Contacts of the strand formed by residues 282 - 285 (chain C) in PDB entry 2VGB
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 282 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114C ILE* 4.2 12.3 - - + -
152C ALA* 4.0 27.6 - - + -
153C ILE 3.4 1.4 + - - +
154C ALA* 3.2 8.2 - - + -
155C LEU* 2.9 28.6 + - - +
280C VAL* 3.6 3.3 - - - +
281C ASP* 1.3 88.1 - - + +
283C VAL* 1.3 66.2 + - - +
284C PHE* 3.7 15.7 - - + -
308C ILE* 3.9 1.5 - - - +
309C LYS* 3.2 11.0 - - + +
311C ILE* 3.6 30.5 - - + -
505C GLN* 4.5 8.7 - - + +
508C LEU* 3.9 33.7 - - + -
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Residues in contact with VAL 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C LEU* 3.4 15.5 - - + +
157C THR* 5.1 2.7 - - - -
272C LEU* 3.8 22.9 - - + -
280C VAL* 5.0 5.2 - - + -
282C ILE* 1.3 74.8 - - - +
284C PHE* 1.3 74.3 + - - +
285C ALA* 3.3 14.6 + - + +
297C VAL* 4.2 10.1 - - + -
301C LEU* 3.8 24.5 - - + -
308C ILE* 3.8 18.2 - - + -
309C LYS 2.9 11.6 + - - +
310C ILE* 4.7 5.4 - - + -
311C ILE* 2.8 29.5 + - - -
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Residues in contact with PHE 284 (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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91C ILE* 3.6 43.5 - - + -
114C ILE* 4.7 2.9 - - + -
116C ARG* 4.1 17.5 - - + -
154C ALA* 3.7 24.0 - - + -
155C LEU 2.9 8.1 + - - +
156C ASP* 3.9 12.9 - - + +
157C THR* 3.0 25.8 + - - -
282C ILE* 3.7 20.1 - - + -
283C VAL* 1.3 70.4 - - - +
285C ALA* 1.3 60.2 + - - +
286C SER 3.6 0.5 + - - -
311C ILE* 3.5 32.8 - - + -
313C LYS* 3.9 16.8 - - + -
334C MET* 3.5 22.0 - - + -
368C VAL* 4.8 2.9 - - + -
508C LEU* 4.8 6.7 - - + -
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Residues in contact with ALA 285 (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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157C THR* 4.3 5.2 - - + -
283C VAL* 3.3 13.2 + - + +
284C PHE* 1.3 69.4 - - - +
286C SER* 1.3 64.0 + - - +
288C VAL* 3.3 19.4 - - + +
294C VAL* 6.3 0.2 - - - -
297C VAL* 3.9 27.8 - - + -
310C ILE* 4.9 5.8 - - + -
311C ILE 2.9 14.7 + - - +
312C SER* 4.6 1.6 - - - -
313C LYS* 2.9 28.8 + - - +
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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