Contacts of the strand formed by residues 396 - 404 (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 PHE 396 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B HIS* 3.0 34.6 + + + -
393B ARG* 2.6 58.1 + - + +
394B LEU 3.0 2.4 + - - +
395B ARG* 1.3 71.5 - - - +
397B THR* 1.3 73.2 + - - +
398B THR* 4.4 9.0 - - + -
425B ILE* 3.6 34.3 - - + -
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Residues in contact with THR 397 (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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389B SER* 4.3 15.4 + - - -
390B MET 3.0 15.7 - - - +
391B ILE* 4.0 18.8 - - + -
392B HIS* 3.8 0.9 - - - -
395B ARG* 4.0 7.5 - - - -
396B PHE* 1.3 90.9 - - - +
398B THR* 1.3 68.5 + - - +
399B ASP* 5.6 0.3 + - - -
469B GLU* 3.8 21.2 + - - +
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Residues in contact with THR 398 (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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389B SER* 3.2 3.1 - - - -
390B MET* 2.7 37.1 + - - +
392B HIS* 2.7 33.8 + - + +
396B PHE* 4.4 12.8 - - + -
397B THR* 1.3 78.7 - - - +
399B ASP* 1.3 68.1 + - - +
400B VAL* 3.6 10.4 + - - +
413B PRO* 6.5 0.9 - - - -
425B ILE* 4.8 4.9 - - + -
427B GLN* 4.8 18.4 + - - +
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Residues in contact with ASP 399 (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 4.2 - - - +
389B SER* 3.6 17.7 - - - -
397B THR* 5.6 0.3 + - - -
398B THR* 1.3 75.8 - - - +
400B VAL* 1.3 65.1 + - - +
413B PRO* 3.9 2.9 - - - +
414B VAL* 3.2 43.4 + - + +
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Residues in contact with VAL 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LYS* 3.5 5.7 - - - +
388B VAL* 2.8 58.5 + - + +
390B MET* 4.1 14.6 - - + +
398B THR* 3.9 14.1 - - - +
399B ASP* 1.3 82.0 - - - +
401B GLN* 1.3 64.4 + - - +
402B LEU* 4.5 0.7 - - + +
411B ILE* 3.9 28.9 - - + -
412B ASP 3.3 11.4 - - - +
413B PRO* 4.3 7.0 - - + -
414B VAL* 3.7 9.8 - - - +
468B PHE* 4.2 11.7 - - + -
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Residues in contact with GLN 401 (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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383B TYR* 4.1 10.3 + - - -
385B SER* 3.0 38.3 + - - +
386B PHE 3.5 7.6 - - - +
387B LYS* 4.8 9.9 - - + +
400B VAL* 1.3 73.4 - - - +
402B LEU* 1.3 59.4 + - - +
403B GLY* 3.8 1.2 + - - +
410B GLU 3.6 1.9 - - - +
411B ILE* 3.4 3.8 - - - -
412B ASP* 2.7 53.0 + - + +
413B PRO 5.6 0.9 - - - +
414B VAL* 4.1 7.5 - - + +
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Residues in contact with LEU 402 (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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385B SER* 3.1 4.1 - - - -
386B PHE* 2.9 44.7 + - + +
388B VAL* 4.0 16.8 - - + -
400B VAL* 4.0 3.7 - - + -
401B GLN* 1.3 71.9 - - - +
403B GLY* 1.3 58.1 + - - +
404B ILE* 4.0 23.1 - - + -
409B VAL* 3.7 30.3 - - + -
410B GLU 3.4 6.5 - - - +
411B ILE* 3.7 15.3 - - + +
453B PHE* 3.8 30.7 - - + -
455B LEU* 5.1 2.9 - - + -
468B PHE* 4.5 11.9 - - + -
478B ILE* 4.1 11.9 - - + -
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Residues in contact with GLY 403 (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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383B TYR* 3.7 22.9 - - - -
384B LYS 3.6 6.3 - - - -
385B SER* 3.9 6.1 - - - -
401B GLN* 3.8 2.9 + - - +
402B LEU* 1.3 73.3 - - - +
404B ILE* 1.3 61.6 + - - +
408B LYS 3.7 1.4 - - - +
409B VAL* 3.3 5.0 - - - +
410B GLU* 2.8 44.5 + - - +
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Residues in contact with ILE 404 (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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383B TYR* 3.3 2.6 - - - -
384B LYS 2.8 39.3 + - - +
386B PHE* 3.9 16.2 - - + -
402B LEU* 4.0 23.1 - - + +
403B GLY* 1.3 78.1 - - - +
405B SER* 1.3 64.9 + - - +
408B LYS 3.7 2.2 - - - -
409B VAL* 4.2 17.3 - - + +
437B LEU* 5.9 0.7 - - + -
478B ILE* 3.6 31.2 - - + +
481B LYS* 3.2 20.6 - - + -
482B VAL* 3.9 18.2 - - + -
485B ILE* 3.9 23.1 - - + -
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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