 5.2 5.9 + - - -
454B LYS* 3.2 24.5 + - + +
455B LEU 3.3 4.9 - - - +
456B THR* 2.9 38.2 + - + -
463B TYR* 4.1 19.4 + + + +
464B LYS* 1.3 78.4 + - - +
466B LEU* 1.3 70.1 + - - +
467B TYR* 3.8 29.8 - - + +
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B MET* 3.3 27.4 - - + -
411B ILE* 3.4 32.1 - - + -
430B ILE* 4.8 6.7 - - + -
432B ILE* 4.2 7.6 - - + -
453B PHE 3.8 0.3 - - - +
454B LYS* 3.3 3.8 - - - -
455B LEU* 2.7 40.4 + - + +
457B TYR* 3.6 32.8 - - + +
464B LYS* 5.9 0.9 - - + -
465B HIS* 1.3 82.2 - - - +
467B TYR* 1.3 63.6 + - - +
468B PHE* 3.5 20.4 - - + -
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Residues in contact with TYR 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ARG* 3.2 34.9 + - + +
395A ARG* 3.5 38.6 - - + -
396A PHE* 3.9 32.1 - + - -
390B MET* 3.6 5.1 - - - +
391B ILE* 2.9 48.1 + - + +
443B ALA* 5.4 0.9 - - + -
452B ILE* 4.6 3.6 - - + -
453B PHE 3.3 7.2 - - - +
454B LYS* 3.2 44.5 + - + -
465B HIS* 3.8 26.2 - - + +
466B LEU* 1.3 78.1 - - - +
468B PHE* 1.3 69.1 + - - +
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Residues in contact with PHE 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B VAL* 3.7 20.4 - - + -
389B SER 3.1 8.3 - - - +
390B MET* 3.7 36.8 - - + -
391B ILE* 4.1 4.3 - - - -
400B VAL* 4.2 10.1 - - + -
402B LEU* 4.5 8.7 - - + -
411B ILE* 3.8 26.7 - - + -
452B ILE* 3.3 4.3 - - - +
453B PHE* 3.1 69.8 + + + -
455B LEU* 4.3 15.7 - - + -
466B LEU* 3.5 34.8 - - + -
467B TYR* 1.3 76.3 - - - +
469B GLU* 1.3 64.1 + - - +
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Residues in contact with GLU 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B VAL* 3.7 2.6 - - - +
389B SER* 2.7 55.5 + - - +
391B ILE* 3.8 21.4 - - + +
397B THR* 3.8 14.9 + - - +
450B HIS* 2.9 30.9 + - + +
451B ALA 3.1 15.3 - - - +
452B ILE* 3.7 9.5 - - + +
453B PHE* 5.6 0.2 - - - -
468B PHE* 1.3 76.8 - - - +
470B SER* 1.3 64.5 + - - +
475B VAL* 4.7 1.6 - - - -
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Residues in contact with SER 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B LYS 3.9 10.4 + - - -
388B VAL* 3.8 18.3 - - - +
449B SER 4.1 4.0 - - - -
450B HIS* 3.6 2.8 - - - -
451B ALA 2.9 27.4 + - - +
469B GLU* 1.3 77.8 - - - +
471B ASP* 1.3 84.6 + - - +
474B THR* 3.5 13.0 + - - +
475B VAL* 3.9 9.8 - - - +
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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