Contacts of the strand formed by residues 285 - 290 (chain C) in PDB entry 6VSB
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 ILE 285 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C VAL* 4.3 12.8 - - + -
37C TYR 4.4 2.5 - - - +
38C TYR* 3.1 46.1 + - + +
220C PHE* 4.0 14.5 - - + -
221C SER* 5.3 0.5 - - - -
222C ALA* 3.6 22.9 + - + +
277C LEU* 3.6 28.5 - - + -
278C LYS 3.5 7.2 - - - +
279C TYR* 3.6 30.7 - - + +
284C THR* 1.3 75.8 + - - +
286C THR* 1.3 60.5 + - - +
287C ASP 3.7 19.1 - - - +
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Residues in contact with THR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C PHE* 3.0 25.2 - - - +
278C LYS* 3.0 35.0 + - + +
280C ASN* 4.2 29.4 + - + +
284C THR* 3.4 4.9 + - - -
285C ILE* 1.3 73.2 - - - +
287C ASP* 1.3 66.0 + - + +
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Residues in contact with ASP 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C PHE* 3.5 15.5 - - - +
277C LEU* 4.0 0.5 - - - -
278C LYS* 3.3 37.7 + - + +
285C ILE* 3.7 10.2 - - - +
286C THR* 1.3 82.6 - - + +
288C ALA* 1.3 86.4 + - - +
306C PHE* 3.2 30.0 - - + -
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C VAL* 4.8 9.0 - - + -
58C PHE* 4.0 31.9 - - + -
220C PHE* 4.1 10.1 - - + -
275C PHE* 4.5 7.9 - - + -
276C LEU 3.4 15.9 - - - +
277C LEU* 4.9 2.7 - - + -
287C ASP* 1.3 95.2 + - - +
289C VAL* 1.3 68.0 + - - +
290C ASP 4.3 0.2 - - - -
306C PHE* 3.7 4.9 - - - -
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Residues in contact with VAL 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C PHE* 3.5 9.7 - - - -
276C LEU* 3.3 48.7 + - + +
288C ALA* 1.3 74.6 - - - +
290C ASP* 1.3 61.1 + - - +
291C CYS* 3.4 3.5 + - - +
297C SER* 4.7 9.2 - - - +
300C LYS* 3.9 31.4 - - + +
301C CYS* 4.6 20.0 - - + +
305C SER 5.2 0.2 - - - +
306C PHE* 3.4 32.1 - - + -
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Residues in contact with ASP 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C PHE* 3.9 15.3 - - + -
273C ARG* 3.3 29.6 - - - +
275C PHE* 3.4 20.1 - - + -
288C ALA 4.3 0.2 - - - -
289C VAL* 1.3 69.7 - - - +
291C CYS* 1.3 55.9 + - - +
292C ALA 3.0 10.0 + - - -
293C LEU* 3.3 18.8 + - + -
297C SER* 3.2 25.6 + - - -
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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